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Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.","rna_preparation_5'_rna_adapter_ligation_protocol":"5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.","rna_preparation_reverse_transcription_protocol":"To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60minutes.","library_generation_pcr_template":"15ul of the first strand cDNA product was used in the PCR","library_generation_pcr_polymerase_type":"Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)","library_generation_pcr_thermocycling_program":"step1","library_generation_pcr_number_cycles":"15","library_generation_pcr_f_primer_sequence":"5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'","library_generation_pcr_r_primer_sequence":"5' CAAGCAGAAGACGGCATACGAGAT 3'","library_generation_pcr_primer_conc":"25uM","library_generation_pcr_product_isolation_protocol":"28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually","original_filename":"GSM751284_UCSF-UBC.Brain_Germinal_Matrix.smRNA-Seq.HuFGM02.bigWig"},"geolst":["GSM751284"]},{"type":"bigWig","name":"smRNA-Seq of Brain Germinal Matrix","url":"http://egg.wustl.edu/d/hg19/GSM751283_0.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":43,"pb":173,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["13155","25003","30014","40138","60001","70004"],"details":{"sample_alias":"Brain Germinal Matrix HuFGM01","sample_common_name":"Brain, Germinal Matrix","molecule":"genomic DNA","disease":"None","biomaterial_provider":"Costello Lab UCSF","biomaterial_type":"Primary Tissue","tissue_type":"Brain-Germinal Matrix","tissue_depot":"NA","collection_method":"NA","donor_id":"HuFGM01","donor_age":"20GW","donor_health_status":"Disease Free","donor_sex":"Male","donor_ethnicity":"Caucasian","note":"Twin of HuFGM02","experiment_type":"smRNA-Seq","extraction_protocol":"Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions.","extraction_protocol_smrna_enrichment":"None","smrna_preparation_initial_smrna_qnty":"2.552ug","smrna_preparation_initial_smrna_qlty":"RIN 6.1","rna_preparation_5'_rna_adapter_sequence":"5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'","rna_preparation_3'_rna_adapter_sequence":"5' ATCTCGTATGCCGTCTTCTGCTTGT 3'","rna_preparation_reverse_transcription_primer_sequence":"5' CAAGCAGAAGACGGCATACGAGAT 3'","rna_preparation_3'_rna_adapter_ligation_protocol":"1ug of total RNA (RN=&gt,7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.","rna_preparation_5'_rna_adapter_ligation_protocol":"5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.","rna_preparation_reverse_transcription_protocol":"To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60minutes.","library_generation_pcr_template":"15ul of the first strand cDNA product was used in the PCR","library_generation_pcr_polymerase_type":"Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)","library_generation_pcr_thermocycling_program":"step1","library_generation_pcr_number_cycles":"15","library_generation_pcr_f_primer_sequence":"5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'","library_generation_pcr_r_primer_sequence":"5' CAAGCAGAAGACGGCATACGAGAT 3'","library_generation_pcr_primer_conc":"25uM","library_generation_pcr_product_isolation_protocol":"28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually","original_filename":"GSM751283_UCSF-UBC.Brain_Germinal_Matrix.smRNA-Seq.HuFGM01.bigWig"},"geolst":["GSM751283"]},{"type":"bigWig","name":"RNA-Seq of Brain Germinal Matrix","url":"http://egg.wustl.edu/d/hg19/GSM751275_0.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":["13155","25002","30014","40137","60001","70009"],"details":{"sample_alias":"Brain Germinal Matrix HuFGM02","sample_common_name":"Brain, Germinal Matrix","molecule":"genomic DNA","disease":"None","biomaterial_provider":"Costello Lab UCSF","biomaterial_type":"Primary Tissue","tissue_type":"Brain-Germinal Matrix","tissue_depot":"NA","collection_method":"NA","donor_id":"HuFGM02","donor_age":"20GW","donor_health_status":"Disease Free","donor_sex":"Male","donor_ethnicity":"NA","experiment_type":"mRNA-Seq","extraction_protocol":"Costello Lab Protocol","extraction_protocol_mrna_enrichment":"Miltenyi-Biotec MACS mRNA purification","rna_preparation_initial_rna_qlty":"RIN 7.1","rna_preparation_initial_rna_qnty":"2ug","rna_preparation_reverse_transcription_primer_sequence":"NNNNNN","rna_preparation_reverse_transcription_protocol":"Invitrogen Superscript II RT","library_generation_pcr_template":"cDNA","library_fragmentation":"COVARIS