[{"type":"bigWig","name":"RNA-Seq of IMR90 (fetal lung fibroblast)","url":"http://egg.wustl.edu/d/hg19/GSM438363_0.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":79,"pg":97,"pb":44,"nr":255,"ng":0,"nb":0,"pth":"rgb(79, 97, 44)","nth":"#800000","thtype":2,"thmin":0,"thmax":10,"thpercentile":97,"height":39,"summeth":1,"smooth":7},"annotation":["11310","25002","30002"],"details":{"disease":"None","biomaterial_provider":"ATCC","biomaterial_type":"Cell Line","line":"IMR90","lineage":"NA","batch":"1","differentiation_stage":"Fetal lung fibroblast","differentiation_method":"NA","passage":"4","medium":"Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)","Sex":"Female","experiment_type":"mRNA-Seq","extraction_protocol":"mirVana miRNA isolation kit (Applied Biosystems), performed as per manufacturer's instructions to isolate total RNA, followed by treatment with DNaseI (Qiagen) for 30 min at room temperature","extraction_protocol_mrna_enrichment":"2 x RiboMinus (Life Technologies) rRNA depletion (5S, 5.8S, 12S, 18S, 28S)","extraction_protocol_fragmentation":"15 min at 70 C with RNA Fragmentation kit (Ambion/Applied Biosystems) as per manufacturer's instructions","mrna_preparation_initial_mrna_qnty":"200 ng","mrna_preparation_fragment_size_range":"50-400 bp","rna_preparation_5'_rna_adapter_sequence":"5' GUUCAGAGUUCUACAGUCCGACGAUC","rna_preparation_3'_rna_adapter_sequence":"5' UCGUAUGCCGUCUUCUGCUUGidT, 5' adenylated (Illumina)","rna_preparation_reverse_transcription_primer_sequence":"5' CAAGCAGAAGACGGCATACGA","rna_preparation_5'_dephosphorylation":"Fragmented RNA was treated with 5 U Antarctic phosphatase (New England Biolabs) for 40 min at 37C in the presence of 40 U RNaseOut followed by phosphatase heat inactivation at 65C for 5 min. The RNA was purified using 66 l SPRI beads (Agencourt) and eluted in 11 l 10 mM Tris buffer pH 8.0.","rna_preparation_5'_phosphorylation":"Phosphorylation was performed by addition of 10 U PNK (New England Biolabs), 1 mM ATP, and 20 U RNaseOut  (Life Technologies) and incubation at 37C for 1 h.","rna_preparation_3'_rna_adapter_ligation_protocol":"1 l of 1:10 diluted adenylated 3 RNA adapter oligonucleotide was added to the phosphorylated RNA and incubated at 70C for 2 min followed by placement on ice. The 3 RNA adapter ligation reaction was performed by addition of 2 l 10x T4 RNA ligase 2 truncated ligation buffer, 1.6 l 100 mM MgCl2, 20 U RNaseOut and 300 U T4 RNA ligase 2 truncated (New England Biolabs) and incubation at 22C for 1 h.","rna_preparation_5'_rna_adapter_ligation_protocol":"Ligation of the 5 RNA adapter was performed by addition to the 3 adapter ligated reaction of 1 l 1:1 diluted, heat denatured (70C 2 min) 5 RNA adapter oligonucleotide, 1 l 10 mM ATP, and 10 U T4 RNA ligase (Promega), and incubation at 20C for 1 h. RNA was purified using 66 l SPRI beads and eluted in 10 l 10 mM Tris buffer pH 8.0.","rna_preparation_reverse_transcription_protocol":"To the RNA ligation products, 2 l 1:5 diluted RT primer was added and heat denatured (70C 2 min), followed by incubation on ice. Added to the denatured RNA/primer solution was 4 l 5x first strand buffer, 1 l 12.5 mM dNTPs, 2 l 100 mM DTT, and 40 U RNaseOut, followed by incubation at 48C for 1 min. To this, 200 U Superscript II reverse transcriptase (Life Technologies) was added, followed by incubation at 44C for 1 h.","library_generation_pcr_template":"The entire reverse transcription reaction was used in the PCR enrichment of the library.","library_generation_pcr_polymerase_type":"Phusion hot-start high fidelity DNA polymerase (New England Biolabs). 1x Phusion polymerase buffer and 4 U Phusion hot-start high fidelity DNA polymerase was used in a 100 l reaction.","library_generation_pcr_thermocycling_program":"98C 30 sec, 98C 10 sec, 60C 30 sec, 72C 15 sec, 72C 10 min","library_generation_pcr_number_cycles":"15","library_generation_pcr_f_primer_sequence":"5' AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA","library_generation_pcr_r_primer_sequence":"5' CAAGCAGAAGACGGCATACGA","library_generation_pcr_primer_conc":"0.25 M","library_generation_pcr_product_isolation_protocol":"PCR products were purified in two steps, first by purification using 180 l SPRI beads and elution in 30 l 10 mM Tris buffer pH 8.0, followed by purification with 39 l SPRI beads and elution in 10 l 10 mM Tris buffer pH 8.0.","original_filename":"GSM438363_UCSD.IMR90.mRNA-Seq.mRNA-seq_imr90_r1.bigWig"},"geolst":["GSM438363"]},{"type":"bigWig","name":"RNA-Seq of H1","url":"http://egg.wustl.edu/d/hg19/GSM484408.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":79,"pg":97,"pb":44,"nr":255,"ng":0,"nb":0,"pth":"rgb(79, 97, 44)","nth":"#800000","thtype":2,"thmin":0,"thmax":10,"thpercentile":97,"height":39,"summeth":1,"smooth":7},"annotation":["11101","25002","30014"],"details":{"molecule":""," disease":"None","biomaterial_provider":"Cellular Dynamics International","biomaterial_type":"Cell Line","line":"H1 (WA01)","lineage":"NA","differentiation_stage":"undifferentiated","differentiation_method":"NA","passage":"NA","medium":"NA","Sex":"Male","batch":"#2","experiment_type":"mRNA-Seq","extraction_protocol":"Invitrogen Trizol RNA extraction","extraction_protocol_mrna_enrichment":"Miltenyi-Biotec mRNA purification","extraction_protocol_fragmentation":"NA","mrna_preparation_initial_mrna_qnty":"NA","mrna_preparation_fragment_size_range":"NA","rna_preparation_5'_rna_adapter_sequence":"NA","rna_preparation_3'_rna_adapter_sequence":"NA","rna_preparation_reverse_transcription_primer_sequence":"NNNNNN","rna_preparation_5'_dephosphorylation":"NA","rna_preparation_5'_phosphorylation":"NA","rna_preparation_3'_rna_adapter_ligation_protocol":"NA","rna_preparation_5'_rna_adapter_ligation_protocol":"NA","rna_preparation_reverse_transcription_protocol":"Invitrogen