[{"type":"categorical","name":"MCF-7 genotype ENCODE/HudsonAlpha","url":"http://egg.wustl.edu/d/hg19/wgEncodeHaibGenotypeMcf7RegionsRep1.gz","public":true,"mode":1,"qtc":{"anglescale":1,"height":15},"annotation":["30015","26002","14028"],"categories":{"1":["normal","#858585"],"2":["homozygous deletion","#ff0000"],"3":["heterozygous deletion","#ff9900"],"4":["amplified","#0000ff"],"-1":["no information","transparent"]},"details":{"project":"wgEncode","grant":"Myers","lab":"HudsonAlpha","composite":"wgEncodeHaibGenotype","dataType":"Genotype","view":"CNV","cell":"MCF-7","treatment":"None","replicate":"1","dccRep":"1","origAssembly":"hg19","dataVersion":"ENCODE Jan 2011 Freeze","dccAccession":"wgEncodeEH001268","dateSubmitted":"2011-01-18","dateUnrestricted":"2011-10-18","subId":"3303","geoSampleAccession":"GSM999333","labVersion":"Illumina 1MDuo","obtainedBy":"UW","tableName":"wgEncodeHaibGenotypeMcf7RegionsRep1","type":"bedLogR","md5sum":"770b9efe3f7975554598b391281e3546","size":"8.9K"},"geolst":["GSM999333"]},{"type":"categorical","name":"MCF-7 genotype ENCODE/HudsonAlpha","url":"http://egg.wustl.edu/d/hg19/wgEncodeHaibGenotypeMcf7RegionsRep2.gz","public":true,"mode":1,"qtc":{"anglescale":1,"height":15},"annotation":["30015","26002","14028"],"categories":{"1":["normal","#858585"],"2":["homozygous deletion","#ff0000"],"3":["heterozygous deletion","#ff9900"],"4":["amplified","#0000ff"],"-1":["no information","transparent"]},"details":{"project":"wgEncode","grant":"Myers","lab":"HudsonAlpha","composite":"wgEncodeHaibGenotype","dataType":"Genotype","view":"CNV","cell":"MCF-7","treatment":"None","replicate":"2","dccRep":"2","origAssembly":"hg19","dataVersion":"ENCODE Jan 2011 Freeze","dccAccession":"wgEncodeEH001268","dateSubmitted":"2011-01-18","dateUnrestricted":"2011-10-18","subId":"3303","geoSampleAccession":"GSM999333","labVersion":"Illumina 1MDuo","obtainedBy":"UW","tableName":"wgEncodeHaibGenotypeMcf7RegionsRep2","type":"bedLogR","md5sum":"d31a40699640bd967a239492b1de384b","size":"9.1K"},"geolst":["GSM999333"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 Max","url":"http://egg.wustl.edu/d/hg19/GSM1010863_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24066","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Rabbit polyclonal IgG, epitope mapping at the C-terminus of Max of human origin. Antibody Target: Max","antibody targetdescription":"The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq).","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-197","controlid":"SL16758,SL13504","labexpid":"SL13485,SL14695","softwareversion":"MACS","cell sex":"F","antibody":"Max","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010863_hg19_wgEncodeHaibTfbsMcf7MaxV0422111RawRep2.bigWig"},"geolst":["GSM1010863"]},{"type":"bigWig","name":"Duke DnaseSeq MCF-7 Hypoxia","url":"http://egg.wustl.edu/d/hg19/GSM1008565_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":77,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23001","30019"],"details":{"datatype":"DnaseSeq","datatype description":"DNaseI HS Sequencing","labversion":"baseAlignCounts.pl v 1","replicate":"1,2","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"Hypoxia_LacAcid_ctrl","treatment description":"Untreated cells grown along side Hypoxia LacAcid treated cells (Crawford)","original_filename":"GSM1008565_hg19_wgEncodeOpenChromDnaseMcf7HypoxlacconBaseOverlapSignal.bigWig"},"geolst":["GSM1008565"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM973676_4.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","protocol":"CIP-TAP","protocol description":"This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs.","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"089WC,090WC","labexpid":"LID46458,LID46459","labversion":"iIDR","readtype":"1x101","readtype description":"Single 101 nt reads","original_filename":"GSM973676_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapPlusRep4.bigWig"},"geolst":["GSM973676"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM973676_3.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","protocol":"CIP-TAP","protocol description":"This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs.","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"089WC,090WC","labexpid":"LID46458,LID46459","labversion":"iIDR","readtype":"1x101","readtype description":"Single 101 nt reads","original_filename":"GSM973676_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapPlusRep3.bigWig"},"geolst":["GSM973676"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM973676_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","protocol":"CIP-TAP","protocol description":"This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs.","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"089WC,090WC","labexpid":"LID46458,LID46459","labversion":"iIDR","readtype":"1x101","readtype description":"Single 101 nt reads","original_filename":"GSM973676_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapMinusRep3.bigWig"},"geolst":["GSM973676"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 NR2F2","url":"http://egg.wustl.edu/d/hg19/GSM1010837_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24681","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Mouse monoclonal IgG, specific for an epitope mapping between amino acids 13-44 at the N-terminus of NR2F2 of human origin. Antibody Target: NR2F2","antibody targetdescription":"This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. (provided by RefSeq)","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-271940","controlid":"SL16758,SL13504","labexpid":"SL13490,SL14697","softwareversion":"MACS","cell sex":"F","antibody":"NR2F2_(SC-271940)","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010837_hg19_wgEncodeHaibTfbsMcf7Nr2f2sc271940V0422111RawRep2.bigWig"},"geolst":["GSM1010837"]},{"type":"bigWig","name":"USC ChipSeq MCF-7 HA-E2F1","url":"http://egg.wustl.edu/d/hg19/GSM935477_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24643","30016"],"details":{"lab":"USC","lab description":"Farnham - University of Southern California","datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"None","treatment description":"No special treatment or protocol applies","antibody":"HA-E2F1","antibody antibodydescription":"Mouse Monoclonal antibody HA.11 clone 16B12 was raised against the twelve amino acid peptide CYPYDVPDYASL. This second-generation HA antibody is an excellent substitute for the 12CA5 monoclonal antibody. The HA.11 antibody recognizes the influenza hemagglutinin epitope (YPYDVPDYA) which has been used extensively as a general epitope tag in expression vectors. The extreme specificity of the antibody allows unambiguous identification and quantitative analysis of the tagged protein. The HA.11 antibody recognizes HA epitopes located in the middle of protein sequences as well as at the N- or C-terminus. Antibody Target: HA-E2F1","antibody targetdescription":"The HA-E2F1 protein is a derivative of E2F1, a member of the E2F family of transcription factors. The E2F family plays a crucial role in the control of cell cycle and action of tumor suppressor proteins and is also a target of the transforming proteins of small DNA tumor viruses. The E2F proteins contain several evolutionary conserved domains found in most members of the family. These domains include a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. This version of E2F1 includes an N terminal HA tag and a modified ER ligand binding domain to allow regulated translocation to the nucleus.","antibody vendorname":"Covance","antibody vendorid":"MMS-101P","control":"UCDavis","control description":"Input library was prepared at UC Davis.","controlid":"wgEncodeEH000762","labversion":"MCF-7 cells stably expressed a tagged HA-E2F1 were fragmented using Bioruptor, precipitated with StaphA and an antibody to the  HA tag,","replicate":"1","softwareversion":"PeakSeq1.0 (fdr 0.001)","original_filename":"GSM935477_hg19_wgEncodeSydhTfbsMcf7Hae2f1UcdSig.bigWig"},"geolst":["GSM935477"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cytosol","url":"http://egg.wustl.edu/d/hg19/GSM973672_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cytosol","localization description":"The fluid between the cells outer membrane and the nucleus","protocol":"None","protocol description":"No special treatment or protocol applies","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"089C,090C","labexpid":"LID46315,LID46316","labversion":"iIDR","readtype":"1x101","readtype description":"Single 101 nt reads","original_filename":"GSM973672_hg19_wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalMinusRep4.bigWig"},"geolst":["GSM973672"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cytosol","url":"http://egg.wustl.edu/d/hg19/GSM973672_3.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cytosol","localization description":"The fluid between the cells outer membrane and the nucleus","protocol":"None","protocol description":"No special treatment or protocol applies","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"089C,090C","labexpid":"LID46315,LID46316","labversion":"iIDR","readtype":"1x101","readtype description":"Single 101 nt reads","original_filename":"GSM973672_hg19_wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalPlusRep3.bigWig"},"geolst":["GSM973672"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cytosol","url":"http://egg.wustl.edu/d/hg19/GSM973672_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cytosol","localization description":"The fluid between the cells outer membrane and the nucleus","protocol":"None","protocol description":"No special treatment or protocol applies","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"089C,090C","labexpid":"LID46315,LID46316","labversion":"iIDR","readtype":"1x101","readtype description":"Single 101 nt reads","original_filename":"GSM973672_hg19_wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalMinusRep3.bigWig"},"geolst":["GSM973672"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cytosol","url":"http://egg.wustl.edu/d/hg19/GSM973672_4.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cytosol","localization description":"The fluid between the cells outer membrane and the nucleus","protocol":"None","protocol description":"No special treatment or protocol applies","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"089C,090C","labexpid":"LID46315,LID46316","labversion":"iIDR","readtype":"1x101","readtype description":"Single 101 nt reads","original_filename":"GSM973672_hg19_wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalPlusRep4.bigWig"},"geolst":["GSM973672"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 PML","url":"http://egg.wustl.edu/d/hg19/GSM1010838_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24688","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Mouse monoclonal IgG, N-terminal epitope corresponding to residues 37-51 of PML of human origin. Antibody Target: PML","antibody targetdescription":"The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-71910","controlid":"SL16757,SL16756","labexpid":"SL16026,SL13722","softwareversion":"MACS","cell sex":"F","antibody":"PML_(SC-71910)","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010838_hg19_wgEncodeHaibTfbsMcf7Pmlsc71910V0422111RawRep2.bigWig"},"geolst":["GSM1010838"]},{"type":"bigWig","name":"UT-A ChipSeq MCF-7 vehicle","url":"http://egg.wustl.edu/d/hg19/GSM822301_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24004","30009"],"details":{"lab":"UT-A","lab description":"Iyer - University of Texas at Austin","datatype":"ChipSeq","datatype description":"ChIP-Seq","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"vehicle","treatment description":"Charcoal stripped hormone-free FBS for 72 hours (Crawford)","antibody":"c-Myc","antibody antibodydescription":"rabbit polyclonal to amino acids 1-262 of c-Myc human origin","antibody targetdescription":"transcription factor","antibody vendorname":"Santa Cruz Biotech","antibody vendorid":"sc-764","controlid":"MCF-7/Input","labversion":"align_on_cluster_bwa.pl v 1","replicate":"1","replicate description":"tier 1","original_filename":"GSM822301_hg19_wgEncodeOpenChromChipMcf7CmycVehBaseOverlapSignal.bigWig"},"geolst":["GSM822301"]},{"type":"bigWig","name":"UT-A ChipSeq MCF-7 vehicle","url":"http://egg.wustl.edu/d/hg19/GSM822301_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24004","30009"],"details":{"lab":"UT-A","lab description":"Iyer - University of Texas at Austin","datatype":"ChipSeq","datatype description":"ChIP-Seq","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"vehicle","treatment description":"Charcoal stripped hormone-free FBS for 72 hours (Crawford)","antibody":"c-Myc","antibody antibodydescription":"rabbit polyclonal to amino acids 1-262 of c-Myc human origin","antibody targetdescription":"transcription factor","antibody vendorname":"Santa Cruz Biotech","antibody vendorid":"sc-764","controlid":"MCF-7/Input","labversion":"align_on_cluster_bwa.pl v 1","replicate":"1","replicate description":"tier 1","original_filename":"GSM822301_hg19_wgEncodeOpenChromChipMcf7CmycVehSig.bigWig"},"geolst":["GSM822301"]},{"type":"bigWig","name":"UT-A ChipSeq MCF-7 CTCF","url":"http://egg.wustl.edu/d/hg19/GSM822305_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24001","30009"],"details":{"lab":"UT-A","lab description":"Iyer - University of Texas at Austin","datatype":"ChipSeq","datatype description":"ChIP-Seq","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","antibody":"CTCF","antibody antibodydescription":"rabbit polyclonal","antibody targetdescription":"CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.","antibody vendorname":"Millipore","antibody vendorid":"07-729","controlid":"MCF-7/Input","labversion":"align_on_cluster_bwa.pl v 1","replicate":"1","replicate description":"tier 1","original_filename":"GSM822305_hg19_wgEncodeOpenChromChipMcf7CtcfBaseOverlapSignal.bigWig"},"geolst":["GSM822305"]},{"type":"bigWig","name":"UT-A ChipSeq MCF-7 CTCF","url":"http://egg.wustl.edu/d/hg19/GSM822305_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24001","30009"],"details":{"lab":"UT-A","lab description":"Iyer - University of Texas at Austin","datatype":"ChipSeq","datatype description":"ChIP-Seq","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","antibody":"CTCF","antibody antibodydescription":"rabbit polyclonal","antibody targetdescription":"CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.","antibody vendorname":"Millipore","antibody vendorid":"07-729","controlid":"MCF-7/Input","labversion":"align_on_cluster_bwa.pl v 1","replicate":"1","replicate description":"tier 1","original_filename":"GSM822305_hg19_wgEncodeOpenChromChipMcf7CtcfSig.bigWig"},"geolst":["GSM822305"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 GATA3","url":"http://egg.wustl.edu/d/hg19/GSM1010783_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24065","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Mouse monoclonal IgG raised against human recombinant GATA-3. Antibody Target:  GATA3","antibody targetdescription":"This gene encodes a protein which belongs to the GATA family of transcription factors.  The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology.  Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq).","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-268","controlid":"SL13504","labexpid":"SL13482,SL14692","softwareversion":"MACS","cell sex":"F","antibody":"GATA3_(SC-268)","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010783_hg19_wgEncodeHaibTfbsMcf7Gata3V0422111RawRep2.bigWig"},"geolst":["GSM1010783"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 GATA3","url":"http://egg.wustl.edu/d/hg19/GSM1010783_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24065","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Mouse monoclonal IgG raised against human recombinant GATA-3. Antibody Target:  GATA3","antibody targetdescription":"This gene encodes a protein which belongs to the GATA family of transcription factors.  The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology.  Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq).","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-268","controlid":"SL13504","labexpid":"SL13482,SL14692","softwareversion":"MACS","cell sex":"F","antibody":"GATA3_(SC-268)","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010783_hg19_wgEncodeHaibTfbsMcf7Gata3V0422111RawRep1.bigWig"},"geolst":["GSM1010783"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM765388_4.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"015WC","labexpid":"LID8686","readtype":"2x76D","readtype description":"Paired 76 n.t. directed reads","replicate":"1","replicate description":"tier 1","original_filename":"GSM765388_wgEncodeCshlLongRnaSeqMcf7CellPapPlusRawSigRep2.bigWig"},"geolst":["GSM765388"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM765388_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"015WC","labexpid":"LID8686","readtype":"2x76D","readtype description":"Paired 76 n.t. directed reads","replicate":"1","replicate description":"tier 1","original_filename":"GSM765388_wgEncodeCshlLongRnaSeqMcf7CellPapMinusRawSigRep1.bigWig"},"geolst":["GSM765388"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM765388_3.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"015WC","labexpid":"LID8686","readtype":"2x76D","readtype description":"Paired 76 n.t. directed reads","replicate":"1","replicate description":"tier 1","original_filename":"GSM765388_wgEncodeCshlLongRnaSeqMcf7CellPapPlusRawSigRep1.bigWig"},"geolst":["GSM765388"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM765388_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"015WC","labexpid":"LID8686","readtype":"2x76D","readtype description":"Paired 76 n.t. directed reads","replicate":"1","replicate description":"tier 1","original_filename":"GSM765388_wgEncodeCshlLongRnaSeqMcf7CellPapMinusRawSigRep2.bigWig"},"geolst":["GSM765388"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cytosol","url":"http://egg.wustl.edu/d/hg19/GSM981252_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089C,090C","labexpid":"LID46857,LID46858","labversion":"iIDR","readtype":"2x101D","readtype description":"Paired 101 nt directed reads","replicate":"3,4","spikeinpool":"Nist14","localization description":"The fluid between the cells outer membrane and the nucleus","original_filename":"GSM981252_hg19_wgEncodeCshlLongRnaSeqMcf7CytosolPapMinusRep3.bigWig"},"geolst":["GSM981252"]},{"type":"bigWig","name":"USC ChipSeq MCF-7 GATA3","url":"http://egg.wustl.edu/d/hg19/GSM825711_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24065","30016"],"details":{"lab":"USC","lab description":"Farnham - University of Southern California","datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"None","treatment description":"No special treatment or protocol applies","antibody":"GATA3_(SC-268)","antibody antibodydescription":"Mouse monoclonal IgG raised against human recombinant GATA-3. Antibody Target:  GATA3","antibody targetdescription":"This gene encodes a protein which belongs to the GATA family of transcription factors.  The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology.  Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq).","antibody vendorname":"Santa Cruz Biotech","antibody vendorid":"sc-268","control":"UCDavis","control description":"Input library was prepared at UC Davis.","controlid":"wgEncodeEH000762","replicate":"1","replicate description":"tier 1","original_filename":"GSM825711_hg19_wgEncodeSydhTfbsMcf7Gata3UcdSig.bigWig"},"geolst":["GSM825711"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 NR2F2","url":"http://egg.wustl.edu/d/hg19/GSM1010837_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24681","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Mouse monoclonal IgG, specific for an epitope mapping between amino acids 13-44 at the N-terminus of NR2F2 of human origin. Antibody Target: NR2F2","antibody targetdescription":"This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. (provided by RefSeq)","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-271940","controlid":"SL16758,SL13504","labexpid":"SL13490,SL14697","softwareversion":"MACS","cell sex":"F","antibody":"NR2F2_(SC-271940)","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010837_hg19_wgEncodeHaibTfbsMcf7Nr2f2sc271940V0422111RawRep1.bigWig"},"geolst":["GSM1010837"]},{"type":"bigWig","name":"RIKEN Cage MCF-7 nucleus","url":"http://egg.wustl.edu/d/hg19/GSM979654_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25004","30011"],"details":{"datatype":"Cage","datatype description":"CAGE 5' RNA Tags","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089N","labexpid":"CThi10052","readtype":"1x50","readtype description":"Single 50 nt reads","replicate":"3","cell sex":"F","localization":"nucleus","localization description":"Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA","original_filename":"GSM979654_hg19_wgEncodeRikenCageMcf7NucleusPapMinusRawRep3.bigWig"},"geolst":["GSM979654"]},{"type":"bigWig","name":"RIKEN Cage MCF-7 nucleus","url":"http://egg.wustl.edu/d/hg19/GSM979654_3.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25004","30011"],"details":{"datatype":"Cage","datatype description":"CAGE 5' RNA Tags","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089N","labexpid":"CThi10052","readtype":"1x50","readtype description":"Single 50 nt reads","replicate":"3","cell sex":"F","localization":"nucleus","localization description":"Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA","original_filename":"GSM979654_hg19_wgEncodeRikenCageMcf7NucleusPapPlusRawRep3.bigWig"},"geolst":["GSM979654"]},{"type":"bigWig","name":"RIKEN Cage MCF-7 nucleus","url":"http://egg.wustl.edu/d/hg19/GSM979654_4.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25004","30011"],"details":{"datatype":"Cage","datatype description":"CAGE 5' RNA Tags","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089N","labexpid":"CThi10052","readtype":"1x50","readtype description":"Single 50 nt reads","replicate":"3","cell sex":"F","localization":"nucleus","localization description":"Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA","original_filename":"GSM979654_hg19_wgEncodeRikenCageMcf7NucleusPapPlusRawRep4.bigWig"},"geolst":["GSM979654"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 p300","url":"http://egg.wustl.edu/d/hg19/GSM1010800_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24011","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Rabbit Polyclonal. Antibody Target: P300","antibody targetdescription":"EP300(c-20)","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-585","controlid":"SL16757,SL13504","labexpid":"SL16335,SL13492","softwareversion":"MACS","cell sex":"F","antibody":"p300","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010800_hg19_wgEncodeHaibTfbsMcf7P300V0422111RawRep2.bigWig"},"geolst":["GSM1010800"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 p300","url":"http://egg.wustl.edu/d/hg19/GSM1010800_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24011","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Rabbit Polyclonal. Antibody Target: P300","antibody targetdescription":"EP300(c-20)","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-585","controlid":"SL16757,SL13504","labexpid":"SL16335,SL13492","softwareversion":"MACS","cell sex":"F","antibody":"p300","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010800_hg19_wgEncodeHaibTfbsMcf7P300V0422111RawRep1.bigWig"},"geolst":["GSM1010800"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM973676_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","protocol":"CIP-TAP","protocol description":"This kind of library was made from RNA < 200 nucleotides that was pre-treated sequentially with Calf Intestinal Alkaline Phosphatase followed by Tobacco Acid Pyrophosphatase. Hence, it will be enriched for capped RNAs.","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"089WC,090WC","labexpid":"LID46458,LID46459","labversion":"iIDR","readtype":"1x101","readtype description":"Single 101 nt reads","original_filename":"GSM973676_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalCiptapMinusRep4.bigWig"},"geolst":["GSM973676"]},{"type":"bigWig","name":"UT-A ChipSeq MCF-7 serum","url":"http://egg.wustl.edu/d/hg19/GSM1006878_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24001","30009"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"rabbit polyclonal. Antibody Target: CTCF","antibody targetdescription":"CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.","antibody vendorname":"Millipore","antibody vendorid":"07-729","controlid":"wgEncodeEH000589","labversion":"baseAlignCounts.pl v 1","replicate":"1,2","cell sex":"F","treatment":"serum_starved_media","treatment description":"Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours","antibody":"CTCF","original_filename":"GSM1006878_hg19_wgEncodeOpenChromChipMcf7CtcfSerumstvdBaseOverlapSignal.bigWig"},"geolst":["GSM1006878"]},{"type":"bigWig","name":"UT-A ChipSeq MCF-7 serum","url":"http://egg.wustl.edu/d/hg19/GSM1006878_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24001","30009"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"rabbit polyclonal. Antibody Target: CTCF","antibody targetdescription":"CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.","antibody vendorname":"Millipore","antibody vendorid":"07-729","controlid":"wgEncodeEH000589","labversion":"baseAlignCounts.pl v 1","replicate":"1,2","cell sex":"F","treatment":"serum_starved_media","treatment description":"Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours","antibody":"CTCF","original_filename":"GSM1006878_hg19_wgEncodeOpenChromChipMcf7CtcfSerumstvdSig.bigWig"},"geolst":["GSM1006878"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM973690_3.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","protocol":"None","protocol description":"No special treatment or protocol applies","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"089WC,090WC","labexpid":"LID46311,LID46312","labversion":"iIDR","readtype":"1x101","readtype description":"Single 101 nt reads","original_filename":"GSM973690_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalPlusRep3.bigWig"},"geolst":["GSM973690"]},{"type":"bigWig","name":"UW DnaseSeq MCF-7 Estradiol","url":"http://egg.wustl.edu/d/hg19/GSM1024764_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":77,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23001","30004"],"details":{"lab":"UW","lab description":"Stamatoyannopoulous - University of Washington","datatype":"DnaseSeq","datatype description":"DNaseI HS Sequencing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"Estradiol_ctrl_0hr","treatment description":"No hormone control, zero timepoint, used to distinguish untreated sample in series (Stam)","labexpid":"DS18267","labversion":"Hotspot-v5.2,lmax-v1.0,WindowDensity-bin20-win+/-75","replicate":"1","original_filename":"GSM1024764_hg19_wgEncodeUwDnaseMcf7Estctrl0hRawRep1.bigWig"},"geolst":["GSM1024764"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM973690_4.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","protocol":"None","protocol description":"No special treatment or protocol applies","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"089WC,090WC","labexpid":"LID46311,LID46312","labversion":"iIDR","readtype":"1x101","readtype description":"Single 101 nt reads","original_filename":"GSM973690_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalPlusRep4.bigWig"},"geolst":["GSM973690"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM973690_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","protocol":"None","protocol description":"No special treatment or protocol applies","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"089WC,090WC","labexpid":"LID46311,LID46312","labversion":"iIDR","readtype":"1x101","readtype description":"Single 101 nt reads","original_filename":"GSM973690_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalMinusRep4.bigWig"},"geolst":["GSM973690"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM973690_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","protocol":"None","protocol description":"No special treatment or protocol applies","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"089WC,090WC","labexpid":"LID46311,LID46312","labversion":"iIDR","readtype":"1x101","readtype description":"Single 101 nt reads","original_filename":"GSM973690_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalMinusRep3.bigWig"},"geolst":["GSM973690"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 GABP","url":"http://egg.wustl.edu/d/hg19/GSM1010864_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24021","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Mouse monoclonal, GABPa(G-1), IgG1. Antibody Target: GABP","antibody targetdescription":"The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence.","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-28312","controlid":"SL16758,SL13504","labexpid":"SL14683,SL13459","softwareversion":"MACS","cell sex":"F","antibody":"GABP","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010864_hg19_wgEncodeHaibTfbsMcf7GabpV0422111RawRep2.bigWig"},"geolst":["GSM1010864"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 CTCF","url":"http://egg.wustl.edu/d/hg19/GSM1010734_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24001","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Goat polyclonal IgG, epitope mapping at the N-terminus of CTCF of human origin. Antibody Target: CTCF","antibody targetdescription":"This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq)","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-5916","controlid":"SL16757,SL13504","labexpid":"SL13463,SL16333","softwareversion":"MACS","cell sex":"F","antibody":"CTCF_(SC-5916)","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010734_hg19_wgEncodeHaibTfbsMcf7CtcfcV0422111RawRep1.bigWig"},"geolst":["GSM1010734"]},{"type":"bigWig","name":"UT-A ChipSeq MCF-7 serum","url":"http://egg.wustl.edu/d/hg19/GSM1006875_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24001","30009"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"rabbit polyclonal. Antibody Target: CTCF","antibody targetdescription":"CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.","antibody vendorname":"Millipore","antibody vendorid":"07-729","controlid":"wgEncodeEH000589","labversion":"baseAlignCounts.pl v 1","replicate":"1,2","cell sex":"F","treatment":"serum_stimulated_media","treatment description":"Grown with normal serum levels (10%), then switched back to normal serum levels (10% FBS) for 3 hours.","antibody":"CTCF","original_filename":"GSM1006875_hg19_wgEncodeOpenChromChipMcf7CtcfSerumstimBaseOverlapSignal.bigWig"},"geolst":["GSM1006875"]},{"type":"bigWig","name":"UT-A ChipSeq MCF-7 serum","url":"http://egg.wustl.edu/d/hg19/GSM1006875_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24001","30009"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"rabbit polyclonal. Antibody Target: CTCF","antibody targetdescription":"CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.","antibody vendorname":"Millipore","antibody vendorid":"07-729","controlid":"wgEncodeEH000589","labversion":"baseAlignCounts.pl v 1","replicate":"1,2","cell sex":"F","treatment":"serum_stimulated_media","treatment description":"Grown with normal serum levels (10%), then switched back to normal serum levels (10% FBS) for 3 hours.","antibody":"CTCF","original_filename":"GSM1006875_hg19_wgEncodeOpenChromChipMcf7CtcfSerumstimSig.bigWig"},"geolst":["GSM1006875"]},{"type":"bigWig","name":"UT-A ChipSeq MCF-7 serum","url":"http://egg.wustl.edu/d/hg19/GSM1006877_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24004","30009"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"rabbit polyclonal to amino acids 1-262 of c-Myc human origin. Antibody Target: c-Myc","antibody targetdescription":"transcription factor","antibody vendorname":"Santa Cruz Biotech","antibody vendorid":"sc-764","controlid":"wgEncodeEH000589","labversion":"baseAlignCounts.pl v 1","replicate":"1,2","cell sex":"F","treatment":"serum_stimulated_media","treatment description":"Grown with normal serum levels (10%), then switched back to normal serum levels (10% FBS) for 3 hours.","antibody":"c-Myc","original_filename":"GSM1006877_hg19_wgEncodeOpenChromChipMcf7CmycSerumstimBaseOverlapSignal.bigWig"},"geolst":["GSM1006877"]},{"type":"bigWig","name":"UW DnaseSeq MCF-7 Estradiol","url":"http://egg.wustl.edu/d/hg19/GSM1024767_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":77,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23001","30004"],"details":{"lab":"UW","lab description":"Stamatoyannopoulous - University of Washington","datatype":"DnaseSeq","datatype description":"DNaseI HS Sequencing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"Estradiol_ctrl_0hr","treatment description":"No hormone control, zero timepoint, used to distinguish untreated sample in series (Stam)","labexpid":"DS18021","labversion":"Hotspot-v5.2,lmax-v1.0,WindowDensity-bin20-win+/-75","replicate":"2","original_filename":"GSM1024767_hg19_wgEncodeUwDnaseMcf7Estctrl0hRawRep2.bigWig"},"geolst":["GSM1024767"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 TCF12","url":"http://egg.wustl.edu/d/hg19/GSM1010861_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24015","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"HEB (A-20) Rabbit polyclonal IgG, 200 ?g/ml. Epitope mapping within the C-terminus of HEB of human origin. Antibody Target: TCF12","antibody targetdescription":"The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined.","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-357","controlid":"SL16757,SL16756","labexpid":"SL16340,SL14574","softwareversion":"MACS","cell sex":"F","antibody":"TCF12","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010861_hg19_wgEncodeHaibTfbsMcf7Tcf12V0422111RawRep2.bigWig"},"geolst":["GSM1010861"]},{"type":"bigWig","name":"RIKEN Cage MCF-7 cytosol","url":"http://egg.wustl.edu/d/hg19/GSM979657_4.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25004","30011"],"details":{"datatype":"Cage","datatype description":"CAGE 5' RNA Tags","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089C","labexpid":"CThi10051","readtype":"1x50","readtype description":"Single 50 nt reads","replicate":"3","cell sex":"F","localization":"cytosol","localization description":"The fluid between the cells outer membrane and the nucleus","original_filename":"GSM979657_hg19_wgEncodeRikenCageMcf7CytosolPapPlusRawRep4.bigWig"},"geolst":["GSM979657"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 JunD","url":"http://egg.wustl.edu/d/hg19/GSM1010892_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24063","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"rabbit polyclonal IgG. Antibody Target: JunD","antibody targetdescription":"The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq)","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-74","controlid":"SL13504","labexpid":"SL14694,SL13484","softwareversion":"MACS","cell sex":"F","antibody":"JunD","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010892_hg19_wgEncodeHaibTfbsMcf7JundV0422111RawRep2.bigWig"},"geolst":["GSM1010892"]},{"type":"bigWig","name":"UNC FaireSeq MCF-7 Hypoxia","url":"http://egg.wustl.edu/d/hg19/GSM864344_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23003","30022"],"details":{"lab":"UNC","lab description":"Lieb - University of North Carolina","datatype":"FaireSeq","datatype description":"FAIRE followed by sequencing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"Hypoxia_LacAcid","treatment description":"24 h with 1% p02 and 10mM Lactate, pH 6.7","controlid":"MCF-7/Input","labversion":"align_on_cluster_bwa.pl v 1","replicate":"1","replicate description":"tier 1","original_filename":"GSM864344_hg19_wgEncodeOpenChromFaireMcf7HypoxlacSig.bigWig"},"geolst":["GSM864344"]},{"type":"bigWig","name":"UNC FaireSeq MCF-7 Hypoxia","url":"http://egg.wustl.edu/d/hg19/GSM864344_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23003","30022"],"details":{"lab":"UNC","lab description":"Lieb - University of North Carolina","datatype":"FaireSeq","datatype description":"FAIRE followed by sequencing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"Hypoxia_LacAcid","treatment description":"24 h with 1% p02 and 10mM Lactate, pH 6.7","controlid":"MCF-7/Input","labversion":"align_on_cluster_bwa.pl v 1","replicate":"1","replicate description":"tier 1","original_filename":"GSM864344_hg19_wgEncodeOpenChromFaireMcf7HypoxlacBaseOverlapSignal.bigWig"},"geolst":["GSM864344"]},{"type":"bigWig","name":"UW RepliSeq MCF-7","url":"http://egg.wustl.edu/d/hg19/GSM923442_8.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23004","30004"],"details":{"lab":"UW","lab description":"Stamatoyannopoulous - University of Washington","datatype":"RepliSeq","datatype description":"Assessment of DNA Replication Timing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","labexpid":"DS9795","phase":"G1b","phase description":"Flow sorted, G1b phase corresponds to the second half of the first DNA content window","replicate":"1","original_filename":"GSM923442_hg19_wgEncodeUwRepliSeqMcf7WaveSignalRep1.bigWig"},"geolst":["GSM923442"]},{"type":"bigWig","name":"UW RepliSeq MCF-7","url":"http://egg.wustl.edu/d/hg19/GSM923442_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23004","30004"],"details":{"lab":"UW","lab description":"Stamatoyannopoulous - University of Washington","datatype":"RepliSeq","datatype description":"Assessment of DNA Replication Timing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","labexpid":"DS9795","phase":"G1b","phase description":"Flow sorted, G1b phase corresponds to the second half of the first DNA content window","replicate":"1","original_filename":"GSM923442_hg19_wgEncodeUwRepliSeqMcf7G1bPctSignalRep1.bigWig"},"geolst":["GSM923442"]},{"type":"bigWig","name":"UW RepliSeq MCF-7","url":"http://egg.wustl.edu/d/hg19/GSM923442_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23004","30004"],"details":{"lab":"UW","lab description":"Stamatoyannopoulous - University of Washington","datatype":"RepliSeq","datatype description":"Assessment of DNA Replication Timing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","labexpid":"DS9795","phase":"G1b","phase description":"Flow sorted, G1b phase corresponds to the second half of the first DNA content window","replicate":"1","original_filename":"GSM923442_hg19_wgEncodeUwRepliSeqMcf7G2PctSignalRep1.bigWig"},"geolst":["GSM923442"]},{"type":"bigWig","name":"UW RepliSeq MCF-7","url":"http://egg.wustl.edu/d/hg19/GSM923442_3.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23004","30004"],"details":{"lab":"UW","lab description":"Stamatoyannopoulous - University of Washington","datatype":"RepliSeq","datatype description":"Assessment of DNA Replication Timing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","labexpid":"DS9795","phase":"G1b","phase description":"Flow sorted, G1b phase corresponds to the second half of the first DNA content window","replicate":"1","original_filename":"GSM923442_hg19_wgEncodeUwRepliSeqMcf7S1PctSignalRep1.bigWig"},"geolst":["GSM923442"]},{"type":"bigWig","name":"UW RepliSeq MCF-7","url":"http://egg.wustl.edu/d/hg19/GSM923442_4.