title: 140718_I232_FCC4MVEACXX_L3_RHUMdztTAAMMRAAPEI-213

description: GC6 Cohort


title: 140718_I232_FCC4MVEACXX_L2_RHUMdztTAAMJRAAPEI-210

status: Public on Apr 10 2018

type: SRA

city: Seattle

first: Daniel

last: Zak

state: WA

address: 188 East Blaine Street, Suite 300

country: USA

institute: Regeneron

description: GC6 Cohort

library_source: transcriptomic

data_processing:
Alignment STAR version STAR_2.3.1d
Sequenced reads were filtered for low-quality sequence and the presence of 'N's, then mapped to hg19 whole genome using star STAR_2.3.1d
Junctions counts were calculated by using an in house script to count the number of reads mapped to all splice junctions in the genome
Gene counts were calculated by using HTSeq count
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file including the raw junction counts for all the detected junctions in the genome and tab delimited gene counts table
Supplementary_files_format_and_content: rawCounts_GeneNames_AllSamples.csv: number of reads mapped to the genes in all samples
Supplementary_files_format_and_content: GC6_juncCounts_raw_Star.txt: number of reads mapped to the splice junctions in all samples

molecule: total RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
Paxgene RNA
GlobinClear Globin transcript reduction followed by Illumina mRNA-Seq

tag: tissue

value: blood

tag: code

tag: subjectid

tag: site

value: MRC

tag: age

tag: gender

value: F

tag: group

value: Control


title: 140718_I232_FCC4MVEACXX_L2_RHUMdztTAAMLRAAPEI-212

description: GC6 Cohort


title: 140718_I232_FCC4MVEACXX_L1_RHUMdztTAAMGRAAPEI-207

description: GC6 Cohort

value: M

value: case (TB)