Superscript II RT protocol","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 forever","library_generation_pcr_number_cycles":"10","library_generation_pcr_f_primer_sequence":"5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT","library_generation_pcr_r_primer_sequence":"5' CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT","library_generation_pcr_primer_conc":"0.4uM","library_generation_pcr_product_isolation_protocol":"8% Novex TBE PAGE gel purification","original_filename":"GSM484408_UCSF-UBC.H1.mRNA-Seq.H1EScd1_batch2_vial2.bigWig","Embargo end date":"2010-10-07"},"geolst":["GSM484408"]},{"type":"bigWig","name":"polyA RNA sequencing of H1 cells","url":"http://egg.wustl.edu/d/hg19/GSM915328_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":79,"pg":97,"pb":44,"nr":255,"ng":0,"nb":0,"pth":"rgb(79, 97, 44)","nth":"#800000","thtype":2,"thmin":0,"thmax":10,"thpercentile":97,"height":9,"summeth":1,"smooth":7},"annotation":["11101","25002","30002"],"details":{"sample alias":"H1_RNA_r1","sample common name":"H1 Cell Line","disease":"None","biomaterial_provider":"Thomson Laboratory","biomaterial_type":"Cell Line","line":"H1","lineage":"NA","differentiation_stage":"embryonic stem cell differentiated by treatment with fibronectin and human collagen","differentiation_method":"H1 cells were cultured on plates coated with fibronectin and human collagen","passage":"5","medium":"50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2.","Sex":"Male","batch":"Replicate 1","experiment_type":"mRNA-Seq","extraction_protocol":"Qiagen RNeasy mini kit, performed as per manufacturer's instructions","cdna_preparation_initial_rna_qnty":"4 g","cdna_preparation_polya_rna/":"Dynabeads oligo(dt)25 (Invitrogen)","cdna_preparation_fragmentation":"PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94C for 4 min","cdna_preparation_fragment_size_range":"200-250","cdna_preparation_first_strand_synthesis_enzyme":"SuperScript III (Invitrogen)","cdna_preparation_first_strand_purification":"Purification with RNAClean XP beads (Agencourt)","cdna_preparation_second_strand_synthesis_enzyme":"DNA Polymerase I (E. coli) (New England Biolabs)","cdna_preparation_second_strand_synthesis_dntp_mix":"dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP","cdna_preparation_purification":"Purification with AMPure XP beads (Agencourt)","dna_preparation_adaptor":"TruSeq Multiplexed Adapters (Illumina)","dna_preparation_adaptor_ligation_protocol":"16C for 16 hours with T4 DNA ligase (New England Biolabs)","dna_preparation_post-ligation_fragment_size_selection":"Two rounds of purification with AMPure XP beads (Agencourt)","dna_preparation_uracil_dna_glycosylase_digestion":"One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps.","library_generation_pcr_polymerase_type":"TruSeq PCR Master Mix (Illumina)","library_generation_pcr_thermocycling_program":"98C 30 sec, 10 cycles of 98C 10 sec, 60C 30 sec, 72C 30 sec, 72C 10 min","library_generation_pcr_number_cycles":"10","library_generation_pcr_primer":"TruSeq PCR Primer Cocktail (Illumina)","library_generation_pcr_product_isolation_protocol":"Purification with AMPure XP beads (Agencourt)","extraction_protocol_mrna_enrichment":"Dynabeads oligo(dt)25 protocol","rna_preparation_reverse_transcription_primer_sequence":"Random hexamers","rna_preparation_reverse_transcription_protocol":"First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)","library_generation_pcr_template":"cDNA","library_generation_pcr_template_conc":"5 ng/L","library_generation_pcr_f_primer_sequence":"5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'","library_generation_pcr_r_primer_sequence":"5' CAAGCAGAAGACGGCATACGAGAT 3'","library_generation_pcr_primer_conc":"200nM","original_filename":"UCSD.H1.mRNA-Seq.polyA-RNA-seq_h1_r1a.bigWig"},"geolst":["GSM915328"]},{"type":"bigWig","name":"polyA RNA sequencing of H1 cells","url":"http://egg.wustl.edu/d/hg19/GSM915329_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":79,"pg":97,"pb":44,"nr":255,"ng":0,"nb":0,"pth":"rgb(79, 97, 44)","nth":"#800000","thtype":2,"thmin":0,"thmax":10,"thpercentile":97,"height":9,"summeth":1,"smooth":7},"annotation":["11101","25002","30002"],"details":{"sample alias":"H1_RNA_r2","sample common name":"H1 Cell Line","disease":"None","biomaterial_provider":"Thomson Laboratory","biomaterial_type":"Cell Line","line":"H1","lineage":"NA","differentiation_stage":"embryonic stem cell differentiated by treatment with fibronectin and human collagen","differentiation_method":"H1 cells were cultured on plates coated with fibronectin and human collagen","passage":"5","medium":"50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2.","Sex":"Male","batch":"Replicate 2","experiment_type":"mRNA-Seq","extraction_protocol":"Qiagen RNeasy mini kit, performed as per manufacturer's instructions","cdna_preparation_initial_rna_qnty":"4 g","cdna_preparation_polya_rna/":"Dynabeads oligo(dt)25 (Invitrogen)","cdna_preparation_fragmentation":"PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94C for 4 min","cdna_preparation_fragment_size_range":"200-250","cdna_preparation_first_strand_synthesis_enzyme":"SuperScript III (Invitrogen)","cdna_preparation_first_strand_purification":"Purification with RNAClean XP beads (Agencourt)","cdna_preparation_second_strand_synthesis_enzyme":"DNA Polymerase I (E. coli) (New England Biolabs)","cdna_preparation_second_strand_synthesis_dntp_mix":"dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP","cdna_preparation_purification":"Purification with AMPure XP beads (Agencourt)","dna_preparation_adaptor":"TruSeq