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23004","30004"],"details":{"lab":"UW","lab description":"Stamatoyannopoulous - University of Washington","datatype":"RepliSeq","datatype description":"Assessment of DNA Replication Timing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","labexpid":"DS9795","phase":"G1b","phase description":"Flow sorted, G1b phase corresponds to the second half of the first DNA content window","replicate":"1","original_filename":"GSM923442_hg19_wgEncodeUwRepliSeqMcf7S2PctSignalRep1.bigWig"},"geolst":["GSM923442"]},{"type":"bigWig","name":"UW RepliSeq MCF-7","url":"http://egg.wustl.edu/d/hg19/GSM923442_5.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23004","30004"],"details":{"lab":"UW","lab description":"Stamatoyannopoulous - University of Washington","datatype":"RepliSeq","datatype description":"Assessment of DNA Replication Timing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","labexpid":"DS9795","phase":"G1b","phase description":"Flow sorted, G1b phase corresponds to the second half of the first DNA content window","replicate":"1","original_filename":"GSM923442_hg19_wgEncodeUwRepliSeqMcf7S3PctSignalRep1.bigWig"},"geolst":["GSM923442"]},{"type":"bigWig","name":"UW RepliSeq MCF-7","url":"http://egg.wustl.edu/d/hg19/GSM923442_6.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23004","30004"],"details":{"lab":"UW","lab description":"Stamatoyannopoulous - University of Washington","datatype":"RepliSeq","datatype description":"Assessment of DNA Replication Timing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","labexpid":"DS9795","phase":"G1b","phase description":"Flow sorted, G1b phase corresponds to the second half of the first DNA content window","replicate":"1","original_filename":"GSM923442_hg19_wgEncodeUwRepliSeqMcf7S4PctSignalRep1.bigWig"},"geolst":["GSM923442"]},{"type":"bigWig","name":"UW RepliSeq MCF-7","url":"http://egg.wustl.edu/d/hg19/GSM923442_7.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23004","30004"],"details":{"lab":"UW","lab description":"Stamatoyannopoulous - University of Washington","datatype":"RepliSeq","datatype description":"Assessment of DNA Replication Timing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","labexpid":"DS9795","phase":"G1b","phase description":"Flow sorted, G1b phase corresponds to the second half of the first DNA content window","replicate":"1","original_filename":"GSM923442_hg19_wgEncodeUwRepliSeqMcf7SumSignalRep1.bigWig"},"geolst":["GSM923442"]},{"type":"bigWig","name":"UW ChipSeq MCF-7 CTCFRep1","url":"http://egg.wustl.edu/d/hg19/GSM1022658_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24001","30004"],"details":{"lab":"UW","lab description":"Stamatoyannopoulous - University of Washington","datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","antibody":"CTCF","antibody antibodydescription":"Rabbit polyclonal. Antibody Target: CTCF","antibody targetdescription":"CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.","antibody vendorname":"Millipore","antibody vendorid":"07-729","treatment":"None","treatment description":"No special treatment or protocol applies","control":"std","control description":"Standard input signal for most experiments.","controlid":"wgEncodeEH000968","labexpid":"DS16200","labversion":"Hotspot-v5.2,lmax-v1.0,WindowDensity-bin20-win+/-75","replicate":"1","original_filename":"GSM1022658_hg19_wgEncodeUwTfbsMcf7CtcfStdRawRep1.bigWig"},"geolst":["GSM1022658"]},{"type":"bigWig","name":"Stam MCF-7 2","url":"http://egg.wustl.edu/d/hg19/GSM736588_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":77,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23001","30004"],"details":{"cell":"MCF-7","cell organism":"Human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell sex":"F","replicate":"2","original_filename":"GSM736588_hg19_wgEncodeUwDnaseMcf7RawRep2.bigWig"},"geolst":["GSM736588"]},{"type":"bigWig","name":"UW DnaseSeq MCF-7 Estradiol","url":"http://egg.wustl.edu/d/hg19/GSM1024783_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":77,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23001","30004"],"details":{"lab":"UW","lab description":"Stamatoyannopoulous - University of Washington","datatype":"DnaseSeq","datatype description":"DNaseI HS Sequencing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"Estradiol_100nM_1hr","treatment description":"1 h with 100 nM Estradiol, hormone treatment (Stam)","labexpid":"DS18025","labversion":"Hotspot-v5.2,lmax-v1.0,WindowDensity-bin20-win+/-75","replicate":"2","original_filename":"GSM1024783_hg19_wgEncodeUwDnaseMcf7Est100nm1hRawRep2.bigWig"},"geolst":["GSM1024783"]},{"type":"bigWig","name":"Duke DnaseSeq MCF-7 Hypoxia","url":"http://egg.wustl.edu/d/hg19/GSM1008565_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":77,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23001","30019"],"details":{"datatype":"DnaseSeq","datatype description":"DNaseI HS Sequencing","labversion":"baseAlignCounts.pl v 1","replicate":"1,2","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"Hypoxia_LacAcid_ctrl","treatment description":"Untreated cells grown along side Hypoxia LacAcid treated cells (Crawford)","original_filename":"GSM1008565_hg19_wgEncodeOpenChromDnaseMcf7HypoxlacconSig.bigWig"},"geolst":["GSM1008565"]},{"type":"bigWig","name":"Stam MCF-7 Input 1","url":"http://egg.wustl.edu/d/hg19/GSM749760_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":200,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","22001","30004"],"details":{"cell":"MCF-7","cell organism":"Human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell sex":"F","antibody":"Input","replicate":"1","original_filename":"GSM749760_hg19_wgEncodeUwTfbsMcf7InputStdRawRep1.bigWig"},"geolst":["GSM749760"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 RevXlinkChromatin","url":"http://egg.wustl.edu/d/hg19/GSM1010854_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24017","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","controlid":"SL16758,SL16757,SL13504,SL16756","labexpid":"SL16758,SL16757,SL13504,SL16756","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","antibody":"RevXlinkChromatin","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,3,2,4","original_filename":"GSM1010854_hg19_wgEncodeHaibTfbsMcf7RxlchV0422111RawRep1.bigWig"},"geolst":["GSM1010854"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 RevXlinkChromatin","url":"http://egg.wustl.edu/d/hg19/GSM1010854_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24017","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","controlid":"SL16758,SL16757,SL13504,SL16756","labexpid":"SL16758,SL16757,SL13504,SL16756","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","antibody":"RevXlinkChromatin","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,3,2,4","original_filename":"GSM1010854_hg19_wgEncodeHaibTfbsMcf7RxlchV0422111RawRep2.bigWig"},"geolst":["GSM1010854"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 RevXlinkChromatin","url":"http://egg.wustl.edu/d/hg19/GSM1010854_3.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24017","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","controlid":"SL16758,SL16757,SL13504,SL16756","labexpid":"SL16758,SL16757,SL13504,SL16756","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","antibody":"RevXlinkChromatin","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,3,2,4","original_filename":"GSM1010854_hg19_wgEncodeHaibTfbsMcf7RxlchV0422111RawRep3.bigWig"},"geolst":["GSM1010854"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 RevXlinkChromatin","url":"http://egg.wustl.edu/d/hg19/GSM1010854_4.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24017","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","controlid":"SL16758,SL16757,SL13504,SL16756","labexpid":"SL16758,SL16757,SL13504,SL16756","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","antibody":"RevXlinkChromatin","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,3,2,4","original_filename":"GSM1010854_hg19_wgEncodeHaibTfbsMcf7RxlchV0422111RawRep4.bigWig"},"geolst":["GSM1010854"]},{"type":"bigWig","name":"UNC FaireSeq MCF-7 vehicle","url":"http://egg.wustl.edu/d/hg19/GSM1011128_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23003","30022"],"details":{"datatype":"FaireSeq","datatype description":"FAIRE-seq Open Chromatin","controlid":"MCF-7/Input","labversion":"baseAlignCounts.pl v 1,fseq v 1.84, iff_MCF7,p-value cutoff: 0.1","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"vehicle","treatment description":"Charcoal stripped hormone-free FBS for 72 hours (Crawford)","replicate":"1,2","original_filename":"GSM1011128_hg19_wgEncodeOpenChromFaireMcf7VehSig.bigWig"},"geolst":["GSM1011128"]},{"type":"bigWig","name":"UNC FaireSeq MCF-7 vehicle","url":"http://egg.wustl.edu/d/hg19/GSM1011128_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23003","30022"],"details":{"datatype":"FaireSeq","datatype description":"FAIRE-seq Open Chromatin","controlid":"MCF-7/Input","labversion":"baseAlignCounts.pl v 1,fseq v 1.84, iff_MCF7,p-value cutoff: 0.1","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"vehicle","treatment description":"Charcoal stripped hormone-free FBS for 72 hours (Crawford)","replicate":"1,2","original_filename":"GSM1011128_hg19_wgEncodeOpenChromFaireMcf7VehBaseOverlapSignal.bigWig"},"geolst":["GSM1011128"]},{"type":"bigWig","name":"UNC FaireSeq MCF-7 Estradiol","url":"http://egg.wustl.edu/d/hg19/GSM1011121_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23003","30022"],"details":{"datatype":"FaireSeq","datatype description":"FAIRE-seq Open Chromatin","controlid":"MCF-7/Input","labversion":"baseAlignCounts.pl v 1,fseq v 1.84, iff_MCF7,p-value cutoff: 0.1","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"Estradiol_10nM_30m","treatment description":"30 min with 10nM 7b-Estradiol (Crawford)","replicate":"1,2","original_filename":"GSM1011121_hg19_wgEncodeOpenChromFaireMcf7Est10nm30mSig.bigWig"},"geolst":["GSM1011121"]},{"type":"bigWig","name":"UW DnaseSeq MCF-7 Estradiol","url":"http://egg.wustl.edu/d/hg19/GSM1024784_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":77,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23001","30004"],"details":{"lab":"UW","lab description":"Stamatoyannopoulous - University of Washington","datatype":"DnaseSeq","datatype description":"DNaseI HS Sequencing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"Estradiol_100nM_1hr","treatment description":"1 h with 100 nM Estradiol, hormone treatment (Stam)","labexpid":"DS18271","labversion":"Hotspot-v5.2,lmax-v1.0,WindowDensity-bin20-win+/-75","replicate":"1","original_filename":"GSM1024784_hg19_wgEncodeUwDnaseMcf7Est100nm1hRawRep1.bigWig"},"geolst":["GSM1024784"]},{"type":"bigWig","name":"Stam MCF-7 1","url":"http://egg.wustl.edu/d/hg19/GSM736581_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":77,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23001","30004"],"details":{"cell":"MCF-7","cell organism":"Human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell sex":"F","replicate":"1","original_filename":"GSM736581_hg19_wgEncodeUwDnaseMcf7RawRep1.bigWig"},"geolst":["GSM736581"]},{"type":"bigWig","name":"USC ChipSeq MCF-7 H3K9me3","url":"http://egg.wustl.edu/d/hg19/GSM945857_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":159,"pg":0,"pb":72,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","22012","30016"],"details":{"lab":"USC","lab description":"Farnham - University of Southern California","datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"None","treatment description":"No special treatment or protocol applies","antibody":"H3K9me3","antibody antibodydescription":"rabbit polyclonal, ChIP grade. Antibody Target: H3K9me3","antibody targetdescription":"Histone H3 (tri methyl K9). Is associated with repressive heterochromatic state (silenced chromatin). NOTE CONTRAST to H3K9me1 which is associated with active and accessible regions.","antibody vendorname":"Abcam","antibody vendorid":"ab8898","control":"UCDavis","control description":"Input library was prepared at UC Davis.","controlid":"wgEncodeEH000762","replicate":"1","original_filename":"GSM945857_hg19_wgEncodeSydhHistoneMcf7H3k09me3UcdSig.bigWig"},"geolst":["GSM945857"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 FOSL2","url":"http://egg.wustl.edu/d/hg19/GSM1010768_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24058","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Fra-2(Q-20) is an affinity purified rabbit polyclonal raised against the N-terminus of Fra-2 of human origin. Recommended for detection of Fra-2 of m, r, h and chicken origin by WB, IP, IF, IHC(P) and ELISA. Antibody Target: FOSL2","antibody targetdescription":"The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation.","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-604","controlid":"SL16758,SL13504","labexpid":"SL13457,SL14682","softwareversion":"MACS","cell sex":"F","antibody":"FOSL2","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010768_hg19_wgEncodeHaibTfbsMcf7Fosl2V0422111RawRep2.bigWig"},"geolst":["GSM1010768"]},{"type":"bigWig","name":"GIS RnaPet MCF-7 cytosol","url":"http://egg.wustl.edu/d/hg19/GSM1006904_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25006","30007"],"details":{"datatype":"RnaPet","datatype description":"RNA Paired-End Tags","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089C,090C","labexpid":"RHM044,RHM045","labversion":"clone-free","readtype":"2x36","readtype description":"Paired 36 nt reads","replicate":"3,4","localization":"cytosol","localization description":"The fluid between the cells outer membrane and the nucleus","original_filename":"GSM1006904_hg19_wgEncodeGisRnaPetMcf7CytosolPapMinusRawRep3.bigWig"},"geolst":["GSM1006904"]},{"type":"bigWig","name":"GIS RnaPet MCF-7 cytosol","url":"http://egg.wustl.edu/d/hg19/GSM1006904_3.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25006","30007"],"details":{"datatype":"RnaPet","datatype description":"RNA Paired-End Tags","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089C,090C","labexpid":"RHM044,RHM045","labversion":"clone-free","readtype":"2x36","readtype description":"Paired 36 nt reads","replicate":"3,4","localization":"cytosol","localization description":"The fluid between the cells outer membrane and the nucleus","original_filename":"GSM1006904_hg19_wgEncodeGisRnaPetMcf7CytosolPapPlusRawRep3.bigWig"},"geolst":["GSM1006904"]},{"type":"bigWig","name":"GIS RnaPet MCF-7 cytosol","url":"http://egg.wustl.edu/d/hg19/GSM1006904_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25006","30007"],"details":{"datatype":"RnaPet","datatype description":"RNA Paired-End Tags","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089C,090C","labexpid":"RHM044,RHM045","labversion":"clone-free","readtype":"2x36","readtype description":"Paired 36 nt reads","replicate":"3,4","localization":"cytosol","localization description":"The fluid between the cells outer membrane and the nucleus","original_filename":"GSM1006904_hg19_wgEncodeGisRnaPetMcf7CytosolPapMinusRawRep4.bigWig"},"geolst":["GSM1006904"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 CEBPB","url":"http://egg.wustl.edu/d/hg19/GSM1010889_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24624","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Rabbit polyclonal IgG, epitope mapping at the C-terminus of CEBPB of rat origin. Antibody Target: CEBPB","antibody targetdescription":"The protein encoded by this intronless gene is a bZIP transcription factor which can bind as a homodimer to certain DNA regulatory regions.  It can also form heterodimers with the related proteins CEBP-alpha, CEBP-delta, and CEBP-gamma.  The encoded protein is important in the regulation of genes involved in immune and inflammatory responses and has been shown to bind to the IL-1 response element in the IL-6 gene, as well as to regulatory regions of several acute-phase and cytokine genes.  In addition, the encoded protein can bind the promoter and upstream element and stimulate the expression of the collagen type I gene (provided by RefSeq).","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-150","controlid":"SL13504","labexpid":"SL13460,SL14684","softwareversion":"MACS","cell sex":"F","antibody":"CEBPB_(SC-150)","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010889_hg19_wgEncodeHaibTfbsMcf7Cebpbsc150V0422111RawRep2.bigWig"},"geolst":["GSM1010889"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 nucleus","url":"http://egg.wustl.edu/d/hg19/GSM973687_4.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"nucleus","localization description":"Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA","protocol":"None","protocol description":"No special treatment or protocol applies","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"089N,090N","labexpid":"LID46313,LID46314","labversion":"iIDR","readtype":"1x101","readtype description":"Single 101 nt reads","original_filename":"GSM973687_hg19_wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalPlusRep4.bigWig"},"geolst":["GSM973687"]},{"type":"bigWig","name":"RIKEN Cage MCF-7 nucleus","url":"http://egg.wustl.edu/d/hg19/GSM979654_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25004","30011"],"details":{"datatype":"Cage","datatype description":"CAGE 5' RNA Tags","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089N","labexpid":"CThi10052","readtype":"1x50","readtype description":"Single 50 nt reads","replicate":"3","cell sex":"F","localization":"nucleus","localization description":"Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA","original_filename":"GSM979654_hg19_wgEncodeRikenCageMcf7NucleusPapMinusRawRep4.bigWig"},"geolst":["GSM979654"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 nucleus","url":"http://egg.wustl.edu/d/hg19/GSM981245_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089N,090N","labexpid":"LID46859,LID46860","labversion":"iIDR","readtype":"2x101D","readtype description":"Paired 101 nt directed reads","replicate":"3,4","spikeinpool":"Nist14","localization description":"Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA","original_filename":"GSM981245_hg19_wgEncodeCshlLongRnaSeqMcf7NucleusPapMinusRep3.bigWig"},"geolst":["GSM981245"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 nucleus","url":"http://egg.wustl.edu/d/hg19/GSM981245_3.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089N,090N","labexpid":"LID46859,LID46860","labversion":"iIDR","readtype":"2x101D","readtype description":"Paired 101 nt directed reads","replicate":"3,4","spikeinpool":"Nist14","localization description":"Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA","original_filename":"GSM981245_hg19_wgEncodeCshlLongRnaSeqMcf7NucleusPapPlusRep3.bigWig"},"geolst":["GSM981245"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 nucleus","url":"http://egg.wustl.edu/d/hg19/GSM981245_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089N,090N","labexpid":"LID46859,LID46860","labversion":"iIDR","readtype":"2x101D","readtype description":"Paired 101 nt directed reads","replicate":"3,4","spikeinpool":"Nist14","localization description":"Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA","original_filename":"GSM981245_hg19_wgEncodeCshlLongRnaSeqMcf7NucleusPapMinusRep4.bigWig"},"geolst":["GSM981245"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cytosol","url":"http://egg.wustl.edu/d/hg19/GSM973681_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cytosol","localization description":"The fluid between the cells outer membrane and the nucleus","protocol":"TAP-Only","protocol description":"This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"089C","labexpid":"LID47162","readtype":"1x101","readtype description":"Single 101 nt reads","replicate":"3","original_filename":"GSM973681_hg19_wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalTapMinusRep3.bigWig"},"geolst":["GSM973681"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cytosol","url":"http://egg.wustl.edu/d/hg19/GSM973681_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cytosol","localization description":"The fluid between the cells outer membrane and the nucleus","protocol":"TAP-Only","protocol description":"This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"089C","labexpid":"LID47162","readtype":"1x101","readtype description":"Single 101 nt reads","replicate":"3","original_filename":"GSM973681_hg19_wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalTapMinusRep4.bigWig"},"geolst":["GSM973681"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cytosol","url":"http://egg.wustl.edu/d/hg19/GSM973681_3.