[{"type":"bedGraph","name":"Bisulfite-Seq of WGBS_Lib 10 derived from human hippocampus middle cells","url":"http://egg.wustl.edu/d/hg19/GSM916050_1.gz","public":true,"mode":"show","qtc":{"anglescale":1,"pr":200,"pg":0,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1,"barplotbg":"#cccccc"},"annotation":["13042","21004","30003","40162","60001","70009"],"details":{"sample alias":"223","sample common name":"Brain, Hippocampus Middle","collection_method":"Post-Mortem","donor_health_status":"no AD present","molecule":"genomic DNA","disease":"no AD present","tissue_type":"Hippocampus Middle","donor_ethnicity":"NA","donor_sex":"Male","biomaterial_type":"Primary Tissue","tissue_depot":"Brain","donor_id":"150","biomaterial_provider":"Rush University Medical Center","donor_age":"73.0 Years","bisulfite_conversion_protocol":"2x5hrs Epitect Kit","dna_preparation_initial_dna_qnty":"5 ug","extraction_protocol_sonication_cycles":"Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes","dna_preparation_adaptor_ligation_protocol":"T4 Ligase (2,000U/ul) 16C o/n","dna_preparation_adaptor_sequence":"Illumina paired end adapter","library_generation_pcr_r_primer_sequence":"PE1.0","dna_preparation_post-ligation_fragment_size_selection":"270-370","bisulfite_conversion_percent":"99.5%","extraction_protocol":"Standard Protocol (Smith et al., Methods 48, 226-232)","library_generation_pcr_primer_conc":"25uM","dna_preparation_fragment_size_range":"150-250","experiment_type":"DNA Methylation","library_generation_pcr_thermocycling_program":"Smith et al., Methods 48, 226-232","library_generation_pcr_product_isolation_protocol":"SPRI Beads","library_generation_pcr_f_primer_sequence":"PE2.0","library_generation_pcr_template_conc":"NA","library_generation_pcr_polymerase_type":"Pfu Turbo Cx hot start","library_generation_pcr_number_cycles":"5-8","extraction_protocol_type_of_sonicator":"Covaris S2 (TM)","original_filename":"BI.Brain_Hippocampus_Middle.Bisulfite-Seq.150.bigWig"},"geolst":["GSM916050"]},{"type":"bedGraph","name":"Bisulfite-Seq of H1","url":"http://egg.wustl.edu/d/hg19/GSM429322_1.gz","public":true,"mode":"show","qtc":{"anglescale":1,"pr":200,"pg":0,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1,"barplotbg":"#cccccc"},"annotation":["11101","21004","30002"],"details":{"molecule":"genomic DNA"," disease":"None","biomaterial_provider":"Thomson Laboratory","biomaterial_type":"Cell Line","line":"H1","lineage":"NA","batch":"Replicate 1","differentiation_stage":"embryonic stem cell","differentiation_method":"NA","passage":"30","medium":"TeSR","Sex":"Male","experiment_type":"DNA Methylation","extraction_protocol":"Qiagen DNeasy mini kit, performed as per manufacturer's instructions'","extraction_protocol_type_of_sonicator":"Diagenode Bioruptor","extraction_protocol_sonication_cycles":"20 cycles of","dna_preparation_initial_dna_qnty":"5 g","dna_preparation_fragment_size_range":"50-500 bp","dna_preparation_adaptor_sequence":"A","dna_preparation_adaptor_ligation_protocol":"Standard Illumina genomic DNA library preparation ligation protocol (15 minutes at room temperature), except the adapters contained methylcytosine and were supplied by Illumina","dna_preparation_post-ligation_fragment_size_selection":"Separation by electrophoresis on a 2% agarose gel followed by excision of 140-210 bp fragments","bisulfite_conversion_protocol":"Standard Human Genetic Signatures MethylEasy Xceed bisulfite conversion kit protocol","bisulfite_conversion_percent":"99.6% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample","library_generation_pcr_template_conc":"One third of the 140-210 nt adapter-ligated, bisulfite converted DNA was used in each 50 l PCR reaction","library_generation_pcr_polymerase_type":"Stratagene Pfu Turbo Cx","library_generation_pcr_thermocycling_program":"95C 