Multiplexed Adapters (Illumina)","dna_preparation_adaptor_ligation_protocol":"16C for 16 hours with T4 DNA ligase (New England Biolabs)","dna_preparation_post-ligation_fragment_size_selection":"Two rounds of purification with AMPure XP beads (Agencourt)","dna_preparation_uracil_dna_glycosylase_digestion":"One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps.","library_generation_pcr_polymerase_type":"TruSeq PCR Master Mix (Illumina)","library_generation_pcr_thermocycling_program":"98C 30 sec, 10 cycles of 98C 10 sec, 60C 30 sec, 72C 30 sec, 72C 10 min","library_generation_pcr_number_cycles":"10","library_generation_pcr_primer":"TruSeq PCR Primer Cocktail (Illumina)","library_generation_pcr_product_isolation_protocol":"Purification with AMPure XP beads (Agencourt)","extraction_protocol_mrna_enrichment":"Dynabeads oligo(dt)25 protocol","rna_preparation_reverse_transcription_primer_sequence":"Random hexamers","rna_preparation_reverse_transcription_protocol":"First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)","library_generation_pcr_template":"cDNA","library_generation_pcr_template_conc":"5 ng/L","library_generation_pcr_f_primer_sequence":"5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'","library_generation_pcr_r_primer_sequence":"5' CAAGCAGAAGACGGCATACGAGAT 3'","library_generation_pcr_primer_conc":"200nM","original_filename":"UCSD.H1.mRNA-Seq.polyA-RNA-seq_h1_r2a.bigWig"},"geolst":["GSM915329"]},{"type":"bigWig","name":"RNA-Seq of H1 Derived Neuronal Progenitor Cultured Cells","url":"http://egg.wustl.edu/d/hg19/GSM706048_0.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":79,"pg":97,"pb":44,"nr":255,"ng":0,"nb":0,"pth":"rgb(79, 97, 44)","nth":"#800000","thtype":2,"thmin":0,"thmax":10,"thpercentile":97,"height":9,"summeth":1,"smooth":7},"annotation":["11309","25002","30002"],"details":{"sample_alias":"H1-NPC_r1","sample_common_name":"H1 Derived Neuronal Progenitor Cultured Cells","disease":"None","biomaterial_provider":"Thomson Laboratory","biomaterial_type":"Cell Line","line":"H1","lineage":"NA","differentiation_stage":"embryonic stem cell differentiated into neural progenitor cells","differentiation_method":"H1 cells were differentiated by culturing in insulin, SB, Noggin","passage":"25","medium":"TeSR","Sex":"Male","batch":"Replicate 1","experiment_type":"mRNA-Seq","extraction_protocol":"RNeasy Blood and Tissue Kit (Qiagen)","extraction_protocol_mrna_enrichment":"Poly(A)Purist MAG Kit (Ambion)","extraction_protocol_fragmentation":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","mrna_preparation_initial_mrna_qnty":"20-100 ng","mrna_preparation_fragment_size_range":"200 nt","rna_preparation_5'_rna_adapter_sequence":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","rna_preparation_3'_rna_adapter_sequence":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","rna_preparation_reverse_transcription_primer_sequence":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","rna_preparation_5'_dephosphorylation":"NA","rna_preparation_5'_phosphorylation":"NA","rna_preparation_3'_rna_adapter_ligation_protocol":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","rna_preparation_5'_rna_adapter_ligation_protocol":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","rna_preparation_reverse_transcription_protocol":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","library_generation_pcr_template":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","library_generation_pcr_polymerase_type":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","library_generation_pcr_thermocycling_program":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","library_generation_pcr_number_cycles":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","library_generation_pcr_f_primer_sequence":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","library_generation_pcr_r_primer_sequence":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","library_generation_pcr_primer_conc":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","library_generation_pcr_product_isolation_protocol":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","original_filename":"GSM706048_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.mRNA-Seq.mRNA-Seq_h1-npc_r1.bigWig"},"geolst":["GSM706048"]},{"type":"bigWig","name":"RNA-Seq of H1 Derived Neuronal Progenitor Cultured Cells","url":"http://egg.wustl.edu/d/hg19/GSM706049_0.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":79,"pg":97,"pb":44,"nr":255,"ng":0,"nb":0,"pth":"rgb(79, 97, 44)","nth":"#800000","thtype":2,"thmin":0,"thmax":10,"thpercentile":97,"height":9,"summeth":1,"smooth":7},"annotation":["11309","25002","30002"],"details":{"sample_alias":"H1-NPC_r2","sample_common_name":"H1 Derived Neuronal Progenitor Cultured Cells","disease":"None","biomaterial_provider":"Thomson Laboratory","biomaterial_type":"Cell Line","line":"H1","lineage":"NA","differentiation_stage":"embryonic stem cell differentiated into neural progenitor cells","differentiation_method":"H1 cells were differentiated by culturing in insulin, SB, Noggin","passage":"27","medium":"TeSR","Sex":"Male","batch":"Replicate 2","experiment_type":"mRNA-Seq","extraction_protocol":"RNeasy Blood and Tissue Kit (Qiagen)","extraction_protocol_mrna_enrichment":"Poly(A)Purist MAG Kit (Ambion)","extraction_protocol_fragmentation":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","mrna_preparation_initial_mrna_qnty":"20-100 ng","mrna_preparation_fragment_size_range":"200 