title: 140718_I232_FCC4MVEACXX_L1_RHUMdztTAAMKRAAPEI-211

description: GC6 Cohort


title: 140711_I266_FCC4MVHACXX_L8_RHUMdztTFORAAPEI-201

description: GC6 Cohort

value: SUN


title: 140711_I266_FCC4MVHACXX_L1_RHUMdztTEURAAPEI-205

description: GC6 Cohort


title: 140718_I232_FCC4MVEACXX_L1_RHUMdztTAAMRRAAPEI-219

description: GC6 Cohort


title: 140711_I266_FCC4MVHACXX_L2_RHUMdztTEZRAAPEI-210

description: GC6 Cohort


title: 140711_I266_FCC4MVHACXX_L3_RHUMdztTFCRAAPEI-213

description: GC6 Cohort


title: 140711_I266_FCC4MVHACXX_L3_RHUMdztTFBRAAPEI-212

description: GC6 Cohort


title: 140711_I266_FCC4MVHACXX_L4_RHUMdztTFGRAAPEI-218

description: GC6 Cohort


title: 140711_I266_FCC4MVHACXX_L2_RHUMdztTFARAAPEI-211

description: GC6 Cohort


title: 140711_I266_FCC4MVHACXX_L2_RHUMdztTEYRAAPEI-209

description: GC6 Cohort


title: 140718_I232_FCC4MVEACXX_L4_RHUMdztTAAMIRAAPEI-209

description: GC6 Cohort


title: 140711_I266_FCC4MVHACXX_L6_RHUMdztTFJRAAPEI-221

description: GC6 Cohort


title: 140718_I232_FCC4MVEACXX_L8_RHUMdztTAANARAAPEI-203

description: GC6 Cohort


title: 140711_I266_FCC4MVHACXX_L4_RHUMdztTFFRAAPEI-216

description: GC6 Cohort


title: 140711_I266_FCC4MVHACXX_L4_RHUMdztTFERAAPEI-215

description: GC6 Cohort


title: 140711_I266_FCC4MVHACXX_L6_RHUMdztTFIRAAPEI-220

description: GC6 Cohort


title: 140711_I266_FCC4MVHACXX_L7_RHUMdztTFLRAAPEI-223

description: GC6 Cohort


title: 140711_I266_FCC4MVHACXX_L6_RHUMdztTFHRAAPEI-219

description: GC6 Cohort


title: 140711_I266_FCC4MVHACXX_L7_RHUMdztTFMRAAPEI-225

description: GC6 Cohort


title: 140711_I266_FCC4MVHACXX_L7_RHUMdztTFKRAAPEI-222

description: GC6 Cohort


title: 140711_I266_FCC4MVHACXX_L8_RHUMdztTFNRAAPEI-227

description: GC6 Cohort


title: 140711_I266_FCC4MVHACXX_L1_RHUMdztTEXRAAPEI-208

description: GC6 Cohort


title: 140718_I232_FCC4MVEACXX_L3_RHUMdztTAAMORAAPEI-215

description: GC6 Cohort


title: 140711_I266_FCC4MVHACXX_L1_RHUMdztTEVRAAPEI-206

description: GC6 Cohort


title: 140718_I232_FCC4MVRACXX_L2_RHUMdztTAALQRAAPEI-215

description: GC6 Cohort


title: 140718_I232_FCC4MVRACXX_L2_RHUMdztTAALPRAAPEI-214

description: GC6 Cohort


title: 140718_I232_FCC4MVRACXX_L1_RHUMdztTAALLRAAPEI-210

description: GC6 Cohort


title: 140718_I232_FCC4MVEACXX_L2_RHUMdztTAAMHRAAPEI-208

description: GC6 Cohort


title: 140718_I232_FCC4MVRACXX_L2_RHUMdztTAALORAAPEI-213

description: GC6 Cohort


title: 140718_I232_FCC4MVRACXX_L3_RHUMdztTAALSRAAPEI-218

description: GC6 Cohort


title: 140711_I266_FCC4MVHACXX_L3_RHUMdztTFDRAAPEI-214

description: GC6 Cohort


title: 140718_I232_FCC4MVRACXX_L4_RHUMdztTAALWRAAPEI-222

description: GC6 Cohort


title: 140718_I232_FCC4MVRACXX_L4_RHUMdztTAALVRAAPEI-221

description: GC6 Cohort


title: 140718_I232_FCC4MVRACXX_L3_RHUMdztTAALTRAAPEI-219

description: GC6 Cohort


title: 140718_I232_FCC4MVRACXX_L4_RHUMdztTAALURAAPEI-220

description: GC6 Cohort


title: 140718_I232_FCC4MVRACXX_L7_RHUMdztTAAMBRAAPEI-202

description: GC6 Cohort


title: 140718_I232_FCC4MVRACXX_L7_RHUMdztTAAMARAAPEI-201

description: GC6 Cohort


title: 140718_I232_FCC4MVRACXX_L6_RHUMdztTAALYRAAPEI-225

description: GC6 Cohort


title: 140718_I232_FCC4MVRACXX_L6_RHUMdztTAALXRAAPEI-223

description: GC6 Cohort


title: 140718_I232_FCC4MVRACXX_L6_RHUMdztTAALZRAAPEI-227

description: GC6 Cohort


title: 140718_I232_FCC4MVRACXX_L8_RHUMdztTAAMFRAAPEI-206

description: GC6 Cohort