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cytosol","localization description":"The fluid between the cells outer membrane and the nucleus","protocol":"TAP-Only","protocol description":"This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"089C","labexpid":"LID47162","readtype":"1x101","readtype description":"Single 101 nt reads","replicate":"3","original_filename":"GSM973681_hg19_wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalTapPlusRep3.bigWig"},"geolst":["GSM973681"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cytosol","url":"http://egg.wustl.edu/d/hg19/GSM973681_4.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cytosol","localization description":"The fluid between the cells outer membrane and the nucleus","protocol":"TAP-Only","protocol description":"This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"089C","labexpid":"LID47162","readtype":"1x101","readtype description":"Single 101 nt reads","replicate":"3","original_filename":"GSM973681_hg19_wgEncodeCshlShortRnaSeqMcf7CytosolShorttotalTapPlusRep4.bigWig"},"geolst":["GSM973681"]},{"type":"bigWig","name":"UT-A ChipSeq MCF-7 serum","url":"http://egg.wustl.edu/d/hg19/GSM1006865_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24634","30009"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"mouse monoclonal, clone 8WG16. Antibody Target: POL2","antibody targetdescription":"RNA Polymerase II","antibody vendorname":"Covance","antibody vendorid":"MMS-126R","controlid":"wgEncodeEH000589","labversion":"baseAlignCounts.pl v 1","replicate":"1,2","cell sex":"F","treatment":"serum_starved_media","treatment description":"Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours","antibody":"Pol2","original_filename":"GSM1006865_hg19_wgEncodeOpenChromChipMcf7Pol2SerumstvdSig.bigWig"},"geolst":["GSM1006865"]},{"type":"bigWig","name":"USC ChipSeq MCF-7 ZNF217","url":"http://egg.wustl.edu/d/hg19/GSM935563_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24667","30016"],"details":{"lab":"USC","lab description":"Farnham - University of Southern California","datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"None","treatment description":"No special treatment or protocol applies","antibody":"ZNF217","antibody antibodydescription":"A rabbit polyclonal antibody raised against a recombinant ZNF217 protein corresponding to the 1562-2207 nucleotides from a human ZNF217 cDNA. Antibody Target: ZNF217","antibody targetdescription":"ZNF217 is an important oncogene based on the high frequency of amplification and overexpression in many cancer types, but its molecular mode of gene regulation is poorly understood. ZNF217 has been purified in complexes that contain repressor proteins such as CtBP2, suggesting that it acts as a transcriptional repressor. ZNF217 contains seven C2H2 zinc finger domains and has been shown to bind to gene promoters","antibody vendorname":"From the lab of Dr. Paul Yaswen","antibody vendorid":"ZNF217","control":"UCDavis","control description":"Input library was prepared at UC Davis.","controlid":"wgEncodeEH000762","replicate":"1","original_filename":"GSM935563_hg19_wgEncodeSydhTfbsMcf7Znf217UcdSig.bigWig"},"geolst":["GSM935563"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 HDAC2","url":"http://egg.wustl.edu/d/hg19/GSM1010825_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","22044","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Goat polyclonal IgG, epitope mapping at the C-terminus of HDAC2 of human origin. Antibody Target: HDAC2","antibody targetdescription":"This gene product belongs to the histone deacetylase family.  Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq)","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-6296","controlid":"SL16757,SL13504","labexpid":"SL16334,SL13483","softwareversion":"MACS","cell sex":"F","antibody":"HDAC2_(SC-6296)","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010825_hg19_wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111RawRep2.bigWig"},"geolst":["GSM1010825"]},{"type":"bigWig","name":"USC ChipSeq MCF-7 Input","url":"http://egg.wustl.edu/d/hg19/GSM945859_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":200,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","22001","30016"],"details":{"lab":"USC","lab description":"Farnham - University of Southern California","datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"None","treatment description":"No special treatment or protocol applies","antibody":"Input","antibody description":"Control signal which may be subtracted from experimental raw signal before peaks are called.","control":"UCDavis","control description":"Input library was prepared at UC Davis.","controlid":"wgEncodeEH000762","labversion":"remapped from hg18, MCF7 cells stably expressed a tagged HA-E2F1 were fragmented using Bioruptor, crosslinks were reversed at 67*C overnight and Input was Qiagen purified, PeakSeq 1.0 (fdr 0.001)","replicate":"1","original_filename":"GSM945859_hg19_wgEncodeSydhHistoneMcf7InputUcdSig.bigWig"},"geolst":["GSM945859"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 ELF1","url":"http://egg.wustl.edu/d/hg19/GSM1010764_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24051","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Rabbit polyclonal IgG, epitope mapping at the C-terminus of Elf-1 of human origin. Antibody Target:  ELF1","antibody targetdescription":"This gene encodes an E26 transformation-specific related transcription factor.  The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes.  Alternative splicing results in multiple transcript variants. (provided by RefSeq)","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-631","controlid":"SL13504","labexpid":"SL13466,SL14690","softwareversion":"MACS","cell sex":"F","antibody":"ELF1_(SC-631)","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010764_hg19_wgEncodeHaibTfbsMcf7Elf1V0422111RawRep2.bigWig"},"geolst":["GSM1010764"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 ELF1","url":"http://egg.wustl.edu/d/hg19/GSM1010764_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24051","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Rabbit polyclonal IgG, epitope mapping at the C-terminus of Elf-1 of human origin. Antibody Target:  ELF1","antibody targetdescription":"This gene encodes an E26 transformation-specific related transcription factor.  The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes.  Alternative splicing results in multiple transcript variants. (provided by RefSeq)","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-631","controlid":"SL13504","labexpid":"SL13466,SL14690","softwareversion":"MACS","cell sex":"F","antibody":"ELF1_(SC-631)","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010764_hg19_wgEncodeHaibTfbsMcf7Elf1V0422111RawRep1.bigWig"},"geolst":["GSM1010764"]},{"type":"bigWig","name":"RIKEN Cage MCF-7 cytosol","url":"http://egg.wustl.edu/d/hg19/GSM979657_3.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25004","30011"],"details":{"datatype":"Cage","datatype description":"CAGE 5' RNA Tags","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089C","labexpid":"CThi10051","readtype":"1x50","readtype description":"Single 50 nt reads","replicate":"3","cell sex":"F","localization":"cytosol","localization description":"The fluid between the cells outer membrane and the nucleus","original_filename":"GSM979657_hg19_wgEncodeRikenCageMcf7CytosolPapPlusRawRep3.bigWig"},"geolst":["GSM979657"]},{"type":"bigWig","name":"USC ChipSeq MCF-7 H3K27ac","url":"http://egg.wustl.edu/d/hg19/GSM945854_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":150,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","22019","30016"],"details":{"lab":"USC","lab description":"Farnham - University of Southern California","datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"None","treatment description":"No special treatment or protocol applies","antibody":"H3K27ac","antibody antibodydescription":"rabbit polyclonal. Antibody Target: H3K27ac","antibody targetdescription":"Histone H3 (acetyl K27). As with H3K9ac, associated with transcriptional initiation and open chromatin structure. It remains unknown whether acetylation has can have different consequences depending on the specific lysine residue targeted. In general, though, there appears to be high redundancy. Histone acetylation is notable for susceptibility to small molecules and drugs that target histone deacetylases.","antibody vendorname":"Abcam","antibody vendorid":"ab4729","control":"UCDavis","control description":"Input library was prepared at UC Davis.","controlid":"wgEncodeEH000762","replicate":"1","original_filename":"GSM945854_hg19_wgEncodeSydhHistoneMcf7H3k27acUcdSig.bigWig"},"geolst":["GSM945854"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 Sin3Ak-20","url":"http://egg.wustl.edu/d/hg19/GSM1010862_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24054","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Rabbit polyclonal, Sin3A (k-20). Antibody Target: SIN3AK20","antibody targetdescription":"Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-994","controlid":"SL16757,SL13504","labexpid":"SL14716,SL13726","softwareversion":"MACS","cell sex":"F","antibody":"Sin3Ak-20","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010862_hg19_wgEncodeHaibTfbsMcf7Sin3ak20V0422111RawRep1.bigWig"},"geolst":["GSM1010862"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 FOXM1","url":"http://egg.wustl.edu/d/hg19/GSM1010769_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24692","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Rabbit polyclonal IgG, epitope mapping at the C-terminus of FOXM1 of human origin. Antibody Target: FOXM1","antibody targetdescription":"The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011)","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-502","controlid":"SL16758,SL13504","labexpid":"SL13462,SL14686","softwareversion":"MACS","cell sex":"F","antibody":"FOXM1_(SC-502)","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010769_hg19_wgEncodeHaibTfbsMcf7Foxm1sc502V0422111RawRep1.bigWig"},"geolst":["GSM1010769"]},{"type":"bigWig","name":"USC ChipSeq MCF-7 TCF7L2","url":"http://egg.wustl.edu/d/hg19/GSM816438_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24071","30016"],"details":{"lab":"USC","lab description":"Farnham - University of Southern California","datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"None","treatment description":"No special treatment or protocol applies","antibody":"TCF7L2","antibody antibodydescription":"Rabbit monoclonal. Antibody Target: TCF7L2","antibody targetdescription":"TCF7L2 (formerly known as TCF4) is a member of the high mobility group (HMG) DNA binding protein family of transcription factors which consists of the following: Lymphoid enhancer factor 1 (LEF1), T Cell Factor 1 (TCF1), TCF3 and TCF4. Note: there is an official TCF-4 http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCF4&search=TCF4","antibody vendorname":"Cell Signaling Technology","antibody vendorid":"2569","control":"UCDavis","control description":"Input library was prepared at UC Davis.","controlid":"wgEncodeEH000762","replicate":"1","replicate description":"tier 1","original_filename":"GSM816438_hg19_wgEncodeSydhTfbsMcf7Tcf7l2UcdSig.bigWig"},"geolst":["GSM816438"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 Egr-1","url":"http://egg.wustl.edu/d/hg19/GSM1010844_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24050","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Rabbit polyclonal, EGR-1 (588). Antibody Target: EGR1","antibody targetdescription":"Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner.","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-110","controlid":"SL16758,SL13504","labexpid":"SL14689,SL13465","softwareversion":"MACS","cell sex":"F","antibody":"Egr-1","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010844_hg19_wgEncodeHaibTfbsMcf7Egr1V0422111RawRep1.bigWig"},"geolst":["GSM1010844"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 TEAD4","url":"http://egg.wustl.edu/d/hg19/GSM1010860_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24680","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Mouse monoclonal IgG, raised against recombinant protein TEF-3 (TEAD4) of human origin. Antibody Target: TEAD4","antibody targetdescription":"Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression.","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-101184","controlid":"SL16757,SL16756","labexpid":"SL14575,SL16341","softwareversion":"MACS","cell sex":"F","antibody":"TEAD4_(SC-101184)","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010860_hg19_wgEncodeHaibTfbsMcf7Tead4sc101184V0422111RawRep1.bigWig"},"geolst":["GSM1010860"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 TEAD4","url":"http://egg.wustl.edu/d/hg19/GSM1010860_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24680","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Mouse monoclonal IgG, raised against recombinant protein TEF-3 (TEAD4) of human origin. Antibody Target: TEAD4","antibody targetdescription":"Member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is preferentially expressed in the skeletal muscle, and binds to the M-CAT regulatory element found in promoters of muscle-specific genes to direct their gene expression.","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-101184","controlid":"SL16757,SL16756","labexpid":"SL14575,SL16341","softwareversion":"MACS","cell sex":"F","antibody":"TEAD4_(SC-101184)","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010860_hg19_wgEncodeHaibTfbsMcf7Tead4sc101184V0422111RawRep2.bigWig"},"geolst":["GSM1010860"]},{"type":"bigWig","name":"Caltech RnaSeq MCF-7 2x75","url":"http://egg.wustl.edu/d/hg19/GSM958745_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30010"],"details":{"lab":"Caltech","lab description":"Wold - California Institute of Technology","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","readtype":"2x75","readtype description":"Paired 75 nt reads","insertlength":"200","insertlength description":"insert length of 200nt","treatment":"None","treatment description":"No special treatment or protocol applies","labexpid":"11581","mapalgorithm":"TH1014","mapalgorithm description":"TopHat v1.0.14","replicate":"1","original_filename":"GSM958745_hg19_wgEncodeCaltechRnaSeqMcf7R2x75Th1014Il200SigRep2V4.bigWig"},"geolst":["GSM958745"]},{"type":"bigWig","name":"Caltech RnaSeq MCF-7 2x75","url":"http://egg.wustl.edu/d/hg19/GSM958745_3.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30010"],"details":{"lab":"Caltech","lab description":"Wold - California Institute of Technology","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","readtype":"2x75","readtype description":"Paired 75 nt reads","insertlength":"200","insertlength description":"insert length of 200nt","treatment":"None","treatment description":"No special treatment or protocol applies","labexpid":"11581","mapalgorithm":"TH1014","mapalgorithm description":"TopHat v1.0.14","replicate":"1","original_filename":"GSM958745_hg19_wgEncodeCaltechRnaSeqMcf7R2x75Th1014Il200SigRep3V4.bigWig"},"geolst":["GSM958745"]},{"type":"bigWig","name":"Caltech RnaSeq MCF-7 2x75","url":"http://egg.wustl.edu/d/hg19/GSM958745_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30010"],"details":{"lab":"Caltech","lab description":"Wold - California Institute of Technology","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","readtype":"2x75","readtype description":"Paired 75 nt reads","insertlength":"200","insertlength description":"insert length of 200nt","treatment":"None","treatment description":"No special treatment or protocol applies","labexpid":"11581","mapalgorithm":"TH1014","mapalgorithm description":"TopHat v1.0.14","replicate":"1","original_filename":"GSM958745_hg19_wgEncodeCaltechRnaSeqMcf7R2x75Th1014Il200SigRep1V4.bigWig"},"geolst":["GSM958745"]},{"type":"bigWig","name":"GIS RnaPet MCF-7 nucleus","url":"http://egg.wustl.edu/d/hg19/GSM1006912_4.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25006","30007"],"details":{"datatype":"RnaPet","datatype description":"RNA Paired-End Tags","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089N,090N","labexpid":"RHM054,RHM055","labversion":"clone-free","readtype":"2x36","readtype description":"Paired 36 nt reads","replicate":"3,4","localization":"nucleus","localization description":"Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA","original_filename":"GSM1006912_hg19_wgEncodeGisRnaPetMcf7NucleusPapPlusRawRep4.bigWig"},"geolst":["GSM1006912"]},{"type":"bigWig","name":"GIS RnaPet MCF-7 nucleus","url":"http://egg.wustl.edu/d/hg19/GSM1006912_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25006","30007"],"details":{"datatype":"RnaPet","datatype description":"RNA Paired-End Tags","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089N,090N","labexpid":"RHM054,RHM055","labversion":"clone-free","readtype":"2x36","readtype description":"Paired 36 nt reads","replicate":"3,4","localization":"nucleus","localization description":"Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA","original_filename":"GSM1006912_hg19_wgEncodeGisRnaPetMcf7NucleusPapMinusRawRep3.bigWig"},"geolst":["GSM1006912"]},{"type":"bigWig","name":"GIS RnaPet MCF-7 nucleus","url":"http://egg.wustl.edu/d/hg19/GSM1006912_3.