nt","rna_preparation_5'_rna_adapter_sequence":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","rna_preparation_3'_rna_adapter_sequence":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","rna_preparation_reverse_transcription_primer_sequence":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","rna_preparation_5'_dephosphorylation":"NA","rna_preparation_5'_phosphorylation":"NA","rna_preparation_3'_rna_adapter_ligation_protocol":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","rna_preparation_5'_rna_adapter_ligation_protocol":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","rna_preparation_reverse_transcription_protocol":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","library_generation_pcr_template":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","library_generation_pcr_polymerase_type":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","library_generation_pcr_thermocycling_program":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","library_generation_pcr_number_cycles":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","library_generation_pcr_f_primer_sequence":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","library_generation_pcr_r_primer_sequence":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","library_generation_pcr_primer_conc":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","library_generation_pcr_product_isolation_protocol":"SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)","original_filename":"GSM706049_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.mRNA-Seq.mRNA-Seq_h1-npc_r2.bigWig"},"geolst":["GSM706049"]},{"type":"bigWig","name":"polyA RNA sequencing of H1 Derived Neuronal Progenitor Cultured Cell","url":"http://egg.wustl.edu/d/hg19/GSM915326_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":79,"pg":97,"pb":44,"nr":255,"ng":0,"nb":0,"pth":"rgb(79, 97, 44)","nth":"#800000","thtype":2,"thmin":0,"thmax":10,"thpercentile":97,"height":9,"summeth":1,"smooth":7},"annotation":["11309","25002","30002"],"details":{"sample alias":"H1-NPC_RNA_r1","sample common name":"H1 Derived Neuronal Progenitor Cultured Cells","disease":"None","biomaterial_provider":"Thomson Laboratory","biomaterial_type":"Cell Line","line":"H1","lineage":"NA","differentiation_stage":"embryonic stem cell differentiated by treatment with fibronectin and human collagen","differentiation_method":"H1 cells were cultured on plates coated with fibronectin and human collagen","passage":"5","medium":"50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2.","Sex":"Male","batch":"Replicate 1","experiment_type":"mRNA-Seq","extraction_protocol":"Qiagen RNeasy mini kit, performed as per manufacturer's instructions","cdna_preparation_initial_rna_qnty":"4 g","cdna_preparation_polya_rna/":"Dynabeads oligo(dt)25 (Invitrogen)","cdna_preparation_fragmentation":"PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94C for 4 min","cdna_preparation_fragment_size_range":"200-250","cdna_preparation_first_strand_synthesis_enzyme":"SuperScript III (Invitrogen)","cdna_preparation_first_strand_purification":"Purification with RNAClean XP beads (Agencourt)","cdna_preparation_second_strand_synthesis_enzyme":"DNA Polymerase I (E. coli) (New England Biolabs)","cdna_preparation_second_strand_synthesis_dntp_mix":"dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP","cdna_preparation_purification":"Purification with AMPure XP beads (Agencourt)","dna_preparation_adaptor":"TruSeq Multiplexed Adapters (Illumina)","dna_preparation_adaptor_ligation_protocol":"16C for 16 hours with T4 DNA ligase (New England Biolabs)","dna_preparation_post-ligation_fragment_size_selection":"Two rounds of purification with AMPure XP beads (Agencourt)","dna_preparation_uracil_dna_glycosylase_digestion":"One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps.","library_generation_pcr_polymerase_type":"TruSeq PCR Master Mix (Illumina)","library_generation_pcr_thermocycling_program":"98C 30 sec, 10 cycles of 98C 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Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)","library_generation_pcr_template":"cDNA","library_generation_pcr_template_conc":"5 ng/L","library_generation_pcr_f_primer_sequence":"5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'","library_generation_pcr_r_primer_sequence":"5' CAAGCAGAAGACGGCATACGAGAT 3'","library_generation_pcr_primer_conc":"200nM","original_filename":"GSM1010952_UCSD.Aorta.mRNA-Seq.STL003.wig"},"geolst":["GSM1010952"]},{"type":"bigWig","name":"RNA-Seq of cDNA_Lib 4 derived from human liver cells","url":"http://egg.wustl.edu/d/hg19/GSM916093_1.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":79,"pg":97,"pb":44,"nr":255,"ng":0,"nb":0,"pth":"rgb(79, 97, 44)","nth":"#800000","thtype":2,"thmin":0,"thmax":10,"thpercentile":97,"height":9,"summeth":1,"smooth":7},"annotation":["13010","25002","30003","40278","60002","70004"],"details":{"sample alias":"BioSam 321 REMC 27","sample common name":"Adult Liver","collection_method":"Surgery","donor_health_status":"patient with metastatic carcinoid","disease":"patient with metastatic carcinoid","tissue_type":"Adult Liver","donor_ethnicity":"Caucasian","donor_sex":"Female","biomaterial_type":"Primary Tissue","tissue_depot":"Liver","donor_id":"Donor 177 REMC 27","biomaterial_provider":"MGH","donor_age":"45.0 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.Adult_Liver.mRNA-Seq.Donor_177_REMC_27.bigWig"},"geolst":["GSM916093"]},{"type":"bedGraph","name":"polyA RNA sequencing of STL001 Liver Cultured Cells","url":"http://egg.wustl.edu/d/hg19/GSM1067795_1.gz","public":true,"mode":1,"qtc":{"anglescale":1,"pr":79,"pg":97,"pb":44,"nr":255,"ng":0,"nb":0,"pth":"rgb(79, 97, 44)","nth":"#800000","thtype":2,"thmin":0,"thmax":10,"thpercentile":97,"height":9,"summeth":1,"smooth":7},"annotation":["13010","25002","30002","40272"],"details":{"sample