title: 140718_I232_FCC4MVRACXX_L8_RHUMdztTAAMERAAPEI-205

description: GC6 Cohort


title: 140718_I232_FCC4MVRACXX_L8_RHUMdztTAAMDRAAPEI-204

description: GC6 Cohort


title: 140718_I232_FCC4MVRACXX_L1_RHUMdztTAALMRAAPEI-211

description: GC6 Cohort


title: 140718_I232_FCC4MVRACXX_L1_RHUMdztTAALNRAAPEI-212

description: GC6 Cohort


title: 140718_I232_FCC4MVRACXX_L7_RHUMdztTAAMCRAAPEI-203

description: GC6 Cohort


title: 140715_I162_FCC4MWCACXX_L1_RHUMdztTAAJWRAAPEI-218

description: GC6 Cohort


title: 140715_I162_FCC4MWCACXX_L2_RHUMdztTAAJZRAAPEI-221

description: GC6 Cohort


title: 140715_I162_FCC4MWCACXX_L3_RHUMdztTAAKBRAAPEI-223

description: GC6 Cohort


title: 140715_I162_FCC4MWCACXX_L3_RHUMdztTAAKCRAAPEI-225

description: GC6 Cohort


title: 140715_I162_FCC4MWCACXX_L3_RHUMdztTAAKDRAAPEI-227

description: GC6 Cohort


title: 140715_I162_FCC4MWCACXX_L8_RHUMdztTAAKORAAPEI-211

description: GC6 Cohort


title: 140715_I162_FCC4MWCACXX_L1_RHUMdztTAAJVRAAPEI-216

description: GC6 Cohort


title: 140715_I162_FCC4MWCACXX_L4_RHUMdztTAAKFRAAPEI-202

description: GC6 Cohort


title: 140715_I162_FCC4MWCACXX_L6_RHUMdztTAAKHRAAPEI-204

description: GC6 Cohort


title: 140715_I162_FCC4MWCACXX_L2_RHUMdztTAAKARAAPEI-222

description: GC6 Cohort


title: 140715_I162_FCC4MWCACXX_L2_RHUMdztTAAJYRAAPEI-220

description: GC6 Cohort


title: 140711_I266_FCC4MVHACXX_L8_RHUMdztTFPRAAPEI-202

description: GC6 Cohort


title: 140718_I232_FCC4MVRACXX_L3_RHUMdztTAALRRAAPEI-216

description: GC6 Cohort


title: 140715_I162_FCC4MWCACXX_L6_RHUMdztTAAKIRAAPEI-205

description: GC6 Cohort


title: 140715_I162_FCC4MWCACXX_L7_RHUMdztTAAKKRAAPEI-207

description: GC6 Cohort


title: 140715_I162_FCC4MWCACXX_L4_RHUMdztTAAKGRAAPEI-203

description: GC6 Cohort


title: 140715_I162_FCC4MWCACXX_L7_RHUMdztTAAKLRAAPEI-208

description: GC6 Cohort


title: 140715_I162_FCC4MWCACXX_L8_RHUMdztTAAKPRAAPEI-212

description: GC6 Cohort


title: 140715_I162_FCC4MWCACXX_L8_RHUMdztTAAKNRAAPEI-210

description: GC6 Cohort


title: 140711_I269_FCC4MWPACXX_L1_RHUMdztTFQRAAPEI-203

description: GC6 Cohort


title: 140711_I269_FCC4MWPACXX_L2_RHUMdztTFVRAAPEI-208

description: GC6 Cohort


title: 140711_I269_FCC4MWPACXX_L2_RHUMdztTFURAAPEI-207

description: GC6 Cohort


title: 140711_I269_FCC4MWPACXX_L3_RHUMdztTFYRAAPEI-211

description: GC6 Cohort


title: 140711_I269_FCC4MWPACXX_L2_RHUMdztTFTRAAPEI-206

description: GC6 Cohort


title: 140711_I269_FCC4MWPACXX_L3_RHUMdztTFXRAAPEI-210

description: GC6 Cohort


title: 140715_I162_FCC4MWCACXX_L1_RHUMdztTAAJXRAAPEI-219

description: GC6 Cohort


title: 140711_I269_FCC4MWPACXX_L4_RHUMdztTGBRAAPEI-214

description: GC6 Cohort


title: 140711_I269_FCC4MWPACXX_L4_RHUMdztTGARAAPEI-213

description: GC6 Cohort


title: 140711_I269_FCC4MWPACXX_L3_RHUMdztTFWRAAPEI-209

description: GC6 Cohort


title: 140711_I269_FCC4MWPACXX_L4_RHUMdztTFZRAAPEI-212

description: GC6 Cohort


title: 140711_I269_FCC4MWPACXX_L6_RHUMdztTGERAAPEI-218

description: GC6 Cohort


title: 140715_I162_FCC4MWCACXX_L4_RHUMdztTAAKERAAPEI-201

description: GC6 Cohort


title: 140715_I162_FCC4MWCACXX_L6_RHUMdztTAAKJRAAPEI-206

description: GC6 Cohort


title: 140711_I269_FCC4MWPACXX_L6_RHUMdztTGDRAAPEI-216

description: GC6 Cohort


title: 140711_I269_FCC4MWPACXX_L6_RHUMdztTGCRAAPEI-215

description: GC6 Cohort


title: 140711_I269_FCC4MWPACXX_L8_RHUMdztTGJRAAPEI-223

description: GC6 Cohort