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25006","30007"],"details":{"datatype":"RnaPet","datatype description":"RNA Paired-End Tags","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089N,090N","labexpid":"RHM054,RHM055","labversion":"clone-free","readtype":"2x36","readtype description":"Paired 36 nt reads","replicate":"3,4","localization":"nucleus","localization description":"Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA","original_filename":"GSM1006912_hg19_wgEncodeGisRnaPetMcf7NucleusPapPlusRawRep3.bigWig"},"geolst":["GSM1006912"]},{"type":"bigWig","name":"UT-A ChipSeq MCF-7 vehicle","url":"http://egg.wustl.edu/d/hg19/GSM822308_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24001","30009"],"details":{"lab":"UT-A","lab description":"Iyer - University of Texas at Austin","datatype":"ChipSeq","datatype description":"ChIP-Seq","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"vehicle","treatment description":"Charcoal stripped hormone-free FBS for 72 hours (Crawford)","antibody":"CTCF","antibody antibodydescription":"rabbit polyclonal","antibody targetdescription":"CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.","antibody vendorname":"Millipore","antibody vendorid":"07-729","controlid":"MCF-7/Input","labversion":"align_on_cluster_bwa.pl v 1","replicate":"1","replicate description":"tier 1","original_filename":"GSM822308_hg19_wgEncodeOpenChromChipMcf7CtcfVehSig.bigWig"},"geolst":["GSM822308"]},{"type":"bigWig","name":"Duke DnaseSeq MCF-7","url":"http://egg.wustl.edu/d/hg19/GSM816627_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":77,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23001","30019"],"details":{"lab":"Duke","lab description":"Crawford - Duke University","datatype":"DnaseSeq","datatype description":"DNase digestion followed by sequencing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"None","treatment description":"No special treatment or protocol applies","controlid":"MCF-7/Input","labversion":"align_on_cluster_bwa.pl v 1","replicate":"1","replicate description":"tier 1","original_filename":"GSM816627_hg19_wgEncodeOpenChromDnaseMcf7Sig.bigWig"},"geolst":["GSM816627"]},{"type":"bigWig","name":"Duke DnaseSeq MCF-7","url":"http://egg.wustl.edu/d/hg19/GSM816627_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":77,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23001","30019"],"details":{"lab":"Duke","lab description":"Crawford - Duke University","datatype":"DnaseSeq","datatype description":"DNase digestion followed by sequencing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"None","treatment description":"No special treatment or protocol applies","controlid":"MCF-7/Input","labversion":"align_on_cluster_bwa.pl v 1","replicate":"1","replicate description":"tier 1","original_filename":"GSM816627_hg19_wgEncodeOpenChromDnaseMcf7BaseOverlapSignal.bigWig"},"geolst":["GSM816627"]},{"type":"bigWig","name":"UW ChipSeq MCF-7 H3K4me3","url":"http://egg.wustl.edu/d/hg19/GSM945269_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":117,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","22009","30004"],"details":{"lab":"UW","lab description":"Stamatoyannopoulous - University of Washington","datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","antibody":"H3K4me3","antibody antibodydescription":"rabbit polyclonal. Antibody Target: H3K4me3","antibody targetdescription":"Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.","antibody vendorname":"Millipore","antibody vendorid":"07-473","treatment":"None","treatment description":"No special treatment or protocol applies","control":"std","control description":"Standard input signal for most experiments.","controlid":"wgEncodeEH000968","labexpid":"DS16201","labversion":"Bowtie 0.12.7","replicate":"2","original_filename":"GSM945269_hg19_wgEncodeUwHistoneMcf7H3k4me3StdRawRep1.bigWig"},"geolst":["GSM945269"]},{"type":"bigWig","name":"UW ChipSeq MCF-7 H3K4me3","url":"http://egg.wustl.edu/d/hg19/GSM945269_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":117,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","22009","30004"],"details":{"lab":"UW","lab description":"Stamatoyannopoulous - University of Washington","datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","antibody":"H3K4me3","antibody antibodydescription":"rabbit polyclonal. Antibody Target: H3K4me3","antibody targetdescription":"Histone H3 (tri methyl K4). Marks promoters that are active or poised to be activated.","antibody vendorname":"Millipore","antibody vendorid":"07-473","treatment":"None","treatment description":"No special treatment or protocol applies","control":"std","control description":"Standard input signal for most experiments.","controlid":"wgEncodeEH000968","labexpid":"DS16201","labversion":"Bowtie 0.12.7","replicate":"2","original_filename":"GSM945269_hg19_wgEncodeUwHistoneMcf7H3k04me3StdRawRep2.bigWig"},"geolst":["GSM945269"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 JunD","url":"http://egg.wustl.edu/d/hg19/GSM1010892_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24063","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"rabbit polyclonal IgG. Antibody Target: JunD","antibody targetdescription":"The protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. It has been proposed to protect cells from p53-dependent senescence and apoptosis. Alternate translation initiation site usage results in the production of different isoforms. (provided by RefSeq)","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-74","controlid":"SL13504","labexpid":"SL14694,SL13484","softwareversion":"MACS","cell sex":"F","antibody":"JunD","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010892_hg19_wgEncodeHaibTfbsMcf7JundV0422111RawRep1.bigWig"},"geolst":["GSM1010892"]},{"type":"bigWig","name":"Duke DnaseSeq MCF-7 Randomized","url":"http://egg.wustl.edu/d/hg19/GSM1008603_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":77,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23001","30019"],"details":{"datatype":"DnaseSeq","datatype description":"DNaseI HS Sequencing","labversion":"baseAlignCounts.pl v 1","replicate":"1,3,2","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"Randomized_shRNA_control","treatment description":"Cells were transduced with a lentivirus expressing an shRNA containing a randomized DNA sequence generated by the siRNA Wizard v3.1 (http://www.sirnawizard.com/scrambled2.php) program. Lentiviral constructs also contained the puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct.","original_filename":"GSM1008603_hg19_wgEncodeOpenChromDnaseMcf7RandshrnaBaseOverlapSignal.bigWig"},"geolst":["GSM1008603"]},{"type":"bigWig","name":"UT-A ChipSeq MCF-7 serum","url":"http://egg.wustl.edu/d/hg19/GSM1006865_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24634","30009"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"mouse monoclonal, clone 8WG16. Antibody Target: POL2","antibody targetdescription":"RNA Polymerase II","antibody vendorname":"Covance","antibody vendorid":"MMS-126R","controlid":"wgEncodeEH000589","labversion":"baseAlignCounts.pl v 1","replicate":"1,2","cell sex":"F","treatment":"serum_starved_media","treatment description":"Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours","antibody":"Pol2","original_filename":"GSM1006865_hg19_wgEncodeOpenChromChipMcf7Pol2SerumstvdBaseOverlapSignal.bigWig"},"geolst":["GSM1006865"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 FOXM1","url":"http://egg.wustl.edu/d/hg19/GSM1010769_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24692","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Rabbit polyclonal IgG, epitope mapping at the C-terminus of FOXM1 of human origin. Antibody Target: FOXM1","antibody targetdescription":"The protein encoded by this gene is a transcriptional activator involved in cell proliferation. The encoded protein is phosphorylated in M phase and regulates the expression of several cell cycle genes, such as cyclin B1 and cyclin D1. Several transcript variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2011)","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-502","controlid":"SL16758,SL13504","labexpid":"SL13462,SL14686","softwareversion":"MACS","cell sex":"F","antibody":"FOXM1_(SC-502)","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010769_hg19_wgEncodeHaibTfbsMcf7Foxm1sc502V0422111RawRep2.bigWig"},"geolst":["GSM1010769"]},{"type":"bigWig","name":"UT-A ChipSeq MCF-7 estrogen","url":"http://egg.wustl.edu/d/hg19/GSM822304_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24004","30009"],"details":{"lab":"UT-A","lab description":"Iyer - University of Texas at Austin","datatype":"ChipSeq","datatype description":"ChIP-Seq","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"estrogen","treatment description":"45 min with 100 nM Estradiol (Crawford)","antibody":"c-Myc","antibody antibodydescription":"rabbit polyclonal to amino acids 1-262 of c-Myc human origin","antibody targetdescription":"transcription factor","antibody vendorname":"Santa Cruz Biotech","antibody vendorid":"sc-764","controlid":"MCF-7/Input","labversion":"align_on_cluster_bwa.pl v 1","replicate":"1","replicate description":"tier 1","original_filename":"GSM822304_hg19_wgEncodeOpenChromChipMcf7CmycEstroBaseOverlapSignal.bigWig"},"geolst":["GSM822304"]},{"type":"bigWig","name":"UT-A ChipSeq MCF-7 estrogen","url":"http://egg.wustl.edu/d/hg19/GSM822304_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24004","30009"],"details":{"lab":"UT-A","lab description":"Iyer - University of Texas at Austin","datatype":"ChipSeq","datatype description":"ChIP-Seq","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"estrogen","treatment description":"45 min with 100 nM Estradiol (Crawford)","antibody":"c-Myc","antibody antibodydescription":"rabbit polyclonal to amino acids 1-262 of c-Myc human origin","antibody targetdescription":"transcription factor","antibody vendorname":"Santa Cruz Biotech","antibody vendorid":"sc-764","controlid":"MCF-7/Input","labversion":"align_on_cluster_bwa.pl v 1","replicate":"1","replicate description":"tier 1","original_filename":"GSM822304_hg19_wgEncodeOpenChromChipMcf7CmycEstroSig.bigWig"},"geolst":["GSM822304"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 Egr-1","url":"http://egg.wustl.edu/d/hg19/GSM1010844_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24050","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Rabbit polyclonal, EGR-1 (588). Antibody Target: EGR1","antibody targetdescription":"Egr-1, Egr-2, Egr-3 and Egr-4 are nuclear transcription factors belonging to the Egr C2H2-type zinc-finger protein family and containing three C2H2-type zinc fingers. As immediate early proteins, Egr transcription factors are rapidly induced by diverse extracellular stimuli. Egr proteins are subject to tight differential control through diverse mechanisms at several levels of regulation including transcriptional, translational and post-translational (including glyco- sylation, phosphorylation and redox) mechanisms and protein-protein inter- action. Egr-1 binds to the DNA sequence 5'-CGCCCCCGC-3' (EGR-site), there- by activating transcription of target genes whose products are required for mitogenisis and differentiation. Egr-2 binds specific DNA sites located in the promoter region of HoxA4. Egr-2 defects cause congenital hypomyelination neuropathy (also designated Charcot-Marie-tooth disease) and Dejerine- Sottas neuropathology (also designated hereditary motor and sensory neuro- pathy III. Egr-3 is involved in muscle spindle development and is expressed in T cells 20 minutes following activation. EGR-4 binds to the EGR consensus motif GCGTGGGCG, functions as a transcriptional repressor, and displays autoregulatory activities, downregulating its on gene promoter in a dose dependent manner.","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-110","controlid":"SL16758,SL13504","labexpid":"SL14689,SL13465","softwareversion":"MACS","cell sex":"F","antibody":"Egr-1","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010844_hg19_wgEncodeHaibTfbsMcf7Egr1V0422111RawRep2.bigWig"},"geolst":["GSM1010844"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 PML","url":"http://egg.wustl.edu/d/hg19/GSM1010838_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24688","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Mouse monoclonal IgG, N-terminal epitope corresponding to residues 37-51 of PML of human origin. Antibody Target: PML","antibody targetdescription":"The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-71910","controlid":"SL16757,SL16756","labexpid":"SL16026,SL13722","softwareversion":"MACS","cell sex":"F","antibody":"PML_(SC-71910)","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010838_hg19_wgEncodeHaibTfbsMcf7Pmlsc71910V0422111RawRep1.bigWig"},"geolst":["GSM1010838"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 SRF","url":"http://egg.wustl.edu/d/hg19/GSM1010839_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24023","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Rabbit polyclonal. Antibody Target: SRF","antibody targetdescription":"Serum response transcription factor","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-335","controlid":"SL16757,SL16756","labexpid":"SL16044,SL13723","softwareversion":"MACS","cell sex":"F","antibody":"SRF","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010839_hg19_wgEncodeHaibTfbsMcf7SrfV0422111RawRep1.bigWig"},"geolst":["GSM1010839"]},{"type":"bigWig","name":"UW ChipSeq MCF-7 Input","url":"http://egg.wustl.edu/d/hg19/GSM945274_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":200,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","22001","30004"],"details":{"lab":"UW","lab description":"Stamatoyannopoulous - University of Washington","datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","antibody":"Input","antibody description":"Control signal which may be subtracted from experimental raw signal before peaks are called.","treatment":"None","treatment description":"No special treatment or protocol applies","control":"std","control description":"Standard input signal for most experiments.","controlid":"wgEncodeEH000968","labexpid":"DS16198","labversion":"Bowtie 0.12.7","replicate":"1","original_filename":"GSM945274_hg19_wgEncodeUwHistoneMcf7InputStdRawRep1.bigWig"},"geolst":["GSM945274"]},{"type":"bigWig","name":"UT-A ChipSeq MCF-7 estrogen","url":"http://egg.wustl.edu/d/hg19/GSM822309_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24001","30009"],"details":{"lab":"UT-A","lab description":"Iyer - University of Texas at Austin","datatype":"ChipSeq","datatype description":"ChIP-Seq","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"estrogen","treatment description":"45 min with 100 nM Estradiol (Crawford)","antibody":"CTCF","antibody antibodydescription":"rabbit polyclonal","antibody targetdescription":"CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.","antibody vendorname":"Millipore","antibody vendorid":"07-729","controlid":"MCF-7/Input","labversion":"align_on_cluster_bwa.pl v 1","replicate":"1","replicate description":"tier 1","original_filename":"GSM822309_hg19_wgEncodeOpenChromChipMcf7CtcfEstroBaseOverlapSignal.bigWig"},"geolst":["GSM822309"]},{"type":"bigWig","name":"UW ChipSeq MCF-7 CTCFRep2","url":"http://egg.wustl.edu/d/hg19/GSM1022663_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24001","30004"],"details":{"lab":"UW","lab description":"Stamatoyannopoulous - University of Washington","datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","antibody":"CTCF","antibody antibodydescription":"Rabbit polyclonal. Antibody Target: CTCF","antibody targetdescription":"CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.","antibody vendorname":"Millipore","antibody vendorid":"07-729","treatment":"None","treatment description":"No special treatment or protocol applies","control":"std","control description":"Standard input signal for most experiments.","controlid":"wgEncodeEH000968","labexpid":"DS16199","labversion":"Hotspot-v5.2,lmax-v1.0,WindowDensity-bin20-win+/-75","replicate":"2","original_filename":"GSM1022663_hg19_wgEncodeUwTfbsMcf7CtcfStdRawRep2.bigWig"},"geolst":["GSM1022663"]},{"type":"bigWig","name":"Duke DnaseSeq MCF-7 Randomized","url":"http://egg.wustl.edu/d/hg19/GSM1008603_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":77,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23001","30019"],"details":{"datatype":"DnaseSeq","datatype description":"DNaseI HS Sequencing","labversion":"baseAlignCounts.pl v 1","replicate":"1,3,2","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"Randomized_shRNA_control","treatment description":"Cells were transduced with a lentivirus expressing an shRNA containing a randomized DNA sequence generated by the siRNA Wizard v3.1 (http://www.sirnawizard.com/scrambled2.php) program. Lentiviral constructs also contained the puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct.","original_filename":"GSM1008603_hg19_wgEncodeOpenChromDnaseMcf7RandshrnaSig.bigWig"},"geolst":["GSM1008603"]},{"type":"bigWig","name":"UT-A ChipSeq MCF-7 Input","url":"http://egg.wustl.edu/d/hg19/GSM822283_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":200,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","22001","30009"],"details":{"lab":"UT-A","lab description":"Iyer - University of Texas at Austin","datatype":"ChipSeq","datatype description":"ChIP-Seq","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","antibody":"Input","antibody description":"Control signal which may be subtracted from experimental raw signal before peaks are called.","controlid":"MCF-7/Input","labversion":"align_on_cluster_bwa.pl v 1","original_filename":"GSM822283_hg19_wgEncodeOpenChromChipMcf7InputSig.bigWig"},"geolst":["GSM822283"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 CEBPB","url":"http://egg.wustl.edu/d/hg19/GSM1010889_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24624","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Rabbit polyclonal IgG, epitope mapping at the C-terminus of CEBPB of rat origin. Antibody Target: CEBPB","antibody targetdescription":"The protein encoded by this intronless gene is a bZIP transcription factor which can bind as a homodimer to certain DNA regulatory regions.  It can also form heterodimers with the related proteins CEBP-alpha, CEBP-delta, and CEBP-gamma.  The encoded protein is important in the regulation of genes involved in immune and inflammatory responses and has been shown to bind to the IL-1 response element in the IL-6 gene, as well as to regulatory regions of several acute-phase and cytokine genes.  In addition, the encoded protein can bind the promoter and upstream element and stimulate the expression of the collagen type I gene (provided by RefSeq).","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-150","controlid":"SL13504","labexpid":"SL13460,SL14684","softwareversion":"MACS","cell sex":"F","antibody":"CEBPB_(SC-150)","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010889_hg19_wgEncodeHaibTfbsMcf7Cebpbsc150V0422111RawRep1.bigWig"},"geolst":["GSM1010889"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM897081_5.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","protocol":"TAP-Only","protocol description":"This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"015WC,016WC","labexpid":"LID20743,LID20744","labversion":"iIDR","readtype":"1x36","readtype description":"Single 36 nt reads","original_filename":"GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapPlusRawRep1.bigWig"},"geolst":["GSM897081"]},{"type":"bigWig","name":"GIS RnaPet MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM1006905_4.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25006","30007"],"details":{"datatype":"RnaPet","datatype description":"RNA Paired-End Tags","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089WC,090WC","labexpid":"RHM046,RHM047","labversion":"iIDR","readtype":"2x36","readtype description":"Paired 36 nt reads","replicate":"3,4","localization":"cell","localization description":"Whole cell","original_filename":"GSM1006905_hg19_wgEncodeGisRnaPetMcf7CellPapPlusRawRep4.bigWig"},"geolst":["GSM1006905"]},{"type":"bigWig","name":"UT-A ChipSeq MCF-7 vehicle","url":"http://egg.wustl.edu/d/hg19/GSM822308_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24001","30009"],"details":{"lab":"UT-A","lab description":"Iyer - University of Texas at Austin","datatype":"ChipSeq","datatype description":"ChIP-Seq","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"vehicle","treatment description":"Charcoal stripped hormone-free FBS for 72 hours (Crawford)","antibody":"CTCF","antibody antibodydescription":"rabbit polyclonal","antibody targetdescription":"CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.","antibody vendorname":"Millipore","antibody vendorid":"07-729","controlid":"MCF-7/Input","labversion":"align_on_cluster_bwa.pl v 1","replicate":"1","replicate description":"tier 1","original_filename":"GSM822308_hg19_wgEncodeOpenChromChipMcf7CtcfVehBaseOverlapSignal.bigWig"},"geolst":["GSM822308"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 nucleus","url":"http://egg.wustl.edu/d/hg19/GSM981245_4.