alias":"STL001LI-01","sample common name":"Adult Liver","disease":"None","biomaterial_provider":"Shin Lin, Stanford University","biomaterial_type":"Primary Tissue","tissue_type":"Liver","tissue_depot":"N/A","collection_method":"Autopsy","donor_id":"STL001","donor_age":"3","donor_health_status":"healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)","donor_sex":"Male","donor_ethnicity":"Caucasian and African American","experiment_type":"mRNA-Seq","extraction_protocol":"Qiagen RNeasy mini kit, performed as per manufacturer's instructions","cdna_preparation_initial_rna_qnty":"4 g","cdna_preparation_polya_rna/":"Dynabeads oligo(dt)25 (Invitrogen)","cdna_preparation_fragmentation":"PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94C for 4 min","cdna_preparation_fragment_size_range":"200-250","cdna_preparation_first_strand_synthesis_enzyme":"SuperScript III (Invitrogen)","cdna_preparation_first_strand_purification":"Purification with RNAClean XP beads (Agencourt)","cdna_preparation_second_strand_synthesis_enzyme":"DNA Polymerase I (E. coli) (New England Biolabs)","cdna_preparation_second_strand_synthesis_dntp_mix":"dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP","cdna_preparation_purification":"Purification with AMPure XP beads (Agencourt)","dna_preparation_adaptor":"TruSeq Multiplexed Adapters (Illumina)","dna_preparation_adaptor_ligation_protocol":"16C for 16 hours with T4 DNA ligase (New England Biolabs)","dna_preparation_post-ligation_fragment_size_selection":"Two rounds of purification with AMPure XP beads (Agencourt)","dna_preparation_uracil_dna_glycosylase_digestion":"One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps.","library_generation_pcr_polymerase_type":"TruSeq PCR Master Mix (Illumina)","library_generation_pcr_thermocycling_program":"98C 30 sec","library_generation_pcr_number_cycles":"10","library_generation_pcr_primer":"TruSeq PCR Primer Cocktail (Illumina)","library_generation_pcr_product_isolation_protocol":"Purification with AMPure XP beads (Agencourt)","extraction_protocol_mrna_enrichment":"Dynabeads oligo(dt)25 protocol","rna_preparation_reverse_transcription_primer_sequence":"Random hexamers","rna_preparation_reverse_transcription_protocol":"First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)","library_generation_pcr_template":"cDNA","library_generation_pcr_template_conc":"5 ng/L","library_generation_pcr_f_primer_sequence":"5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'","library_generation_pcr_r_primer_sequence":"5' CAAGCAGAAGACGGCATACGAGAT 3'","library_generation_pcr_primer_conc":"200nM","original_filename":"GSM1067795_UCSD.Adult_Liver.mRNA-Seq.STL001.wig"},"geolst":["GSM1067795"]},{"type":"bedGraph","name":"polyA RNA sequencing of STL002 Small Bowel Cells","url":"http://egg.wustl.edu/d/hg19/GSM1120313_1.gz","public":true,"mode":1,"qtc":{"anglescale":1,"pr":79,"pg":97,"pb":44,"nr":255,"ng":0,"nb":0,"pth":"rgb(79, 97, 44)","nth":"#800000","thtype":2,"thmin":0,"thmax":10,"thpercentile":97,"height":9,"summeth":1,"smooth":7},"annotation":["13207","25002","30002","40271"],"details":{"sample common name":"Small Intestine","sra sample accession":"SRS366519","disease":"iron deficiency, bipolar","biomaterial_provider":"Shin Lin, Stanford University","biomaterial_type":"Primary Tissue","tissue_type":"Small Intestine","tissue_depot":"N/A","collection_method":"Autopsy","donor_id":"STL002","donor_age":"30","donor_health_status":"iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)","donor_sex":"Female","donor_ethnicity":"Caucasian","experiment_type":"mRNA-Seq","extraction_protocol":"Qiagen RNeasy mini kit, performed as per manufacturer's instructions","cdna_preparation_initial_rna_qnty":"4 g","cdna_preparation_polya_rna/":"Dynabeads oligo(dt)25 (Invitrogen)","cdna_preparation_fragmentation":"PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94C for 4 min","cdna_preparation_fragment_size_range":"200-250","cdna_preparation_first_strand_synthesis_enzyme":"SuperScript III (Invitrogen)","cdna_preparation_first_strand_purification":"Purification with RNAClean XP beads (Agencourt)","cdna_preparation_second_strand_synthesis_enzyme":"DNA Polymerase I (E. coli) (New England Biolabs)","cdna_preparation_second_strand_synthesis_dntp_mix":"dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP","cdna_preparation_purification":"Purification with AMPure XP beads (Agencourt)","dna_preparation_adaptor":"TruSeq Multiplexed Adapters (Illumina)","dna_preparation_adaptor_ligation_protocol":"16C for 16 hours with T4 DNA ligase (New England Biolabs)","dna_preparation_post-ligation_fragment_size_selection":"Two rounds of purification with AMPure XP beads (Agencourt)","dna_preparation_uracil_dna_glycosylase_digestion":"One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps.","library_generation_pcr_polymerase_type":"TruSeq PCR Master Mix (Illumina)","library_generation_pcr_thermocycling_program":"98C 30 sec","library_generation_pcr_number_cycles":"10","library_generation_pcr_primer":"TruSeq PCR Primer Cocktail (Illumina)","library_generation_pcr_product_isolation_protocol":"Purification with AMPure XP beads (Agencourt)","extraction_protocol_mrna_enrichment":"Dynabeads oligo(dt)25 protocol","rna_preparation_reverse_transcription_primer_sequence":"Random hexamers","rna_preparation_reverse_transcription_protocol":"First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)","library_generation_pcr_template":"cDNA","library_generation_pcr_template_conc":"5 ng/L","library_generation_pcr_f_primer_sequence":"5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'","library_generation_pcr_r_primer_sequence":"5' CAAGCAGAAGACGGCATACGAGAT 