title: 140711_I269_FCC4MWPACXX_L7_RHUMdztTGHRAAPEI-221

description: GC6 Cohort


title: 140711_I269_FCC4MWPACXX_L7_RHUMdztTGGRAAPEI-220

description: GC6 Cohort


title: 140711_I269_FCC4MWPACXX_L7_RHUMdztTGFRAAPEI-219

description: GC6 Cohort


title: 140711_I269_FCC4MWPACXX_L8_RHUMdztTGKRAAPEI-225

description: GC6 Cohort


title: 140708_I175_FCC4MY9ACXX_L7_RHUMdztTBGRAAPEI-209

description: GC6 Cohort


title: 140711_I269_FCC4MWPACXX_L8_RHUMdztTGIRAAPEI-222

description: GC6 Cohort


title: 140709_I232_FCC4MUWACXX_L7_RHUMdztTCYRAAPEI-205

description: GC6 Cohort


title: 140711_I269_FCC4MWPACXX_L1_RHUMdztTFSRAAPEI-205

description: GC6 Cohort


title: 140708_I175_FCC4MY9ACXX_L8_RHUMdztTBJRAAPEI-212

description: GC6 Cohort


title: 140708_I175_FCC4MY9ACXX_L1_RHUMdztTAXRAAPEI-227

description: GC6 Cohort


title: 140708_I175_FCC4MY9ACXX_L8_RHUMdztTBKRAAPEI-213

description: GC6 Cohort


title: 140708_I175_FCC4MY9ACXX_L7_RHUMdztTBHRAAPEI-210

description: GC6 Cohort


title: 140715_I162_FCC4MWCACXX_L7_RHUMdztTAAKMRAAPEI-209

description: GC6 Cohort


title: 140708_I175_FCC4MY9ACXX_L5_RHUMdztTDZRAAPEI-208

description: GC6 Cohort


title: 140708_I175_FCC4MY9ACXX_L4_RHUMdztTBCRABPEI-205

description: GC6 Cohort


title: iPSC_C45

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

description: Single Cell RNA-seq data

data_processing:
Basecalls performed using BCL2FASTQ Conversion Software 1.8.4 in the CASAVA 1.8.2 pipeline.
Sequence reads were aligned to the human genome (hg19) using TopHat2 software.
The sequenced short reads were trimmed by Trimmomatic 0.3.3 and mapped to the human reference genome hg19 using TopHat 2.0.14 and Bowtie 2.2.5.
RPKM counts for each gene were obtained using the RPKMforgenes software.
Genome_build: hg19
Supplementary_files_format_and_content: Calculation of gene expression value and normalization were performed by RPKMforgenes (10th, Dec, 2012). The processed data file contains Gene name, Refseq ID, RPKM, and Raw counts columns (from left to right), and the expression level was represented by RPKM.

source_name: Human induced Pluripotent Stem cell

extract_protocol:
We obtained EGFP (+)/DAPI (-) cells on day 3, and TRA-1-60 (+)/DAPI (-) cells on days 7-28 by sorting with FACS Aria II. RNA extraction and cDNA synthesis of single cells were performed using SMARTer Ultra Low Input RNA for Illumina Sequencing (Clontech) with the C1 Single-Cell Auto-prep and IFC for 10-17 µm (Fluidigm) according to the manufacturer’s instructions.
Sequencing libraries were constructed using the Nextera XT DNA Sample Prep kit (Illumina) and Nextera XT Index kit (Illumina) according to Fluidigm’s instruction, which was modified from Illumina’s original protocol. The libraries were sequenced with the TruSeq SBS kit v3 and TruSeq SR Cluster kit v3 (Illumina) in 100-cycle Single-Read mode of HiSeq 2500 (Illumina).

treatment_protocol: Human iPSCs were routinely maintained in Primate ESC medium (ReproCELL) supplemented with 4 ng/ml recombinant human basic fibroblast growth factor (bFGF, Wako) on mitomycin C-inactivated SNL feeder cells (McMahon and Bradley, 1990) or in StemFiT medium (Ajinomoto) on Laminin 511 E8 (Nippi)-coated plate. HDFs were maintained in Dulbecco’s modified eagle medium (DMEM, Life Technologies) containing 10% fetal bovine serum (FBS, Life Technologies) and 0.5% Penicillin/Streptomycin (Pen/Strep, Life Technologies).