E210","library_fragment_size_range":"181-281bp","library_generation_pcr_polymerase_type":"Phusion","library_generation_pcr_thermocycling_program":"98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold","library_generation_pcr_number_cycles":"15","library_generation_pcr_f_primer_sequence":"AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT","library_generation_pcr_r_primer_sequence":"CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT","library_generation_pcr_primer_conc":"0.5uM","library_generation_pcr_product_isolation_protocol":"8% Novex TBE PAGE gel purification","original_filename":"GSM751275_UCSF-UBC.Brain_Germinal_Matrix.mRNA-Seq.HuFGM02.bigWig"},"geolst":["GSM751275"]},{"type":"bigWig","name":"HudsonAlpha RnaSeq PFSK-1 longPolyA","url":"http://egg.wustl.edu/d/hg19/GSM923430_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":["13142","25002","30015"],"details":{"lab":"HudsonAlpha","lab description":"Myers - 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Hudson Alpha Institute for Biotechnology","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"PFSK-1","cell organism":"human","cell description":"neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433)","cell karyotype":"cancer","cell lineage":"ectoderm","cell sex":"M","treatment":"None","treatment description":"No special treatment or protocol applies","rnaextract":"longPolyA","rnaextract description":"Poly(A)+ RNA longer than 200 nt","labexpid":"SL530","labversion":"cufflinks_v_0.9","mapalgorithm":"bow125","mapalgorithm description":"bowtie v0.12.5","readtype":"1x36","readtype description":"Single 36 nt reads","replicate":"1","original_filename":"GSM923430_hg19_wgEncodeHaibRnaSeqPfsk1RawRep1.bigWig"},"geolst":["GSM923430"]},{"type":"bigWig","name":"RNA-Seq of cDNA_Lib 3 derived from human hippocampus middle cells","url":"http://egg.wustl.edu/d/hg19/GSM916094_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":["13042","25002","30003","40162","60001","70009"],"details":{"sample alias":"223","sample common name":"Brain, Hippocampus Middle","collection_method":"Post-Mortem","donor_health_status":"no AD present","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","rna_preparation_5'_rna_adapter_ligation_protocol":"NA","rna_preparation_3'_rna adapter_ligation_protocol":"NA","rna_preparation_5'_rna_adapter_sequence":"NA","library_generation_pcr_f_primer_sequence":"AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT","rna_preparation_3'_rna_adapter_sequence":"NA","mrna_preparation_initial_mrna_qnty":"200ng","library_generation_pcr_product_isolation_protocol":"1.8X SPRI cleanup (no size selection)","rna_preparation_5'_dephosphorylation":"NA","extraction_protocol_mrna_enrichment":"Dynabeads mRNA purification kit (Invitrogen)","library_generation_pcr_thermocycling_program":"95C  2mins, 10 cycles of:  98C for 30 sec, 55C for 30 sec, 72C for 1 min, then 72C for 10 min, hold 4C","rna_preparation_reverse_transcription_primer_sequence":"NNNNNN","extraction_protocol":"Qiagen AllPrep DNA/RNA/Protein Mini Kit","library_generation_pcr_template":"Adapter ligated cDNA made by reverse transcription of RNA","library_generation_pcr_polymerase_type":"PFU Ultra II","library_generation_pcr_number_cycles":"10","library_generation_pcr_primer_conc":"0.83 uM","library_generation_pcr_r_primer_sequence":"CAAGCAGAAGACGGCATACGAGAT","extraction_protocol_fragmentation":"98C for 40 min in 0.2 mM sodium citrate, pH 6.4 (Ambion), followed by concentrating it to 3.5 ul, mixing with 1 ul 2 uM SMART tagged random primer, incubating at 70deg C for 10 min and chilling on ice for 2 min.","rna_preparation_5'_phosphorylation":"NA","experiment_type":"mRNA-Seq","rna_preparation_reverse_transcription_protocol":"We synthesized first-strand cDNA with this RNA primer mix by adding 4 ul 5x first-strand buffer, 2 ul 100 mM DTT, 1 ul 10 mM dNTPs, 4 ug of actinomycin D, 200 U SuperScript III and 20 U SUPERase-In, incubating at room temperature for 10 min followed by 1 h at 55degC. We cleaned up first-strand cDNA by PCIA extraction twice, ethanol precipitation with 0.1 volumes 5 M ammonium acetate to remove dNTPs and resuspension in 104 ul H2O. We synthesized second-strand cDNA by adding 4 ul of 5x first-strand buffer, 2 ul of 100 mM DTT, 4 ul of 10 mM dNTPs with dTTP replaced by dUTP (Sigma), 30 ul of 5x second-strand buffer, 40 U of Escherichia coli DNA polymerase, 10 U of E. coli DNA ligase and 2 U of E. coli RNase H, and incubating at 16degC for 2 h.","mrna_preparation_fragment_size_range":"400bp","original_filename":"BI.Brain_Hippocampus_Middle.mRNA-Seq.150.bigWig"},"geolst":["GSM916094"]},{"type":"bigWig","name":"Caltech RnaSeq GM12892 