2 min, 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min, 72C 10 min","library_generation_pcr_number_cycles":"4","library_generation_pcr_f_primer_sequence":"5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT","library_generation_pcr_r_primer_sequence":"5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT","library_generation_pcr_primer_conc":"25 M","library_generation_pcr_product_isolation_protocol":"Separation by electrophoresis on a 2% agarose gel followed by excision of 180-300 bp fragments.","original_filename":"GSM429322_UCSD.H1.Bisulfite-Seq.combined.bigWig","Embargo end date":"2010-07-13"},"geolst":["GSM429322"]},{"type":"bigWig","name":"DNase hypersensitivity of H1","url":"http://egg.wustl.edu/d/hg19/GSM878621.bigWig","public":true,"mode":"show","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":["11101","23001","30004"],"details":{"sample_alias":"H1-13","sample_common_name":"H1 Cell Line","molecule":"genomic DNA","disease":"None","biomaterial_provider":"James Thompson Laboratory","biomaterial_type":"Cell Line","line":"H1","lineage":"Embryonic Stem Cell","differentiation_stage":"None","differentiation_method":"None","passage":"Between 20 and 40","medium":"mTeSER","Sex":"Male","batch":"H1U","experiment_type":"Chromatin Accessibility","extraction_protocol":"Qiagen minElut","dnase_protocol":""},"geolst":["GSM878621"]},{"type":"bigWig","name":"HudsonAlpha ChipSeq H1-hESC SP1","url":"http://egg.wustl.edu/d/hg19/GSM803377_1.bigWig","public":true,"mode":"show","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":["11101","24027","30015"],"details":{"lab":"HudsonAlpha","lab description":"Myers - Hudson Alpha Institute for Biotechnology","datatype":"ChipSeq","datatype description":"ChIP-Seq","cell":"H1-hESC","cell organism":"human","cell description":"embryonic stem cells","cell karyotype":"normal","cell lineage":"inner cell mass","cell sex":"M","antibody":"SP1","antibody antibodydescription":"Sp1(E-3) is a mouse monoclonal antibody raised against amino acids 121-345 mapping near the N-terminus of Sp1 ofhuman origin. Recommended for detection of Sp1 of m, r and h origin by WB, IP, IF and ELISA.","antibody targetdescription":"SP1 is a transcription factor that binds to GC box promoters elements and selectively activates mRNA synthesis from genes that contain functional recognition sites. It can interact with G/C-rich motifs from the serotonin receptor promoter.","antibody vendorname":"Santa Cruz Biotech","antibody vendorid":"sc-17824","treatment":"None","treatment description":"No special treatment or protocol applies","protocol":"PCR1x","protocol description":"1-cycle of PCR (Myers)","controlid":"SL1398","labexpid":"SL1166","replicate":"1","replicate description":"tier 1","original_filename":"GSM803377_hg19_wgEncodeHaibTfbsH1hescSp1Pcr1xRawRep1.bigWig"},"geolst":["GSM803377"]},{"type":"bigWig","name":"Duke DnaseSeq Cerebrum frontal","url":"http://egg.wustl.edu/d/hg19/GSM1008578_1.bigWig","public":true,"mode":"show","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":["13237","23001","30019"],"details":{"datatype":"DnaseSeq","datatype description":"DNaseI HS Sequencing","labversion":"baseAlignCounts.pl v 1","replicate":"1,2","cell":"Cerebrum_frontal_OC","cell organism":"human","cell description":"Primary frozen frontal cerebrum tissue from NICHD donor IDs 1104 (Rep B1), 602 (Rep B2), 1442 (Rep B3), all Caucasian","cell karyotype":"normal","cell sex":"M","original_filename":"GSM1008578_hg19_wgEncodeOpenChromDnaseCerebrumfrontalocBaseOverlapSignal.bigWig"},"geolst":["GSM1008578"]},{"type":"native_track","list":[{"name":"refGene","mode":"full","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":"chr12,53772218,chr12,53777124"},{"type":"native_metadata_terms","list":["Assay","Sample"]}]