tag: cell type

value: Human induced Pluripotent Stem cell


title: iPSC_C39

description: Single Cell RNA-seq data


title: iPSC_C37

description: Single Cell RNA-seq data


title: iPSC_C49

description: Single Cell RNA-seq data


title: iPSC_C61

description: Single Cell RNA-seq data


title: iPSC_C43

description: Single Cell RNA-seq data


title: 140708_I175_FCC4MY9ACXX_L5_RHUMdztTEARAAPEI-209

description: GC6 Cohort


title: 140708_I175_FCC4MY9ACXX_L8_RHUMdztTBIRAAPEI-211

description: GC6 Cohort


title: 140708_I175_FCC4MY9ACXX_L4_RHUMdztTBDRAAPEI-206

description: GC6 Cohort


title: 140708_I175_FCC4MY9ACXX_L3_RHUMdztTAZRAAPEI-202

description: GC6 Cohort


title: 140708_I175_FCC4MY9ACXX_L7_RHUMdztTBFRAAPEI-208

description: GC6 Cohort


title: iPSC_C32

description: Single Cell RNA-seq data


title: iPSC_C67

description: Single Cell RNA-seq data


title: iPSC_C33

description: Single Cell RNA-seq data


title: 140711_I269_FCC4MWPACXX_L1_RHUMdztTFRRAAPEI-204

description: GC6 Cohort


title: 140708_I175_FCC4MY9ACXX_L3_RHUMdztTBBRAAPEI-204

description: GC6 Cohort


title: iPSC_C55

description: Single Cell RNA-seq data


title: iPSC_C31

description: Single Cell RNA-seq data


title: 140708_I175_FCC4MY9ACXX_L3_RHUMdztTBARAAPEI-203

description: GC6 Cohort


title: iPSC_C27

description: Single Cell RNA-seq data


title: 140708_I175_FCC4MY9ACXX_L2_RHUMdztTAORABPEI-215

description: GC6 Cohort


title: 140708_I175_FCC4MY9ACXX_L4_RHUMdztTBERAAPEI-207

description: GC6 Cohort


title: 140708_I175_FCC4MY9ACXX_L2_RHUMdztTAPRABPEI-216

description: GC6 Cohort


title: iPSC_C25

description: Single Cell RNA-seq data


title: iPSC_C26

description: Single Cell RNA-seq data


title: 140708_I175_FCC4MY9ACXX_L2_RHUMdztTAYRABPEI-201

description: GC6 Cohort


title: iPSC_C21

description: Single Cell RNA-seq data


title: 140708_I175_FCC4MY9ACXX_L1_RHUMdztTAMRABPEI-213

description: GC6 Cohort


title: 140724_I269_FCC4N24ACXX_L2_RHUMdztTAAOARAAPEI-205

description: GC6 Cohort


title: iPSC_C20

description: Single Cell RNA-seq data


title: iPSC_C09

description: Single Cell RNA-seq data


title: iPSC_C15

description: Single Cell RNA-seq data


title: iPSC_C19

description: Single Cell RNA-seq data


title: 140708_I175_FCC4MY9ACXX_L1_RHUMdztTANRABPEI-214

description: GC6 Cohort


title: 140724_I269_FCC4N24ACXX_L2_RHUMdztTAANZRAAPEI-204

description: GC6 Cohort


title: 140724_I269_FCC4N24ACXX_L2_RHUMdztTAAOCRAAPEI-207

description: GC6 Cohort


title: iPSC_C08

description: Single Cell RNA-seq data


title: iPSC_C07

description: Single Cell RNA-seq data


title: 140724_I269_FCC4N24ACXX_L1_RHUMdztTAANWRAAPEI-201

description: GC6 Cohort


title: 140724_I269_FCC4N24ACXX_L1_RHUMdztTAANXRAAPEI-202

description: GC6 Cohort


title: 140724_I269_FCC4N24ACXX_L1_RHUMdztTAANYRAAPEI-203

description: GC6 Cohort


title: 140715_I272_FCC4N4PACXX_L1_RHUMdztTAAIHRAAPEI-227

description: GC6 Cohort


title: iPSC_C03

description: Single Cell RNA-seq data


title: 140715_I272_FCC4N4PACXX_L1_RHUMdztTAAIGRAAPEI-225

description: GC6 Cohort


title: Day28_C61

description: Single Cell RNA-seq data

source_name: Intermediate reprogrammed cells

value: TRA-1-60(+) cells on day 28


title: iPSC_C02