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089N,090N","labexpid":"LID46859,LID46860","labversion":"iIDR","readtype":"2x101D","readtype description":"Paired 101 nt directed reads","replicate":"3,4","spikeinpool":"Nist14","localization description":"Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA","original_filename":"GSM981245_hg19_wgEncodeCshlLongRnaSeqMcf7NucleusPapPlusRep4.bigWig"},"geolst":["GSM981245"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 TAF1","url":"http://egg.wustl.edu/d/hg19/GSM1010811_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24028","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Mouse monoclonal (p250). Antibody Target: TAF1","antibody targetdescription":"TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250.","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-735","controlid":"SL16757,SL16756","labexpid":"SL14572,SL16339","softwareversion":"MACS","cell sex":"F","antibody":"TAF1","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010811_hg19_wgEncodeHaibTfbsMcf7Taf1V0422111RawRep1.bigWig"},"geolst":["GSM1010811"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 TAF1","url":"http://egg.wustl.edu/d/hg19/GSM1010811_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24028","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Mouse monoclonal (p250). Antibody Target: TAF1","antibody targetdescription":"TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa. Also designated TAF250.","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-735","controlid":"SL16757,SL16756","labexpid":"SL14572,SL16339","softwareversion":"MACS","cell sex":"F","antibody":"TAF1","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010811_hg19_wgEncodeHaibTfbsMcf7Taf1V0422111RawRep2.bigWig"},"geolst":["GSM1010811"]},{"type":"bigWig","name":"UT-A ChipSeq MCF-7 serum","url":"http://egg.wustl.edu/d/hg19/GSM1006876_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24634","30009"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"mouse monoclonal, clone 8WG16. Antibody Target: POL2","antibody targetdescription":"RNA Polymerase II","antibody vendorname":"Covance","antibody vendorid":"MMS-126R","controlid":"wgEncodeEH000589","labversion":"baseAlignCounts.pl v 1","replicate":"1,2","cell sex":"F","treatment":"serum_stimulated_media","treatment description":"Grown with normal serum levels (10%), then switched back to normal serum levels (10% FBS) for 3 hours.","antibody":"Pol2","original_filename":"GSM1006876_hg19_wgEncodeOpenChromChipMcf7Pol2SerumstimBaseOverlapSignal.bigWig"},"geolst":["GSM1006876"]},{"type":"bigWig","name":"USC ChipSeq MCF-7 Input","url":"http://egg.wustl.edu/d/hg19/GSM935485_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":200,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","22001","30016"],"details":{"lab":"USC","lab description":"Farnham - University of Southern California","datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"None","treatment description":"No special treatment or protocol applies","antibody":"Input","antibody description":"Control signal which may be subtracted from experimental raw signal before peaks are called.","control":"UCDavis","control description":"Input library was prepared at UC Davis.","controlid":"wgEncodeEH000762","labversion":"MCF7 cells stably expressed a tagged HA-E2F1 were fragmented using Bioruptor, crosslinks were reversed at 67*C overnight and Input was Qiagen purified,","replicate":"1","softwareversion":"PeakSeq1.0 (fdr 0.001)","original_filename":"GSM935485_hg19_wgEncodeSydhTfbsMcf7InputUcdSig.bigWig"},"geolst":["GSM935485"]},{"type":"bigWig","name":"RIKEN Cage MCF-7 cytosol","url":"http://egg.wustl.edu/d/hg19/GSM979657_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25004","30011"],"details":{"datatype":"Cage","datatype description":"CAGE 5' RNA Tags","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089C","labexpid":"CThi10051","readtype":"1x50","readtype description":"Single 50 nt reads","replicate":"3","cell sex":"F","localization":"cytosol","localization description":"The fluid between the cells outer membrane and the nucleus","original_filename":"GSM979657_hg19_wgEncodeRikenCageMcf7CytosolPapMinusRawRep3.bigWig"},"geolst":["GSM979657"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 Sin3Ak-20","url":"http://egg.wustl.edu/d/hg19/GSM1010862_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24054","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Rabbit polyclonal, Sin3A (k-20). Antibody Target: SIN3AK20","antibody targetdescription":"Co-repressor interacting with HDAC1, N-coR, SMRT, and MeCP2","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-994","controlid":"SL16757,SL13504","labexpid":"SL14716,SL13726","softwareversion":"MACS","cell sex":"F","antibody":"Sin3Ak-20","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010862_hg19_wgEncodeHaibTfbsMcf7Sin3ak20V0422111RawRep2.bigWig"},"geolst":["GSM1010862"]},{"type":"bigWig","name":"UT-A ChipSeq MCF-7 estrogen","url":"http://egg.wustl.edu/d/hg19/GSM822309_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24001","30009"],"details":{"lab":"UT-A","lab description":"Iyer - University of Texas at Austin","datatype":"ChipSeq","datatype description":"ChIP-Seq","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"estrogen","treatment description":"45 min with 100 nM Estradiol (Crawford)","antibody":"CTCF","antibody antibodydescription":"rabbit polyclonal","antibody targetdescription":"CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.","antibody vendorname":"Millipore","antibody vendorid":"07-729","controlid":"MCF-7/Input","labversion":"align_on_cluster_bwa.pl v 1","replicate":"1","replicate description":"tier 1","original_filename":"GSM822309_hg19_wgEncodeOpenChromChipMcf7CtcfEstroSig.bigWig"},"geolst":["GSM822309"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM897081_8.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","protocol":"TAP-Only","protocol description":"This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"015WC,016WC","labexpid":"LID20743,LID20744","labversion":"iIDR","readtype":"1x36","readtype description":"Single 36 nt reads","original_filename":"GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapPlusRawRep4.bigWig"},"geolst":["GSM897081"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM897081_3.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","protocol":"TAP-Only","protocol description":"This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"015WC,016WC","labexpid":"LID20743,LID20744","labversion":"iIDR","readtype":"1x36","readtype description":"Single 36 nt reads","original_filename":"GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapMinusRawRep3.bigWig"},"geolst":["GSM897081"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM897081_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","protocol":"TAP-Only","protocol description":"This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"015WC,016WC","labexpid":"LID20743,LID20744","labversion":"iIDR","readtype":"1x36","readtype description":"Single 36 nt reads","original_filename":"GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapMinusRawRep2.bigWig"},"geolst":["GSM897081"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM897081_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","protocol":"TAP-Only","protocol description":"This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"015WC,016WC","labexpid":"LID20743,LID20744","labversion":"iIDR","readtype":"1x36","readtype description":"Single 36 nt reads","original_filename":"GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapMinusRawRep1.bigWig"},"geolst":["GSM897081"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM897081_7.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","protocol":"TAP-Only","protocol description":"This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"015WC,016WC","labexpid":"LID20743,LID20744","labversion":"iIDR","readtype":"1x36","readtype description":"Single 36 nt reads","original_filename":"GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapPlusRawRep3.bigWig"},"geolst":["GSM897081"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM897081_6.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","protocol":"TAP-Only","protocol description":"This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"015WC,016WC","labexpid":"LID20743,LID20744","labversion":"iIDR","readtype":"1x36","readtype description":"Single 36 nt reads","original_filename":"GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapPlusRawRep2.bigWig"},"geolst":["GSM897081"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM897081_4.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","protocol":"TAP-Only","protocol description":"This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"015WC,016WC","labexpid":"LID20743,LID20744","labversion":"iIDR","readtype":"1x36","readtype description":"Single 36 nt reads","original_filename":"GSM897081_hg19_wgEncodeCshlShortRnaSeqMcf7CellShorttotalTapMinusRawRep4.bigWig"},"geolst":["GSM897081"]},{"type":"bigWig","name":"GIS RnaPet MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM1006905_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25006","30007"],"details":{"datatype":"RnaPet","datatype description":"RNA Paired-End Tags","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089WC,090WC","labexpid":"RHM046,RHM047","labversion":"iIDR","readtype":"2x36","readtype description":"Paired 36 nt reads","replicate":"3,4","localization":"cell","localization description":"Whole cell","original_filename":"GSM1006905_hg19_wgEncodeGisRnaPetMcf7CellPapMinusRawRep3.bigWig"},"geolst":["GSM1006905"]},{"type":"bigWig","name":"GIS RnaPet MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM1006905_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25006","30007"],"details":{"datatype":"RnaPet","datatype description":"RNA Paired-End Tags","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089WC,090WC","labexpid":"RHM046,RHM047","labversion":"iIDR","readtype":"2x36","readtype description":"Paired 36 nt reads","replicate":"3,4","localization":"cell","localization description":"Whole cell","original_filename":"GSM1006905_hg19_wgEncodeGisRnaPetMcf7CellPapMinusRawRep4.bigWig"},"geolst":["GSM1006905"]},{"type":"bigWig","name":"GIS RnaPet MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM1006905_3.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25006","30007"],"details":{"datatype":"RnaPet","datatype description":"RNA Paired-End Tags","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089WC,090WC","labexpid":"RHM046,RHM047","labversion":"iIDR","readtype":"2x36","readtype description":"Paired 36 nt reads","replicate":"3,4","localization":"cell","localization description":"Whole cell","original_filename":"GSM1006905_hg19_wgEncodeGisRnaPetMcf7CellPapPlusRawRep3.bigWig"},"geolst":["GSM1006905"]},{"type":"bigWig","name":"UT-A ChipSeq MCF-7 Pol2","url":"http://egg.wustl.edu/d/hg19/GSM822295_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24003","30009"],"details":{"lab":"UT-A","lab description":"Iyer - University of Texas at Austin","datatype":"ChipSeq","datatype description":"ChIP-Seq","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","antibody":"Pol2","antibody antibodydescription":"mouse monoclonal, clone 8WG16","antibody targetdescription":"RNA Polymerase II","antibody vendorname":"Covance","antibody vendorid":"MMS-126R","controlid":"MCF-7/Input","labversion":"align_on_cluster_bwa.pl v 1","replicate":"1","replicate description":"tier 1","original_filename":"GSM822295_hg19_wgEncodeOpenChromChipMcf7Pol2Sig.bigWig"},"geolst":["GSM822295"]},{"type":"bigWig","name":"UT-A ChipSeq MCF-7 Pol2","url":"http://egg.wustl.edu/d/hg19/GSM822295_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24003","30009"],"details":{"lab":"UT-A","lab description":"Iyer - University of Texas at Austin","datatype":"ChipSeq","datatype description":"ChIP-Seq","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","antibody":"Pol2","antibody antibodydescription":"mouse monoclonal, clone 8WG16","antibody targetdescription":"RNA Polymerase II","antibody vendorname":"Covance","antibody vendorid":"MMS-126R","controlid":"MCF-7/Input","labversion":"align_on_cluster_bwa.pl v 1","replicate":"1","replicate description":"tier 1","original_filename":"GSM822295_hg19_wgEncodeOpenChromChipMcf7Pol2BaseOverlapSignal.bigWig"},"geolst":["GSM822295"]},{"type":"bigWig","name":"UT-A ChipSeq MCF-7 serum","url":"http://egg.wustl.edu/d/hg19/GSM1006866_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24004","30009"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"rabbit polyclonal to amino acids 1-262 of c-Myc human origin. Antibody Target: c-Myc","antibody targetdescription":"transcription factor","antibody vendorname":"Santa Cruz Biotech","antibody vendorid":"sc-764","controlid":"wgEncodeEH000589","labversion":"baseAlignCounts.pl v 1","replicate":"1,2","cell sex":"F","treatment":"serum_starved_media","treatment description":"Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours","antibody":"c-Myc","original_filename":"GSM1006866_hg19_wgEncodeOpenChromChipMcf7CmycSerumstvdBaseOverlapSignal.bigWig"},"geolst":["GSM1006866"]},{"type":"bigWig","name":"GIS RnaPet MCF-7 nucleus","url":"http://egg.wustl.edu/d/hg19/GSM1006912_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25006","30007"],"details":{"datatype":"RnaPet","datatype description":"RNA Paired-End Tags","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089N,090N","labexpid":"RHM054,RHM055","labversion":"clone-free","readtype":"2x36","readtype description":"Paired 36 nt reads","replicate":"3,4","localization":"nucleus","localization description":"Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA","original_filename":"GSM1006912_hg19_wgEncodeGisRnaPetMcf7NucleusPapMinusRawRep4.bigWig"},"geolst":["GSM1006912"]},{"type":"bigWig","name":"Duke DnaseSeq MCF-7 CTCF","url":"http://egg.wustl.edu/d/hg19/GSM1008581_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":77,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23001","30019"],"details":{"datatype":"DnaseSeq","datatype description":"DNaseI HS Sequencing","labversion":"baseAlignCounts.pl v 1","replicate":"1,3,2","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"CTCF_shRNA_knockdown","treatment description":"CTCF (CCCTC-binding factor) transcript levels were knocked down in cells using lentiviral transduction to express an shRNA targeting the CTCF gene. The lentiviral construct also contained a puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. By western blot, CTCF protein levels in the knockdown cells were <10% of cell lines transduced with a randomized shRNA lentiviral construct.","original_filename":"GSM1008581_hg19_wgEncodeOpenChromDnaseMcf7CtcfshrnaSig.bigWig"},"geolst":["GSM1008581"]},{"type":"bigWig","name":"Duke DnaseSeq MCF-7 CTCF","url":"http://egg.wustl.edu/d/hg19/GSM1008581_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":77,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23001","30019"],"details":{"datatype":"DnaseSeq","datatype description":"DNaseI HS Sequencing","labversion":"baseAlignCounts.pl v 1","replicate":"1,3,2","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"CTCF_shRNA_knockdown","treatment description":"CTCF (CCCTC-binding factor) transcript levels were knocked down in cells using lentiviral transduction to express an shRNA targeting the CTCF gene. The lentiviral construct also contained a puromycin resistance selectable marker and cells were treated 2 times, for three days each, to select for cells containing the retroviral construct. By western blot, CTCF protein levels in the knockdown cells were <10% of cell lines transduced with a randomized shRNA lentiviral construct.","original_filename":"GSM1008581_hg19_wgEncodeOpenChromDnaseMcf7CtcfshrnaBaseOverlapSignal.bigWig"},"geolst":["GSM1008581"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cytosol","url":"http://egg.wustl.edu/d/hg19/GSM981252_4.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089C,090C","labexpid":"LID46857,LID46858","labversion":"iIDR","readtype":"2x101D","readtype description":"Paired 101 nt directed reads","replicate":"3,4","spikeinpool":"Nist14","localization description":"The fluid between the cells outer membrane and the nucleus","original_filename":"GSM981252_hg19_wgEncodeCshlLongRnaSeqMcf7CytosolPapPlusRep4.bigWig"},"geolst":["GSM981252"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cytosol","url":"http://egg.wustl.edu/d/hg19/GSM981252_3.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089C,090C","labexpid":"LID46857,LID46858","labversion":"iIDR","readtype":"2x101D","readtype description":"Paired 101 nt directed reads","replicate":"3,4","spikeinpool":"Nist14","localization description":"The fluid between the cells outer membrane and the nucleus","original_filename":"GSM981252_hg19_wgEncodeCshlLongRnaSeqMcf7CytosolPapPlusRep3.bigWig"},"geolst":["GSM981252"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cytosol","url":"http://egg.wustl.edu/d/hg19/GSM981252_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089C,090C","labexpid":"LID46857,LID46858","labversion":"iIDR","readtype":"2x101D","readtype description":"Paired 101 nt directed reads","replicate":"3,4","spikeinpool":"Nist14","localization description":"The fluid between the cells outer membrane and the nucleus","original_filename":"GSM981252_hg19_wgEncodeCshlLongRnaSeqMcf7CytosolPapMinusRep4.bigWig"},"geolst":["GSM981252"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 NRSF","url":"http://egg.wustl.edu/d/hg19/GSM1010891_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24014","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Mouse monoclonal. Antibody Target: NRSF","antibody targetdescription":"Neuron-restrictive silencer transcription factor","antibody vendorname":"David Anderson, Caltech","antibody vendorid":"(Made by Protein Expression Center: pec@caltech.edu)","controlid":"SL13504","labexpid":"SL14698,SL13491","softwareversion":"MACS","cell sex":"F","antibody":"NRSF","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010891_hg19_wgEncodeHaibTfbsMcf7NrsfV0422111RawRep1.bigWig"},"geolst":["GSM1010891"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 GABP","url":"http://egg.wustl.edu/d/hg19/GSM1010864_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24021","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Mouse monoclonal, GABPa(G-1), IgG1. Antibody Target: GABP","antibody targetdescription":"The transcription factor GA-binding protein (GABP) is composed of two subunits, alpha and beta. Alpha binds to a specific DNA sequence.","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-28312","controlid":"SL16758,SL13504","labexpid":"SL14683,SL13459","softwareversion":"MACS","cell sex":"F","antibody":"GABP","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010864_hg19_wgEncodeHaibTfbsMcf7GabpV0422111RawRep1.bigWig"},"geolst":["GSM1010864"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 NRSF","url":"http://egg.wustl.edu/d/hg19/GSM1010891_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24014","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Mouse monoclonal. Antibody Target: NRSF","antibody targetdescription":"Neuron-restrictive silencer transcription factor","antibody vendorname":"David Anderson, Caltech","antibody vendorid":"(Made by Protein Expression Center: pec@caltech.edu)","controlid":"SL13504","labexpid":"SL14698,SL13491","softwareversion":"MACS","cell sex":"F","antibody":"NRSF","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010891_hg19_wgEncodeHaibTfbsMcf7NrsfV0422111RawRep2.bigWig"},"geolst":["GSM1010891"]},{"type":"bigWig","name":"UT-A ChipSeq MCF-7 serum","url":"http://egg.wustl.edu/d/hg19/GSM1006866_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24004","30009"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"rabbit polyclonal to amino acids 1-262 of c-Myc human origin. Antibody Target: c-Myc","antibody targetdescription":"transcription factor","antibody vendorname":"Santa Cruz Biotech","antibody vendorid":"sc-764","controlid":"wgEncodeEH000589","labversion":"baseAlignCounts.pl v 1","replicate":"1,2","cell sex":"F","treatment":"serum_starved_media","treatment description":"Grown with normal serum levels (10%), then switched to media containing low level of FBS (0.05%) for 72 hours","antibody":"c-Myc","original_filename":"GSM1006866_hg19_wgEncodeOpenChromChipMcf7CmycSerumstvdSig.bigWig"},"geolst":["GSM1006866"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 Max","url":"http://egg.wustl.edu/d/hg19/GSM1010863_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24066","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Rabbit polyclonal IgG, epitope mapping at the C-terminus of Max of human origin. Antibody Target: Max","antibody targetdescription":"The protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper (bHLHZ) family of transcription factors. It is able to form homodimers and heterodimers with other family members, which include Mad, Mxi1 and Myc. Myc is an oncoprotein implicated in cell proliferation, differentiation and apoptosis. The homodimers and heterodimers compete for a common DNA target site (the E box) and rearrangement among these dimer forms provides a complex system of transcriptional regulation. Multiple alternatively spliced transcript variants have been described for this gene but the full-length nature for some of them is unknown (RefSeq).","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-197","controlid":"SL16758,SL13504","labexpid":"SL13485,SL14695","softwareversion":"MACS","cell sex":"F","antibody":"Max","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010863_hg19_wgEncodeHaibTfbsMcf7MaxV0422111RawRep1.bigWig"},"geolst":["GSM1010863"]},{"type":"bigWig","name":"RIKEN Cage MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM849364_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25004","30011"],"details":{"lab":"RIKEN","lab description":"Carninci - RIKEN Omics Science Center","datatype":"Cage","datatype description":"CAGE","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"015WC","labexpid":"K07","replicate":"1","replicate description":"tier 1","original_filename":"GSM849364_hg19_wgEncodeRikenCageMcf7CellPapMinusRawRep2.bigWig"},"geolst":["GSM849364"]},{"type":"bigWig","name":"RIKEN Cage MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM849364_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25004","30011"],"details":{"lab":"RIKEN","lab description":"Carninci - RIKEN Omics Science Center","datatype":"Cage","datatype description":"CAGE","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"015WC","labexpid":"K07","replicate":"1","replicate description":"tier 1","original_filename":"GSM849364_hg19_wgEncodeRikenCageMcf7CellPapMinusSignalRep1.bigWig"},"geolst":["GSM849364"]},{"type":"bigWig","name":"RIKEN Cage MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM849364_3.