3'","library_generation_pcr_primer_conc":"200nM","original_filename":"GSM1120313_UCSD.Small_Intestine.mRNA-Seq.STL002.wig"},"geolst":["GSM1120313"]},{"type":"bedGraph","name":"polyA RNA sequencing of STL001 Small Bowel Cultured Cells","url":"http://egg.wustl.edu/d/hg19/GSM1010940_1.gz","public":true,"mode":1,"qtc":{"anglescale":1,"pr":79,"pg":97,"pb":44,"nr":255,"ng":0,"nb":0,"pth":"rgb(79, 97, 44)","nth":"#800000","thtype":2,"thmin":0,"thmax":10,"thpercentile":97,"height":9,"summeth":1,"smooth":7},"annotation":["13207","25002","30002","40272"],"details":{"sample alias":"STL001SB-01","sample common name":"Small Intestine","disease":"None","biomaterial_provider":"Shin Lin, Stanford University","biomaterial_type":"Primary Tissue","tissue_type":"Small Intestine","tissue_depot":"N/A","collection_method":"Autopsy","donor_id":"STL001","donor_age":"3","donor_health_status":"healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)","donor_sex":"Male","donor_ethnicity":"Caucasian and African American","experiment_type":"mRNA-Seq","extraction_protocol":"Qiagen RNeasy mini kit, performed as per manufacturer's instructions","cdna_preparation_initial_rna_qnty":"4 g","cdna_preparation_polya_rna/":"Dynabeads oligo(dt)25 (Invitrogen)","cdna_preparation_fragmentation":"PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94C for 4 min","cdna_preparation_fragment_size_range":"200-250","cdna_preparation_first_strand_synthesis_enzyme":"SuperScript III (Invitrogen)","cdna_preparation_first_strand_purification":"Purification with RNAClean XP beads (Agencourt)","cdna_preparation_second_strand_synthesis_enzyme":"DNA Polymerase I (E. coli) (New England Biolabs)","cdna_preparation_second_strand_synthesis_dntp_mix":"dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP","cdna_preparation_purification":"Purification with AMPure XP beads (Agencourt)","dna_preparation_adaptor":"TruSeq Multiplexed Adapters (Illumina)","dna_preparation_adaptor_ligation_protocol":"16C for 16 hours with T4 DNA ligase (New England Biolabs)","dna_preparation_post-ligation_fragment_size_selection":"Two rounds of purification with AMPure XP beads (Agencourt)","dna_preparation_uracil_dna_glycosylase_digestion":"One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps.","library_generation_pcr_polymerase_type":"TruSeq PCR Master Mix (Illumina)","library_generation_pcr_thermocycling_program":"98C 30 sec","library_generation_pcr_number_cycles":"10","library_generation_pcr_primer":"TruSeq PCR Primer Cocktail (Illumina)","library_generation_pcr_product_isolation_protocol":"Purification with AMPure XP beads (Agencourt)","extraction_protocol_mrna_enrichment":"Dynabeads oligo(dt)25 protocol","rna_preparation_reverse_transcription_primer_sequence":"Random hexamers","rna_preparation_reverse_transcription_protocol":"First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)","library_generation_pcr_template":"cDNA","library_generation_pcr_template_conc":"5 ng/L","library_generation_pcr_f_primer_sequence":"5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'","library_generation_pcr_r_primer_sequence":"5' CAAGCAGAAGACGGCATACGAGAT 3'","library_generation_pcr_primer_conc":"200nM","original_filename":"GSM1010940_UCSD.Small_Intestine.mRNA-Seq.STL001.wig"},"geolst":["GSM1010940"]},{"type":"bedGraph","name":"polyA RNA sequencing of STL001 Lung Cells","url":"http://egg.wustl.edu/d/hg19/GSM1120308_1.gz","public":true,"mode":1,"qtc":{"anglescale":1,"pr":79,"pg":97,"pb":44,"nr":255,"ng":0,"nb":0,"pth":"rgb(79, 97, 44)","nth":"#800000","thtype":2,"thmin":0,"thmax":10,"thpercentile":97,"height":9,"summeth":1,"smooth":7},"annotation":["13301","25002","30002","40272"],"details":{"sample common name":"Lung","sra sample accession":"SRS366510","disease":"None","biomaterial_provider":"Shin Lin, Stanford University","biomaterial_type":"Primary Tissue","tissue_type":"Lung","tissue_depot":"N/A","collection_method":"Autopsy","donor_id":"STL001","donor_age":"3","donor_health_status":"healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)","donor_sex":"Male","donor_ethnicity":"Caucasian and African American","experiment_type":"mRNA-Seq","extraction_protocol":"Qiagen RNeasy mini kit, performed as per manufacturer's instructions","cdna_preparation_initial_rna_qnty":"4 g","cdna_preparation_polya_rna/":"Dynabeads oligo(dt)25 (Invitrogen)","cdna_preparation_fragmentation":"PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94C for 4 min","cdna_preparation_fragment_size_range":"200-250","cdna_preparation_first_strand_synthesis_enzyme":"SuperScript III (Invitrogen)","cdna_preparation_first_strand_purification":"Purification with RNAClean XP beads (Agencourt)","cdna_preparation_second_strand_synthesis_enzyme":"DNA Polymerase I (E. coli) (New England Biolabs)","cdna_preparation_second_strand_synthesis_dntp_mix":"dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP","cdna_preparation_purification":"Purification with AMPure XP beads (Agencourt)","dna_preparation_adaptor":"TruSeq Multiplexed Adapters (Illumina)","dna_preparation_adaptor_ligation_protocol":"16C for 16 hours with T4 DNA ligase (New England Biolabs)","dna_preparation_post-ligation_fragment_size_selection":"Two rounds of purification with AMPure XP beads (Agencourt)","dna_preparation_uracil_dna_glycosylase_digestion":"One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps.","library_generation_pcr_polymerase_type":"TruSeq PCR Master Mix (Illumina)","library_generation_pcr_thermocycling_program":"98C 30 sec","library_generation_pcr_number_cycles":"10","library_generation_pcr_primer":"TruSeq PCR Primer Cocktail (Illumina)","library_generation_pcr_product_isolation_protocol":"Purification with AMPure XP beads (Agencourt)","extraction_protocol_mrna_enrichment":"Dynabeads oligo(dt)25 protocol","rna_preparation_reverse_transcription_primer_sequence":"Random hexamers","rna_preparation_reverse_transcription_protocol":"First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. 