description: Single Cell RNA-seq data


title: 140715_I272_FCC4N4PACXX_L1_RHUMdztTAAIFRAAPEI-223

description: GC6 Cohort


title: Day28_C55

description: Single Cell RNA-seq data


title: 140715_I272_FCC4N4PACXX_L2_RHUMdztTAAIKRAAPEI-203

description: GC6 Cohort


title: Day28_C45

description: Single Cell RNA-seq data


title: Day28_C44

description: Single Cell RNA-seq data


title: 140715_I272_FCC4N4PACXX_L2_RHUMdztTAAIJRAAPEI-202

description: GC6 Cohort


title: 140715_I272_FCC4N4PACXX_L2_RHUMdztTAAIIRAAPEI-201

description: GC6 Cohort


title: 140724_I269_FCC4N24ACXX_L2_RHUMdztTAAOBRAAPEI-206

description: GC6 Cohort


title: iPSC_C14

description: Single Cell RNA-seq data


title: 140715_I272_FCC4N4PACXX_L3_RHUMdztTAAINRAAPEI-206

description: GC6 Cohort


title: Day28_C43

description: Single Cell RNA-seq data


title: Day28_C49

description: Single Cell RNA-seq data


title: 140715_I272_FCC4N4PACXX_L3_RHUMdztTAAIMRAAPEI-205

description: GC6 Cohort


title: 140715_I272_FCC4N4PACXX_L4_RHUMdztTAAIQRAAPEI-209

description: GC6 Cohort


title: Day28_C38

description: Single Cell RNA-seq data


title: Day28_C39

description: Single Cell RNA-seq data


title: Day28_C32

description: Single Cell RNA-seq data


title: Day28_C33

description: Single Cell RNA-seq data


title: 140715_I272_FCC4N4PACXX_L4_RHUMdztTAAIPRAAPEI-208

description: GC6 Cohort


title: 140715_I272_FCC4N4PACXX_L4_RHUMdztTAAIORAAPEI-207

description: GC6 Cohort


title: 140715_I272_FCC4N4PACXX_L3_RHUMdztTAAILRAAPEI-204

description: GC6 Cohort


title: Day28_C31

description: Single Cell RNA-seq data


title: 140715_I272_FCC4N4PACXX_L6_RHUMdztTAAITRAAPEI-212

description: GC6 Cohort


title: 140715_I272_FCC4N4PACXX_L7_RHUMdztTAAIWRAAPEI-215

description: GC6 Cohort


title: Day28_C25

description: Single Cell RNA-seq data


title: 140715_I272_FCC4N4PACXX_L6_RHUMdztTAAISRAAPEI-211

description: GC6 Cohort


title: Day28_C26

description: Single Cell RNA-seq data


title: Day28_C20

description: Single Cell RNA-seq data


title: Day28_C15

description: Single Cell RNA-seq data


title: 140715_I272_FCC4N4PACXX_L7_RHUMdztTAAIVRAAPEI-214

description: GC6 Cohort


title: 140715_I272_FCC4N4PACXX_L7_RHUMdztTAAIURAAPEI-213

description: GC6 Cohort


title: 140715_I272_FCC4N4PACXX_L8_RHUMdztTAAIZRAAPEI-219

description: GC6 Cohort


title: 140715_I272_FCC4N4PACXX_L8_RHUMdztTAAIYRAAPEI-218

description: GC6 Cohort


title: Day28_C13

description: Single Cell RNA-seq data


title: Day28_C08

description: Single Cell RNA-seq data


title: Day28_C07

description: Single Cell RNA-seq data


title: Day28_C21

description: Single Cell RNA-seq data


title: 140724_I269_FCC4N6KACXX_L7_RHUMdztTAAOARAAPEI-205

description: GC6 Cohort


title: 140715_I272_FCC4N4PACXX_L8_RHUMdztTAAIXRAAPEI-216

description: GC6 Cohort


title: Day28_C03

description: Single Cell RNA-seq data


title: Day28_C02

description: Single Cell RNA-seq data


title: 140724_I269_FCC4N6KACXX_L7_RHUMdztTAAOBRAAPEI-206

description: GC6 Cohort


title: 140724_I269_FCC4N6KACXX_L7_RHUMdztTAANZRAAPEI-204

description: GC6 Cohort


title: Day28_C27

description: Single Cell RNA-seq data


title: Day20_C74

description: Single Cell RNA-seq data

value: TRA-1-60(+) cells on day 20