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25004","30011"],"details":{"lab":"RIKEN","lab description":"Carninci - RIKEN Omics Science Center","datatype":"Cage","datatype description":"CAGE","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"015WC","labexpid":"K07","replicate":"1","replicate description":"tier 1","original_filename":"GSM849364_hg19_wgEncodeRikenCageMcf7CellPapPlusRawRep2.bigWig"},"geolst":["GSM849364"]},{"type":"bigWig","name":"RIKEN Cage MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM849364_4.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25004","30011"],"details":{"lab":"RIKEN","lab description":"Carninci - RIKEN Omics Science Center","datatype":"Cage","datatype description":"CAGE","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"015WC","labexpid":"K07","replicate":"1","replicate description":"tier 1","original_filename":"GSM849364_hg19_wgEncodeRikenCageMcf7CellPapPlusSignalRep1.bigWig"},"geolst":["GSM849364"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 FOSL2","url":"http://egg.wustl.edu/d/hg19/GSM1010768_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24058","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Fra-2(Q-20) is an affinity purified rabbit polyclonal raised against the N-terminus of Fra-2 of human origin. Recommended for detection of Fra-2 of m, r, h and chicken origin by WB, IP, IF, IHC(P) and ELISA. Antibody Target: FOSL2","antibody targetdescription":"The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation.","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-604","controlid":"SL16758,SL13504","labexpid":"SL13457,SL14682","softwareversion":"MACS","cell sex":"F","antibody":"FOSL2","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010768_hg19_wgEncodeHaibTfbsMcf7Fosl2V0422111RawRep1.bigWig"},"geolst":["GSM1010768"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 nucleus","url":"http://egg.wustl.edu/d/hg19/GSM973687_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"nucleus","localization description":"Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA","protocol":"None","protocol description":"No special treatment or protocol applies","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"089N,090N","labexpid":"LID46313,LID46314","labversion":"iIDR","readtype":"1x101","readtype description":"Single 101 nt reads","original_filename":"GSM973687_hg19_wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalMinusRep4.bigWig"},"geolst":["GSM973687"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 nucleus","url":"http://egg.wustl.edu/d/hg19/GSM973687_3.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"nucleus","localization description":"Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA","protocol":"None","protocol description":"No special treatment or protocol applies","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"089N,090N","labexpid":"LID46313,LID46314","labversion":"iIDR","readtype":"1x101","readtype description":"Single 101 nt reads","original_filename":"GSM973687_hg19_wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalPlusRep3.bigWig"},"geolst":["GSM973687"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 nucleus","url":"http://egg.wustl.edu/d/hg19/GSM973687_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"nucleus","localization description":"Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA","protocol":"None","protocol description":"No special treatment or protocol applies","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"089N,090N","labexpid":"LID46313,LID46314","labversion":"iIDR","readtype":"1x101","readtype description":"Single 101 nt reads","original_filename":"GSM973687_hg19_wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalMinusRep3.bigWig"},"geolst":["GSM973687"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 CTCF","url":"http://egg.wustl.edu/d/hg19/GSM1010734_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24001","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Goat polyclonal IgG, epitope mapping at the N-terminus of CTCF of human origin. Antibody Target: CTCF","antibody targetdescription":"This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. (provided by RefSeq)","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-5916","controlid":"SL16757,SL13504","labexpid":"SL13463,SL16333","softwareversion":"MACS","cell sex":"F","antibody":"CTCF_(SC-5916)","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010734_hg19_wgEncodeHaibTfbsMcf7CtcfcV0422111RawRep2.bigWig"},"geolst":["GSM1010734"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 HDAC2","url":"http://egg.wustl.edu/d/hg19/GSM1010825_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","22044","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Goat polyclonal IgG, epitope mapping at the C-terminus of HDAC2 of human origin. Antibody Target: HDAC2","antibody targetdescription":"This gene product belongs to the histone deacetylase family.  Histone deacetylases act via the formation of large multiprotein complexes, and are responsible for the deacetylation of lysine residues at the N-terminal regions of core histones (H2A, H2B, H3 and H4). This protein forms transcriptional repressor complexes by associating with many different proteins, including YY1, a mammalian zinc-finger transcription factor. (provided by RefSeq)","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-6296","controlid":"SL16757,SL13504","labexpid":"SL16334,SL13483","softwareversion":"MACS","cell sex":"F","antibody":"HDAC2_(SC-6296)","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010825_hg19_wgEncodeHaibTfbsMcf7Hdac2sc6296V0422111RawRep1.bigWig"},"geolst":["GSM1010825"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 TCF12","url":"http://egg.wustl.edu/d/hg19/GSM1010861_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24015","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"HEB (A-20) Rabbit polyclonal IgG, 200 ?g/ml. Epitope mapping within the C-terminus of HEB of human origin. Antibody Target: TCF12","antibody targetdescription":"The protein encoded by this gene is a member of the basic helix-loop-helix (bHLH) E-protein family that recognizes the consensus binding site (E-box) CANNTG. This encoded protein is expressed in many tissues, among them skeletal muscle, thymus, B- and T-cells, and may participate in regulating lineage-specific gene expression through the formation of heterodimers with other bHLH E-proteins. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined.","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-357","controlid":"SL16757,SL16756","labexpid":"SL16340,SL14574","softwareversion":"MACS","cell sex":"F","antibody":"TCF12","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010861_hg19_wgEncodeHaibTfbsMcf7Tcf12V0422111RawRep1.bigWig"},"geolst":["GSM1010861"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 nucleus","url":"http://egg.wustl.edu/d/hg19/GSM973682_4.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"nucleus","localization description":"Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA","protocol":"TAP-Only","protocol description":"This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"089N","labexpid":"LID47164","readtype":"1x101","readtype description":"Single 101 nt reads","replicate":"3","original_filename":"GSM973682_hg19_wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalTapPlusRep4.bigWig"},"geolst":["GSM973682"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 nucleus","url":"http://egg.wustl.edu/d/hg19/GSM973682_3.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"nucleus","localization description":"Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA","protocol":"TAP-Only","protocol description":"This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"089N","labexpid":"LID47164","readtype":"1x101","readtype description":"Single 101 nt reads","replicate":"3","original_filename":"GSM973682_hg19_wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalTapPlusRep3.bigWig"},"geolst":["GSM973682"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 nucleus","url":"http://egg.wustl.edu/d/hg19/GSM973682_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"nucleus","localization description":"Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA","protocol":"TAP-Only","protocol description":"This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"089N","labexpid":"LID47164","readtype":"1x101","readtype description":"Single 101 nt reads","replicate":"3","original_filename":"GSM973682_hg19_wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalTapMinusRep4.bigWig"},"geolst":["GSM973682"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 nucleus","url":"http://egg.wustl.edu/d/hg19/GSM973682_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"nucleus","localization description":"Large membrane bound part of cell containing chromosomes and the bulk of the cell's DNA","protocol":"TAP-Only","protocol description":"This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.","rnaextract":"shortTotal","rnaextract description":"Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation","biorep":"089N","labexpid":"LID47164","readtype":"1x101","readtype description":"Single 101 nt reads","replicate":"3","original_filename":"GSM973682_hg19_wgEncodeCshlShortRnaSeqMcf7NucleusShorttotalTapMinusRep3.bigWig"},"geolst":["GSM973682"]},{"type":"bigWig","name":"UT-A ChipSeq MCF-7 serum","url":"http://egg.wustl.edu/d/hg19/GSM1006877_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24004","30009"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"rabbit polyclonal to amino acids 1-262 of c-Myc human origin. Antibody Target: c-Myc","antibody targetdescription":"transcription factor","antibody vendorname":"Santa Cruz Biotech","antibody vendorid":"sc-764","controlid":"wgEncodeEH000589","labversion":"baseAlignCounts.pl v 1","replicate":"1,2","cell sex":"F","treatment":"serum_stimulated_media","treatment description":"Grown with normal serum levels (10%), then switched back to normal serum levels (10% FBS) for 3 hours.","antibody":"c-Myc","original_filename":"GSM1006877_hg19_wgEncodeOpenChromChipMcf7CmycSerumstimSig.bigWig"},"geolst":["GSM1006877"]},{"type":"bigWig","name":"Duke DnaseSeq MCF-7 Hypoxia","url":"http://egg.wustl.edu/d/hg19/GSM816670_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":77,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23001","30019"],"details":{"lab":"Duke","lab description":"Crawford - Duke University","datatype":"DnaseSeq","datatype description":"DNase digestion followed by sequencing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"Hypoxia_LacAcid","treatment description":"Hypoxia and Lactic acidosis: 1% p02 and 10 mM Lactate, pH of 6.7 for 24 hours (Crawford)","labversion":"align_on_cluster_bwa.pl v 1","replicate":"1","replicate description":"tier 1","original_filename":"GSM816670_hg19_wgEncodeOpenChromDnaseMcf7HypoxlacSig.bigWig"},"geolst":["GSM816670"]},{"type":"bigWig","name":"Duke DnaseSeq MCF-7 Hypoxia","url":"http://egg.wustl.edu/d/hg19/GSM816670_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":77,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23001","30019"],"details":{"lab":"Duke","lab description":"Crawford - Duke University","datatype":"DnaseSeq","datatype description":"DNase digestion followed by sequencing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"Hypoxia_LacAcid","treatment description":"Hypoxia and Lactic acidosis: 1% p02 and 10 mM Lactate, pH of 6.7 for 24 hours (Crawford)","labversion":"align_on_cluster_bwa.pl v 1","replicate":"1","replicate description":"tier 1","original_filename":"GSM816670_hg19_wgEncodeOpenChromDnaseMcf7HypoxlacBaseOverlapSignal.bigWig"},"geolst":["GSM816670"]},{"type":"bigWig","name":"USC ChipSeq MCF-7 H3K27me3B","url":"http://egg.wustl.edu/d/hg19/GSM970218_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","22030","30016"],"details":{"lab":"USC","lab description":"Farnham - University of Southern California","datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"None","treatment description":"No special treatment or protocol applies","antibody":"H3K27me3B","antibody antibodydescription":"rabbit monoclonal. Antibody Target: H3K27me3","antibody targetdescription":"Histone H3 (tri-methyl K27) marks repressed chromatin regions","antibody vendorname":"Cell Signaling","antibody vendorid":"9733S","control":"UCDavis","control description":"Input library was prepared at UC Davis.","controlid":"wgEncodeEH000762","labversion":"PeakSeq1.0","original_filename":"GSM970218_hg19_wgEncodeSydhHistoneMcf7H3k27me3bUcdSig.bigWig"},"geolst":["GSM970218"]},{"type":"bigWig","name":"UT-A ChipSeq MCF-7 serum","url":"http://egg.wustl.edu/d/hg19/GSM1006876_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24634","30009"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"mouse monoclonal, clone 8WG16. Antibody Target: POL2","antibody targetdescription":"RNA Polymerase II","antibody vendorname":"Covance","antibody vendorid":"MMS-126R","controlid":"wgEncodeEH000589","labversion":"baseAlignCounts.pl v 1","replicate":"1,2","cell sex":"F","treatment":"serum_stimulated_media","treatment description":"Grown with normal serum levels (10%), then switched back to normal serum levels (10% FBS) for 3 hours.","antibody":"Pol2","original_filename":"GSM1006876_hg19_wgEncodeOpenChromChipMcf7Pol2SerumstimSig.bigWig"},"geolst":["GSM1006876"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 Rad21","url":"http://egg.wustl.edu/d/hg19/GSM1010791_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24052","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Rabbit polyclonal. Antibody Target: RAD21","antibody targetdescription":"Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14","antibody vendorname":"abcam","antibody vendorid":"ab992","controlid":"SL16757,SL16756","labexpid":"SL13724,SL16336","softwareversion":"MACS","cell sex":"F","antibody":"Rad21","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010791_hg19_wgEncodeHaibTfbsMcf7Rad21V0422111RawRep2.bigWig"},"geolst":["GSM1010791"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 Rad21","url":"http://egg.wustl.edu/d/hg19/GSM1010791_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24052","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Rabbit polyclonal. Antibody Target: RAD21","antibody targetdescription":"Synthetic peptide (Human) conjugated to KLH - which represents a portion of human Rad21 encoded within exon 14","antibody vendorname":"abcam","antibody vendorid":"ab992","controlid":"SL16757,SL16756","labexpid":"SL13724,SL16336","softwareversion":"MACS","cell sex":"F","antibody":"Rad21","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010791_hg19_wgEncodeHaibTfbsMcf7Rad21V0422111RawRep1.bigWig"},"geolst":["GSM1010791"]},{"type":"bigWig","name":"UNC FaireSeq MCF-7 Estradiol","url":"http://egg.wustl.edu/d/hg19/GSM1011121_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","23003","30022"],"details":{"datatype":"FaireSeq","datatype description":"FAIRE-seq Open Chromatin","controlid":"MCF-7/Input","labversion":"baseAlignCounts.pl v 1,fseq v 1.84, iff_MCF7,p-value cutoff: 0.1","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"Estradiol_10nM_30m","treatment description":"30 min with 10nM 7b-Estradiol (Crawford)","replicate":"1,2","original_filename":"GSM1011121_hg19_wgEncodeOpenChromFaireMcf7Est10nm30mBaseOverlapSignal.bigWig"},"geolst":["GSM1011121"]},{"type":"bigWig","name":"USC ChipSeq MCF-7 GATA3","url":"http://egg.wustl.edu/d/hg19/GSM935445_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24065","30016"],"details":{"lab":"USC","lab description":"Farnham - University of Southern California","datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"None","treatment description":"No special treatment or protocol applies","antibody":"GATA3_(SC-269)","antibody antibodydescription":"Mouse monoclonal IgG raised against human recombinant GATA-3 (amino acids 1-264). Antibody Target: GATA3","antibody targetdescription":"This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is a n important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia (provided by RefSeq)","antibody vendorname":"Santa Cruz Biotech","antibody vendorid":"sc-269","control":"UCDavis","control description":"Input library was prepared at UC Davis.","controlid":"wgEncodeEH000762","replicate":"1","original_filename":"GSM935445_hg19_wgEncodeSydhTfbsMcf7Gata3sc269UcdSig.bigWig"},"geolst":["GSM935445"]},{"type":"bigWig","name":"RIKEN Cage MCF-7 cytosol","url":"http://egg.wustl.edu/d/hg19/GSM979657_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25004","30011"],"details":{"datatype":"Cage","datatype description":"CAGE 5' RNA Tags","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089C","labexpid":"CThi10051","readtype":"1x50","readtype description":"Single 50 nt reads","replicate":"3","cell sex":"F","localization":"cytosol","localization description":"The fluid between the cells outer membrane and the nucleus","original_filename":"GSM979657_hg19_wgEncodeRikenCageMcf7CytosolPapMinusRawRep4.bigWig"},"geolst":["GSM979657"]},{"type":"bigWig","name":"GIS RnaPet MCF-7 cytosol","url":"http://egg.wustl.edu/d/hg19/GSM1006904_4.