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Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)","library_generation_pcr_template":"cDNA","library_generation_pcr_template_conc":"5 ng/L","library_generation_pcr_f_primer_sequence":"5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'","library_generation_pcr_r_primer_sequence":"5' CAAGCAGAAGACGGCATACGAGAT 3'","library_generation_pcr_primer_conc":"200nM","original_filename":"GSM1120310_UCSD.Psoas_Muscle.mRNA-Seq.STL001.wig"},"geolst":["GSM1120310"]},{"type":"bedGraph","name":"polyA RNA sequencing of STL003 Psoas Cultured Cells","url":"http://egg.wustl.edu/d/hg19/GSM1010968_1.gz","public":true,"mode":1,"qtc":{"anglescale":1,"pr":79,"pg":97,"pb":44,"nr":255,"ng":0,"nb":0,"pth":"rgb(79, 97, 44)","nth":"#800000","thtype":2,"thmin":0,"thmax":10,"thpercentile":97,"height":9,"summeth":1,"smooth":7},"annotation":["13218","25002","30002","40216"],"details":{"sample alias":"STL003PO-01","sample common name":"Psoas Muscle","disease":"None","biomaterial_provider":"Shin Lin, Stanford University","biomaterial_type":"Primary Tissue","tissue_type":"Psoas Muscle","tissue_depot":"N/A","collection_method":"Autopsy","donor_id":"STL003","donor_age":"34","donor_health_status":"polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)","donor_sex":"Male","donor_ethnicity":"Caucasian","experiment_type":"mRNA-Seq","extraction_protocol":"Qiagen RNeasy mini kit, performed as per manufacturer's instructions","cdna_preparation_initial_rna_qnty":"4 g","cdna_preparation_polya_rna/":"Dynabeads oligo(dt)25 (Invitrogen)","cdna_preparation_fragmentation":"PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94C for 4 min","cdna_preparation_fragment_size_range":"200-250","cdna_preparation_first_strand_synthesis_enzyme":"SuperScript III (Invitrogen)","cdna_preparation_first_strand_purification":"Purification with RNAClean XP beads (Agencourt)","cdna_preparation_second_strand_synthesis_enzyme":"DNA Polymerase I (E. coli) (New England Biolabs)","cdna_preparation_second_strand_synthesis_dntp_mix":"dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP","cdna_preparation_purification":"Purification with AMPure XP beads (Agencourt)","dna_preparation_adaptor":"TruSeq Multiplexed Adapters (Illumina)","dna_preparation_adaptor_ligation_protocol":"16C for 16 hours with T4 DNA ligase (New England Biolabs)","dna_preparation_post-ligation_fragment_size_selection":"Two rounds of purification with AMPure XP beads (Agencourt)","dna_preparation_uracil_dna_glycosylase_digestion":"One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps.","library_generation_pcr_polymerase_type":"TruSeq PCR Master Mix (Illumina)","library_generation_pcr_thermocycling_program":"98C 30 sec","library_generation_pcr_number_cycles":"10","library_generation_pcr_primer":"TruSeq PCR Primer Cocktail (Illumina)","library_generation_pcr_product_isolation_protocol":"Purification with AMPure XP beads (Agencourt)","extraction_protocol_mrna_enrichment":"Dynabeads oligo(dt)25 protocol","rna_preparation_reverse_transcription_primer_sequence":"Random hexamers","rna_preparation_reverse_transcription_protocol":"First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)","library_generation_pcr_template":"cDNA","library_generation_pcr_template_conc":"5 ng/L","library_generation_pcr_f_primer_sequence":"5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'","library_generation_pcr_r_primer_sequence":"5' CAAGCAGAAGACGGCATACGAGAT 3'","library_generation_pcr_primer_conc":"200nM","original_filename":"GSM1010968_UCSD.Psoas_Muscle.mRNA-Seq.STL003.wig"},"geolst":["GSM1010968"]},{"type":"bedGraph","name":"polyA RNA sequencing of STL002 Pancreas Cells","url":"http://egg.wustl.edu/d/hg19/GSM1120309_1.gz","public":true,"mode":1,"qtc":{"anglescale":1,"pr":79,"pg":97,"pb":44,"nr":255,"ng":0,"nb":0,"pth":"rgb(79, 97, 44)","nth":"#800000","thtype":2,"thmin":0,"thmax":10,"thpercentile":97,"height":9,"summeth":1,"smooth":7},"annotation":["13208","25002","30002","40271"],"details":{"sample common name":"Pancreas","sra sample accession":"SRS366517","disease":"iron deficiency, bipolar","biomaterial_provider":"Shin Lin, Stanford University","biomaterial_type":"Primary Tissue","tissue_type":"Pancreas","tissue_depot":"N/A","collection_method":"Autopsy","donor_id":"STL002","donor_age":"30","donor_health_status":"iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)","donor_sex":"Female","donor_ethnicity":"Caucasian","experiment_type":"mRNA-Seq","extraction_protocol":"Qiagen RNeasy mini kit, performed as per manufacturer's instructions","cdna_preparation_initial_rna_qnty":"4 g","cdna_preparation_polya_rna/":"Dynabeads oligo(dt)25 (Invitrogen)","cdna_preparation_fragmentation":"PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94C for 4 min","cdna_preparation_fragment_size_range":"200-250","cdna_preparation_first_strand_synthesis_enzyme":"SuperScript III (Invitrogen)","cdna_preparation_first_strand_purification":"Purification with RNAClean XP beads (Agencourt)","cdna_preparation_second_strand_synthesis_enzyme":"DNA Polymerase I (E. coli) (New England Biolabs)","cdna_preparation_second_strand_synthesis_dntp_mix":"dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP","cdna_preparation_purification":"Purification with AMPure XP beads (Agencourt)","dna_preparation_adaptor":"TruSeq Multiplexed Adapters (Illumina)","dna_preparation_adaptor_ligation_protocol":"16C for 16 hours with T4 DNA ligase (New England