2x75","url":"http://egg.wustl.edu/d/hg19/GSM958748_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":["13064","25002","30010"],"details":{"lab":"Caltech","lab description":"Wold - California Institute of Technology","datatype":"RnaSeq","datatype description":"Sequencing analysis of RNA expression","cell":"GM12892","cell organism":"human","cell description":"B-lymphocyte, lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1463, treatment: Epstein-Barr Virus transformed","cell lineage":"mesoderm","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":"11039","mapalgorithm":"TH1014","mapalgorithm description":"TopHat v1.0.14","replicate":"1","original_filename":"GSM958748_hg19_wgEncodeCaltechRnaSeqGm12892R2x75Th1014Il200SigRep3V4.bigWig"},"geolst":["GSM958748"]},{"type":"bigWig","name":"Caltech RnaSeq GM12892 2x75","url":"http://egg.wustl.edu/d/hg19/GSM958748_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":["13064","25002","30010"],"details":{"lab":"Caltech","lab description":"Wold - 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from Invitrogen as per manufacturer's instuctions.","smrna_preparation_initial_smrna_qnty":"1000 ng","extraction_protocol_smrna_enrichment":"The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised.  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The ligation reaction was incubated at 16oC overnight.","rna_preparation_5'_rna_adapter_ligation_protocol":"5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen).  Ligation reaction was incubated at 16oC overnight.","rna_preparation_reverse_transcription_protocol":"To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins.  Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen).  Reaction was heated at 48oC for 3mins.  1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr.  After 1hr of incubation, tube was placed on ice.  12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul.","library_generation_pcr_template":"cDNA","library_generation_pcr_polymerase_type":"Phusion","library_generation_pcr_thermocycling_program":"98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold","library_generation_pcr_number_cycles":"15","library_generation_pcr_f_primer_sequence":"5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'","library_generation_pcr_r_primer_sequence":"5' ATCTCGTATGCCGTCTTCTGCTTGT 3'","library_generation_pcr_primer_conc":"0.5uM","library_generation_pcr_product_isolation_protocol":"8% Novex TBE PAGE gel purification","original_filename":"GSM669586_UCSF-UBC.Breast_Luminal_Epithelial_Cells.smRNA-Seq.RM080.bigWig"},"geolst":["GSM669586"]},{"type":"bigWig","name":"smRNA-Seq of breast myoepithelial cells","url":"http://egg.wustl.edu/d/hg19/GSM669587_0.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":0,"pg":43,"pb":173,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":0,"thmin":0,"thmax":10,"thpercentile":90,"height":10,"summeth":1},"annotation":["13005","25003","30014","40013","60002","70002"],"details":{"sample_alias":"Breast Myo Epi RM080","sample_common_name":"Breast, Myoepithelial Cells","disease":"None","biomaterial_provider":"Thea Tlsty Lab UCSF","biomaterial_type":"Primary Cell","cell_type":"myo epithelial cell","markers":"CD10+","donor_id":"RM080","donor_age":"33","donor_health_status":"Disease Free","donor_sex":"Female","donor_ethnicity":"African-American","passage_if_expanded":"NA","karyotype":"46, XX","parity":"2","location":"Left","experiment_type":"smRNA-Seq","extraction_protocol":"Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions.","smrna_preparation_initial_smrna_qnty":"1000 ng","extraction_protocol_smrna_enrichment":"The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised.  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After 1hr of incubation, tube was placed on ice.  12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul.","library_generation_pcr_template":"cDNA","library_generation_pcr_polymerase_type":"Phusion","library_generation_pcr_thermocycling_program":"98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold","library_generation_pcr_number_cycles":"15","library_generation_pcr_f_primer_sequence":"5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'","library_generation_pcr_r_primer_sequence":"5' ATCTCGTATGCCGTCTTCTGCTTGT 3'","library_generation_pcr_primer_conc":"0.5uM","library_generation_pcr_product_isolation_protocol":"8% Novex TBE PAGE gel purification","original_filename":"GSM669587_UCSF-UBC.Breast_Myoepithelial_Cells.smRNA-Seq.RM080.bigWig"},"geolst":["GSM669587"]},{"type":"bigWig","name":"RNA-Seq of breast myoepithelial 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