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25006","30007"],"details":{"datatype":"RnaPet","datatype description":"RNA Paired-End Tags","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","biorep":"089C,090C","labexpid":"RHM044,RHM045","labversion":"clone-free","readtype":"2x36","readtype description":"Paired 36 nt reads","replicate":"3,4","localization":"cytosol","localization description":"The fluid between the cells outer membrane and the nucleus","original_filename":"GSM1006904_hg19_wgEncodeGisRnaPetMcf7CytosolPapPlusRawRep4.bigWig"},"geolst":["GSM1006904"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq MCF-7 SRF","url":"http://egg.wustl.edu/d/hg19/GSM1010839_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","24023","30015"],"details":{"datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","antibody antibodydescription":"Rabbit polyclonal. Antibody Target: SRF","antibody targetdescription":"Serum response transcription factor","antibody vendorname":"Santa Cruz Biotechnology","antibody vendorid":"sc-335","controlid":"SL16757,SL16756","labexpid":"SL16044,SL13723","softwareversion":"MACS","cell sex":"F","antibody":"SRF","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"v042211.1","protocol description":"Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)","replicate":"1,2","original_filename":"GSM1010839_hg19_wgEncodeHaibTfbsMcf7SrfV0422111RawRep2.bigWig"},"geolst":["GSM1010839"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM767851_2.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","rnaextract":"longNonPolyA","rnaextract description":"Poly(A)- RNA longer than 200 nt","biorep":"015WC","labexpid":"LID8824","readtype":"2x76D","readtype description":"Paired 76 n.t. directed reads","replicate":"1","replicate description":"tier 1","original_filename":"GSM767851_wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaMinusRawSigRep2.bigWig"},"geolst":["GSM767851"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM767851_3.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","rnaextract":"longNonPolyA","rnaextract description":"Poly(A)- RNA longer than 200 nt","biorep":"015WC","labexpid":"LID8824","readtype":"2x76D","readtype description":"Paired 76 n.t. directed reads","replicate":"1","replicate description":"tier 1","original_filename":"GSM767851_wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaPlusRawSigRep1.bigWig"},"geolst":["GSM767851"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM767851_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","rnaextract":"longNonPolyA","rnaextract description":"Poly(A)- RNA longer than 200 nt","biorep":"015WC","labexpid":"LID8824","readtype":"2x76D","readtype description":"Paired 76 n.t. directed reads","replicate":"1","replicate description":"tier 1","original_filename":"GSM767851_wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaMinusRawSigRep1.bigWig"},"geolst":["GSM767851"]},{"type":"bigWig","name":"CSHL RnaSeq MCF-7 cell","url":"http://egg.wustl.edu/d/hg19/GSM767851_4.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","25002","30006"],"details":{"lab":"CSHL","lab description":"Gingeras - Cold Spring Harbor Laboratory","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757)","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","localization":"cell","localization description":"Whole cell","rnaextract":"longNonPolyA","rnaextract description":"Poly(A)- RNA longer than 200 nt","biorep":"015WC","labexpid":"LID8824","readtype":"2x76D","readtype description":"Paired 76 n.t. directed reads","replicate":"1","replicate description":"tier 1","original_filename":"GSM767851_wgEncodeCshlLongRnaSeqMcf7CellLongnonpolyaPlusRawSigRep2.bigWig"},"geolst":["GSM767851"]},{"type":"bigWig","name":"USC ChipSeq MCF-7 H3K36me3B","url":"http://egg.wustl.edu/d/hg19/GSM970217_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":0,"pb":230,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["14028","22033","30016"],"details":{"lab":"USC","lab description":"Farnham - University of Southern California","datatype":"ChipSeq","datatype description":"Chromatin IP Sequencing","cell":"MCF-7","cell organism":"human","cell description":"mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"F","treatment":"None","treatment description":"No special treatment or protocol applies","antibody":"H3K36me3B","antibody antibodydescription":"rabbit polyclonal. Antibody Target: H3K36me3","antibody targetdescription":"Histone H3 (tri-methyl K36) marks actively transcribed chromatin regions","antibody vendorname":"Cell Signaling","antibody vendorid":"9763S","control":"UCDavis","control description":"Input library was prepared at UC Davis.","controlid":"wgEncodeEH000762","labversion":"PeakSeq1.0","original_filename":"GSM970217_hg19_wgEncodeSydhHistoneMcf7H3k36me3bUcdSig.bigWig"},"geolst":["GSM970217"]},{"type":"interaction","name":"ENCODE GIS ChIA-PET MCF-7 ERalpha a rep1","url":"http://egg.wustl.edu/d/hg19/wgEncodeGisChiaPetMcf7EraaInteractionsRep1.gz","public":true,"mode":4,"qtc":{"anglescale":1,"textcolor":"#000000","thtype":0,"fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"pr":184,"pg":0,"pb":138,"nr":0,"ng":99,"nb":133,"pcolorscore":0,"ncolorscore":0,"pfilterscore":0,"nfilterscore":0,"height":50},"annotation":["14028","27001","30007"],"details":{"project":"wgEncode","grant":"Ruan","lab":"GIS-Ruan","composite":"wgEncodeGisChiaPet","dataType":"ChiaPet","view":"Interactions","cell":"MCF-7","antibody":"ERalpha_a","replicate":"1","dataVersion":"ENCODE Mar 2012 Freeze","dccAccession":"wgEncodeEH001429","dateSubmitted":"2011-09-20","dateUnrestricted":"2012-04-20","subId":"4843","labExpId":"IHM001T_hg19","tableName":"wgEncodeGisChiaPetMcf7EraaInteractionsRep1","type":"bed","md5sum":"8c004bab76f6a1f655a60095d5a5ebf2","size":"155K"}},{"type":"interaction","name":"gisChiaPet MCF7 RNAPII saturated rep2","url":"http://egg.wustl.edu/d/hg19/GSM832459.gz","public":true,"mode":4,"qtc":{"anglescale":1,"textcolor":"#000000","thtype":0,"fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"pr":184,"pg":0,"pb":138,"nr":0,"ng":99,"nb":133,"pcolorscore":4,"ncolorscore":0,"pfilterscore":0,"nfilterscore":0,"height":50},"annotation":["27001","14028","30007"],"details":{"Publication":"Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation","Journal":"Cell 148(1-2):84","Year":"2012","Institution":"Genome Institute of Singapore","PI":"Michael Snyder, Yijun Ruan","Assay":"ChIA-PET","Factor":"PolII","Sample":"MCF-7"},"geolst":["GSM832459","GSE33664"]},{"type":"interaction","name":"MCF-7 5C ENCODE/UW rep1","url":"http://egg.wustl.edu/d/hg19/wgEncodeUw5CMcf7Uw5cmycMatrixRep1.gz","public":true,"mode":4,"qtc":{"anglescale":1,"textcolor":"#000000","thtype":0,"fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"pr":184,"pg":0,"pb":138,"nr":0,"ng":99,"nb":133,"pcolorscore":0,"ncolorscore":0,"pfilterscore":0,"nfilterscore":0,"height":50},"annotation":["14028","27002","30004"],"details":{"project":"wgEncode","grant":"Stam","lab":"UW","composite":"wgEncodeUw5C","dataType":"5C","view":"Matrix","cell":"MCF-7","replicate":"1","dataVersion":"ENCODE Mar 2012 Freeze","dccAccession":"wgEncodeEH002104","dateSubmitted":"2011-03-09","dateUnrestricted":"2011-12-08","subId":"3813","geoSampleAccession":"GSM970292","region":"UW-5C-Myc-Region","type":"matrix","md5sum":"65253d1494c9466b29e2c39be78bfd95","size":"66K","original filename":"wgEncodeUw5CMcf7Uw5cmycMatrixRep1.matrix.tgz","download":"http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUw5C/"},"geolst":["GSM970292","GSE39505"]},{"type":"interaction","name":"ENCODE GIS ChIA-PET MCF-7 CTCF rep1","url":"http://egg.wustl.edu/d/hg19/wgEncodeGisChiaPetMcf7CtcfInteractionsRep1.gz","public":true,"mode":4,"qtc":{"anglescale":1,"textcolor":"#000000","thtype":0,"fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"pr":184,"pg":0,"pb":138,"nr":0,"ng":99,"nb":133,"pcolorscore":13,"ncolorscore":0,"pfilterscore":0,"nfilterscore":0,"height":50},"annotation":["14028","27001","30007"],"details":{"project":"wgEncode","grant":"Ruan","lab":"GIS-Ruan","composite":"wgEncodeGisChiaPet","dataType":"ChiaPet","view":"Interactions","cell":"MCF-7","antibody":"CTCF","replicate":"1","dataVersion":"ENCODE Mar 2012 Freeze","dccAccession":"wgEncodeEH002076","dateSubmitted":"2011-06-08","dateResubmitted":"2011-08-30","dateUnrestricted":"2012-03-08","subId":"4305","labExpId":"CHM076M","tableName":"wgEncodeGisChiaPetMcf7CtcfInteractionsRep1","type":"bed","md5sum":"9f67b2d5bf6fc29519e20a41b1a3031b","size":"1.9M"}},{"type":"interaction","name":"ENCODE GIS ChIA-PET MCF-7 CTCF rep2","url":"http://egg.wustl.edu/d/hg19/wgEncodeGisChiaPetMcf7CtcfInteractionsRep2.gz","public":true,"mode":4,"qtc":{"anglescale":1,"textcolor":"#000000","thtype":0,"fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"pr":184,"pg":0,"pb":138,"nr":0,"ng":99,"nb":133,"pcolorscore":4,"ncolorscore":0,"pfilterscore":0,"nfilterscore":0,"height":50},"annotation":["14028","27001","30007"],"details":{"project":"wgEncode","grant":"Ruan","lab":"GIS-Ruan","composite":"wgEncodeGisChiaPet","dataType":"ChiaPet","view":"Interactions","cell":"MCF-7","antibody":"CTCF","replicate":"2","dataVersion":"ENCODE Mar 2012 Freeze","dccAccession":"wgEncodeEH002076","dateSubmitted":"2011-06-08","dateResubmitted":"2011-08-30","dateUnrestricted":"2012-03-08","subId":"4306","labExpId":"CHM077M","tableName":"wgEncodeGisChiaPetMcf7CtcfInteractionsRep2","type":"bed","md5sum":"3535501126bb760dcd068bec547ee21b","size":"771K"}},{"type":"interaction","name":"MCF-7 5C ENCODE/UW rep1","url":"http://egg.wustl.edu/d/hg19/wgEncodeUw5CMcf7Uw5cmycMatrixRep2.gz","public":true,"mode":4,"qtc":{"anglescale":1,"textcolor":"#000000","thtype":0,"fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"pr":184,"pg":0,"pb":138,"nr":0,"ng":99,"nb":133,"pcolorscore":0,"ncolorscore":0,"pfilterscore":0,"nfilterscore":0,"height":50},"annotation":["14028","27002","30004"],"details":{"project":"wgEncode","grant":"Stam","lab":"UW","composite":"wgEncodeUw5C","dataType":"5C","view":"Matrix","cell":"MCF-7","replicate":"2","dataVersion":"ENCODE Mar 2012 Freeze","dccAccession":"wgEncodeEH002104","dateSubmitted":"2011-03-09","dateUnrestricted":"2011-12-08","subId":"3813","geoSampleAccession":"GSM970292","region":"UW-5C-Myc-Region","type":"matrix","md5sum":"8e8d819fcb6dc0b43a60104d9d8035cb","size":"62K","original filename":"wgEncodeUw5CMcf7Uw5cmycMatrixRep2.matrix.tgz","download":"http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUw5C/"},"geolst":["GSM970292","GSE39505"]},{"type":"interaction","name":"ENCODE GIS ChIA-PET MCF-7 POL2 rep4","url":"http://egg.wustl.edu/d/hg19/wgEncodeGisChiaPetMcf7Pol2InteractionsRep4.gz","public":true,"mode":4,"qtc":{"anglescale":1,"textcolor":"#000000","thtype":0,"fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"pr":184,"pg":0,"pb":138,"nr":0,"ng":99,"nb":133,"pcolorscore":14,"ncolorscore":0,"pfilterscore":0,"nfilterscore":0,"height":50},"annotation":["14028","27001","30007"],"details":{"project":"wgEncode","grant":"Ruan","lab":"GIS-Ruan","composite":"wgEncodeGisChiaPet","dataType":"ChiaPet","view":"Interactions","cell":"MCF-7","antibody":"Pol2","replicate":"4","dataVersion":"ENCODE Mar 2012 Freeze","dccAccession":"wgEncodeEH001430","dateSubmitted":"2011-01-20","dateResubmitted":"2011-09-27","dateUnrestricted":"2011-10-20","subId":"4304","labExpId":"CHM163M_L4","tableName":"wgEncodeGisChiaPetMcf7Pol2InteractionsRep4","type":"bed","md5sum":"280ba3becf3ef81b30af7eefa60e96d9","size":"8.3M"}},{"type":"interaction","name":"ENCODE GIS ChIA-PET MCF-7 POL2 rep2","url":"http://egg.wustl.edu/d/hg19/wgEncodeGisChiaPetMcf7Pol2InteractionsRep2.gz","public":true,"mode":4,"qtc":{"anglescale":1,"textcolor":"#000000","thtype":0,"fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"pr":184,"pg":0,"pb":138,"nr":0,"ng":99,"nb":133,"pcolorscore":4,"ncolorscore":0,"pfilterscore":0,"nfilterscore":0,"height":50},"annotation":["14028","27001","30007"],"details":{"project":"wgEncode","grant":"Ruan","lab":"GIS-Ruan","composite":"wgEncodeGisChiaPet","dataType":"ChiaPet","view":"Interactions","cell":"MCF-7","antibody":"Pol2","replicate":"2","dataVersion":"ENCODE Mar 2012 Freeze","dccAccession":"wgEncodeEH001430","dateSubmitted":"2011-01-20","dateResubmitted":"2011-09-23","dateUnrestricted":"2011-10-20","subId":"4842","labExpId":"CHM053T_hg19","tableName":"wgEncodeGisChiaPetMcf7Pol2InteractionsRep2","type":"bed","md5sum":"2eb1c0e7222800da2918bb3f1d1437e2","size":"165K"}},{"type":"interaction","name":"ENCODE GIS ChIA-PET MCF-7 POL2 rep3","url":"http://egg.wustl.edu/d/hg19/wgEncodeGisChiaPetMcf7Pol2InteractionsRep3.gz","public":true,"mode":4,"qtc":{"anglescale":1,"textcolor":"#000000","thtype":0,"fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"pr":184,"pg":0,"pb":138,"nr":0,"ng":99,"nb":133,"pcolorscore":18,"ncolorscore":0,"pfilterscore":0,"nfilterscore":0,"height":50},"annotation":["14028","27001","30007"],"details":{"project":"wgEncode","grant":"Ruan","lab":"GIS-Ruan","composite":"wgEncodeGisChiaPet","dataType":"ChiaPet","view":"Interactions","cell":"MCF-7","antibody":"Pol2","replicate":"3","dataVersion":"ENCODE Mar 2012 Freeze","dccAccession":"wgEncodeEH001430","dateSubmitted":"2011-06-08","dateResubmitted":"2011-09-27","dateUnrestricted":"2012-03-08","subId":"4303","labExpId":"CHM160M_L4","tableName":"wgEncodeGisChiaPetMcf7Pol2InteractionsRep3","type":"bed","md5sum":"49595aa0f557ad62c403b15867e3d94e","size":"6.1M"}},{"type":"interaction","name":"ENCODE GIS ChIA-PET MCF-7 POL2 rep1","url":"http://egg.wustl.edu/d/hg19/wgEncodeGisChiaPetMcf7Pol2InteractionsRep1.gz","public":true,"mode":4,"qtc":{"anglescale":1,"textcolor":"#000000","thtype":0,"fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"pr":184,"pg":0,"pb":138,"nr":0,"ng":99,"nb":133,"pcolorscore":0,"ncolorscore":0,"pfilterscore":0,"nfilterscore":0,"height":50},"annotation":["14028","27001","30007"],"details":{"project":"wgEncode","grant":"Ruan","lab":"GIS-Ruan","composite":"wgEncodeGisChiaPet","dataType":"ChiaPet","view":"Interactions","cell":"MCF-7","antibody":"Pol2","replicate":"1","dataVersion":"ENCODE Mar 2012 Freeze","dccAccession":"wgEncodeEH001430","dateSubmitted":"2011-01-20","dateResubmitted":"2011-09-26","dateUnrestricted":"2011-10-20","subId":"4841","labExpId":"CHM040M_hg19","tableName":"wgEncodeGisChiaPetMcf7Pol2InteractionsRep1","type":"bed","md5sum":"820fc9a1b53b1edc7d4cfe91749849e9","size":"171K"}},{"type":"interaction","name":"gisChiaPet MCF7 RNAPII pilot rep2","url":"http://egg.wustl.edu/d/hg19/GSM832457.gz","public":true,"mode":4,"qtc":{"anglescale":1,"textcolor":"#000000","thtype":0,"fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"pr":184,"pg":0,"pb":138,"nr":0,"ng":99,"nb":133,"pcolorscore":4,"ncolorscore":0,"pfilterscore":0,"nfilterscore":0,"height":50},"annotation":["27001","14028","30007"],"details":{"Publication":"Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation","Journal":"Cell 148(1-2):84","Year":"2012","Institution":"Genome Institute of Singapore","PI":"Michael Snyder, Yijun Ruan","Assay":"ChIA-PET","Factor":"PolII","Sample":"MCF-7"},"geolst":["GSM832457","GSE33664"]},{"type":"interaction","name":"ENCODE GIS ChIA-PET MCF-7 ERalpha a rep2","url":"http://egg.wustl.edu/d/hg19/wgEncodeGisChiaPetMcf7EraaInteractionsRep2.gz","public":true,"mode":4,"qtc":{"anglescale":1,"textcolor":"#000000","thtype":0,"fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"pr":184,"pg":0,"pb":138,"nr":0,"ng":99,"nb":133,"pcolorscore":0,"ncolorscore":0,"pfilterscore":0,"nfilterscore":0,"height":50},"annotation":["14028","27001","30007"],"details":{"project":"wgEncode","grant":"Ruan","lab":"GIS-Ruan","composite":"wgEncodeGisChiaPet","dataType":"ChiaPet","view":"Interactions","cell":"MCF-7","antibody":"ERalpha_a","replicate":"2","dataVersion":"ENCODE Mar 2012 Freeze","dccAccession":"wgEncodeEH001429","dateSubmitted":"2011-09-21","dateUnrestricted":"2012-04-21","subId":"4830","labExpId":"IHH015T_hg19","tableName":"wgEncodeGisChiaPetMcf7EraaInteractionsRep2","type":"bed","md5sum":"34ed7a1ba956f10a0ddf3250f42df63d","size":"197K"}},{"type":"interaction","name":"ENCODE GIS ChIA-PET MCF-7 ERalpha a rep3","url":"http://egg.wustl.edu/d/hg19/wgEncodeGisChiaPetMcf7EraaInteractionsRep3.gz","public":true,"mode":4,"qtc":{"anglescale":1,"textcolor":"#000000","thtype":0,"fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"pr":184,"pg":0,"pb":138,"nr":0,"ng":99,"nb":133,"pcolorscore":0,"ncolorscore":0,"pfilterscore":0,"nfilterscore":0,"height":50},"annotation":["14028","27001","30007"],"details":{"project":"wgEncode","grant":"Ruan","lab":"GIS-Ruan","composite":"wgEncodeGisChiaPet","dataType":"ChiaPet","view":"Interactions","cell":"MCF-7","antibody":"ERalpha_a","replicate":"3","dataVersion":"ENCODE Mar 2012 Freeze","dccAccession":"wgEncodeEH001429","dateSubmitted":"2011-09-24","dateUnrestricted":"2012-04-23","subId":"4874","labExpId":"IHM096M","tableName":"wgEncodeGisChiaPetMcf7EraaInteractionsRep3","type":"bed","md5sum":"621587fe9a5ced0c95a3920a92e35349","size":"84K"}},{"type":"interaction","name":"gisChiaPet MCF7 RNAPII pilot rep1","url":"http://egg.wustl.edu/d/hg19/GSM832456.gz","public":true,"mode":4,"qtc":{"anglescale":1,"textcolor":"#000000","thtype":0,"fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"pr":184,"pg":0,"pb":138,"nr":0,"ng":99,"nb":133,"pcolorscore":2,"ncolorscore":0,"pfilterscore":0,"nfilterscore":0,"height":50},"annotation":["27001","14028","30007"],"details":{"Publication":"Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation","Journal":"Cell 148(1-2):84","Year":"2012","Institution":"Genome Institute of Singapore","PI":"Michael Snyder, Yijun Ruan","Assay":"ChIA-PET","Factor":"PolII","Sample":"MCF-7"},"geolst":["GSM832456","GSE33664"]},{"type":"interaction","name":"gisChiaPet MCF7 RNAPII saturated rep1","url":"http://egg.wustl.edu/d/hg19/GSM832458.gz","public":true,"mode":4,"qtc":{"anglescale":1,"textcolor":"#000000","thtype":0,"fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"pr":184,"pg":0,"pb":138,"nr":0,"ng":99,"nb":133,"pcolorscore":7,"ncolorscore":0,"pfilterscore":0,"nfilterscore":0,"height":50},"annotation":["27001","14028","30007"],"details":{"Publication":"Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation","Journal":"Cell 148(1-2):84","Year":"2012","Institution":"Genome Institute of Singapore","PI":"Michael Snyder, Yijun Ruan","Assay":"ChIA-PET","Factor":"PolII","Sample":"MCF-7"},"geolst":["GSM832458","GSE33664"]},{"type":"native_track","list":[{"name":"rmsk_all","mode":7,"defaultmode":7,"qtc":{"anglescale":1,"pr":0,"pg":77,"pb":0,"nr":0,"ng":0,"nb":230,"pth":"#800000","nth":"#000099","thtype":0,"thmin":0,"thmax":10,"thpercentile":95,"height":50,"summeth":1,"textcolor":"#000000","fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"bedcolor":"#336666","scorescalelst":[{"type":0},{"type":0}]},"showscoreidx":2,"scorenamelst":["Smith-Waterman score","SW score normalized by length","1-divergence%"],"scorescalelst":[{"type":0},{"type":0},{"type":0}],"categories":{"1":["SINE - short interspersed nuclear element","#cc0000"],"2":["LINE - long interspersed nuclear element","#FF6600"],"3":["LTR - long terminal repeat element","#006600"],"4":["DNA transposon","#4A72E8"],"5":["Simple repeat, micro-satellite","#AB833B"],"6":["Satellite repeat","#660000"],"7":["Low complexity repeat","#663333"],"8":["RNA repeat","#cc33ff"],"9":["Other repeats","#488E8E"],"10":["Unknown","#5C5C5C"],"-1":["no information","transparent"]}},{"name":"refGene","mode":3,"qtc":{"anglescale":1,"pr":0,"pg":77,"pb":0,"nr":0,"ng":0,"nb":230,"pth":"#800000","nth":"#000099","thtype":0,"thmin":0,"thmax":10,"thpercentile":95,"height":50,"summeth":1,"textcolor":"rgb(0,0,0)","fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"bedcolor":"rgb(0,77,153)"}}]},{"type":"coordinate_override","coord":"chr7,27053398,chr7,27373766"},{"type":"native_metadata_terms","list":["Assay","Sample"]}]