Biolabs)","dna_preparation_post-ligation_fragment_size_selection":"Two rounds of purification with AMPure XP beads (Agencourt)","dna_preparation_uracil_dna_glycosylase_digestion":"One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps.","library_generation_pcr_polymerase_type":"TruSeq PCR Master Mix (Illumina)","library_generation_pcr_thermocycling_program":"98C 30 sec","library_generation_pcr_number_cycles":"10","library_generation_pcr_primer":"TruSeq PCR Primer Cocktail (Illumina)","library_generation_pcr_product_isolation_protocol":"Purification with AMPure XP beads (Agencourt)","extraction_protocol_mrna_enrichment":"Dynabeads oligo(dt)25 protocol","rna_preparation_reverse_transcription_primer_sequence":"Random hexamers","rna_preparation_reverse_transcription_protocol":"First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)","library_generation_pcr_template":"cDNA","library_generation_pcr_template_conc":"5 ng/L","library_generation_pcr_f_primer_sequence":"5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'","library_generation_pcr_r_primer_sequence":"5' CAAGCAGAAGACGGCATACGAGAT 3'","library_generation_pcr_primer_conc":"200nM","original_filename":"GSM1120309_UCSD.Pancreas.mRNA-Seq.STL002.wig"},"geolst":["GSM1120309"]},{"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":79,"pg":97,"pb":44,"nr":255,"ng":0,"nb":0,"pth":"rgb(79, 97, 44)","nth":"#800000","thtype":2,"thmin":0,"thmax":10,"thpercentile":97,"height":9,"summeth":1,"smooth":7},"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":"RNA-Seq of Neurospheres  Ganglionic Eminence Derived HuFNSC01","url":"http://egg.wustl.edu/d/hg19/GSM751271_0.bigWig","public":true,"mode":1,"qtc":{"anglescale":1,"pr":79,"pg":97,"pb":44,"nr":255,"ng":0,"nb":0,"pth":"rgb(79, 97, 44)","nth":"#800000","thtype":2,"thmin":0,"thmax":10,"thpercentile":97,"height":9,"summeth":1,"smooth":7},"annotation":["13031","25002","30014","40115","60002","70009"],"details":{"sample_alias":"Neurospheres, Ganglionic Eminence Derived HuFNSC01","sample_common_name":"Neurosphere Cultured Cells, Ganglionic Eminence Derived","molecule":"genomic DNA","disease":"None","biomaterial_provider":"Keith Ligon, Harvard","biomaterial_type":"Primary Cell Culture","cell_type":"Neurospheres, Ganglionic Eminence Derived","markers":"NA","culture_conditions":"Neurocult+EGF+FGF","donor_id":"HuFNSC01","donor_age":"17GW","donor_health_status":"Disease Free","donor_sex":"Female","donor_ethnicity":"NA","passage_if_expanded":"3","karyotype":"","parity":"NA","note":"Twin of HuFNSC02","experiment_type":"mRNA-Seq","extraction_protocol":"Costello Lab Protocol","extraction_protocol_mrna_enrichment":"Miltenyi-Biotec MACS mRNA purification","rna_preparation_initial_rna_qlty":"RIN 9.6","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":"10","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":"GSM751271_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.mRNA-Seq.HuFNSC01.bigWig"},"geolst":["GSM751271"]},{"type":"bedGraph","name":"polyA RNA sequencing of STL003 Adrenal Cultured Cells","url":"http://egg.wustl.edu/d/hg19/GSM1010950_1.gz","public":true,"mode":1,"qtc":{"anglescale":1,"pr":79,"pg":97,"pb":44,"nr":255,"ng":0,"nb":0,"pth":"rgb(79, 97, 44)","nth":"#800000","thtype":2,"thmin":0,"thmax":10,"thpercentile":97,"height":9,"summeth":1,"smooth":7},"annotation":["13212","25002","30002","40216"],"details":{"sample alias":"STL003AD-01","sample common name":"Adrenal Gland","disease":"None","biomaterial_provider":"Shin Lin, Stanford University","biomaterial_type":"Primary Tissue","tissue_type":"Adrenal Gland","tissue_depot":"N/A","collection_method":"Autopsy","donor_id":"STL003","donor_age":"34","donor_health_status":"polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)","donor_sex":"Male","donor_ethnicity":"Caucasian","experiment_type":"mRNA-Seq","extraction_protocol":"Qiagen RNeasy mini kit, performed as per manufacturer's instructions","cdna_preparation_initial_rna_qnty":"4 g","cdna_preparation_polya_rna/":"Dynabeads oligo(dt)25 (Invitrogen)","cdna_preparation_fragmentation":"PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94C for 4 min","cdna_preparation_fragment_size_range":"200-250","cdna_preparation_first_strand_synthesis_enzyme":"SuperScript III (Invitrogen)","cdna_preparation_first_strand_purification":"Purification with RNAClean XP beads (Agencourt)","cdna_preparation_second_strand_synthesis_enzyme":"DNA Polymerase I (E. coli) (New England Biolabs)","cdna_preparation_second_strand_synthesis_dntp_mix":"dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP","cdna_preparation_purification":"Purification with AMPure XP beads (Agencourt)","dna_preparation_adaptor":"TruSeq Multiplexed Adapters (Illumina)","dna_preparation_adaptor_ligation_protocol":"16C for 16 hours with T4 DNA ligase (New England Biolabs)","dna_preparation_post-ligation_fragment_size_selection":"Two rounds of purification with AMPure XP beads (Agencourt)","dna_preparation_uracil_dna_glycosylase_digestion":"One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps.","library_generation_pcr_polymerase_type":"TruSeq PCR Master Mix (Illumina)","library_generation_pcr_thermocycling_program":"98C 30 sec","library_generation_pcr_number_cycles":"10","library_generation_pcr_primer":"TruSeq PCR Primer Cocktail (Illumina)","library_generation_pcr_product_isolation_protocol":"Purification with AMPure XP beads (Agencourt)","extraction_protocol_mrna_enrichment":"Dynabeads oligo(dt)25 protocol","rna_preparation_reverse_transcription_primer_sequence":"Random hexamers","rna_preparation_reverse_transcription_protocol":"First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. 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