title: 140724_I272_FCC4NC6ACXX_L2_RHUMdztTAANFRAAPEI-208

description: GC6 Cohort


title: Day28_C01

description: Single Cell RNA-seq data


title: Day20_C68

description: Single Cell RNA-seq data


title: Day28_C14

description: Single Cell RNA-seq data


title: 140715_I272_FCC4N4PACXX_L6_RHUMdztTAAIRRAAPEI-210

description: GC6 Cohort


title: 140724_I272_FCC4NC6ACXX_L2_RHUMdztTAANERAAPEI-207

description: GC6 Cohort


title: Day20_C62

description: Single Cell RNA-seq data


title: Day20_C61

description: Single Cell RNA-seq data


title: Day20_C57

description: Single Cell RNA-seq data


title: 140724_I272_FCC4NC6ACXX_L3_RHUMdztTAANHRAAPEI-210

description: GC6 Cohort


title: 140724_I272_FCC4NC6ACXX_L4_RHUMdztTAANMRAAPEI-215

description: GC6 Cohort


title: Day20_C56

description: Single Cell RNA-seq data


title: 140724_I272_FCC4NC6ACXX_L4_RHUMdztTAANLRAAPEI-214

description: GC6 Cohort


title: Day20_C51

description: Single Cell RNA-seq data


title: 140724_I272_FCC4NC6ACXX_L2_RHUMdztTAANGRAAPEI-209

description: GC6 Cohort


title: Day20_C50

description: Single Cell RNA-seq data


title: 140724_I272_FCC4NC6ACXX_L6_RHUMdztTAANPRAAPEI-219

description: GC6 Cohort


title: 140724_I269_FCC4N6KACXX_L7_RHUMdztTAAOCRAAPEI-207

description: GC6 Cohort


title: 140724_I272_FCC4NC6ACXX_L7_RHUMdztTAANSRAAPEI-222

description: GC6 Cohort


title: Day20_C37

description: Single Cell RNA-seq data


title: Day20_C45

description: Single Cell RNA-seq data


title: 140724_I272_FCC4NC6ACXX_L7_RHUMdztTAANRRAAPEI-221

description: GC6 Cohort


title: Day20_C32

description: Single Cell RNA-seq data


title: Day20_C25

description: Single Cell RNA-seq data


title: 140724_I272_FCC4NC6ACXX_L8_RHUMdztTAANURAAPEI-225

description: GC6 Cohort


title: Day20_C20

description: Single Cell RNA-seq data


title: Day20_C19

description: Single Cell RNA-seq data


title: 140724_I272_FCC4NC6ACXX_L7_RHUMdztTAANQRAAPEI-220

description: GC6 Cohort


title: 140724_I272_FCC4NC6ACXX_L6_RHUMdztTAANNRAAPEI-216

description: GC6 Cohort


title: 140724_I272_FCC4NC6ACXX_L8_RHUMdztTAANTRAAPEI-223

description: GC6 Cohort


title: 140724_I272_FCC4NC6ACXX_L3_RHUMdztTAANJRAAPEI-212

description: GC6 Cohort


title: 140724_I272_FCC4NC6ACXX_L1_RHUMdztTAANDRAAPEI-206

description: GC6 Cohort


title: Day20_C15

description: Single Cell RNA-seq data


title: Day20_C55

description: Single Cell RNA-seq data


title: Day20_C27

description: Single Cell RNA-seq data


title: Day20_C14

description: Single Cell RNA-seq data


title: 140724_I272_FCC4NC6ACXX_L3_RHUMdztTAANIRAAPEI-211

description: GC6 Cohort


title: 140724_I272_FCC4NC6ACXX_L1_RHUMdztTAANCRAAPEI-205

description: GC6 Cohort


title: Day20_C09

description: Single Cell RNA-seq data


title: Day20_C08

description: Single Cell RNA-seq data


title: 140724_I272_FCC4NC6ACXX_L6_RHUMdztTAANORAAPEI-218

description: GC6 Cohort


title: Day20_C33

description: Single Cell RNA-seq data


title: 140718_I266_FCC4RDRACXX_L1_RHUMdztTAAKRRAAPEI-214

description: GC6 Cohort


title: 140724_I272_FCC4NC6ACXX_L4_RHUMdztTAANKRAAPEI-213

description: GC6 Cohort


title: 140718_I266_FCC4RDRACXX_L8_RHUMdztTAALJRAAPEI-208

description: GC6 Cohort


title: 140724_I272_FCC4NC6ACXX_L8_RHUMdztTAANVRAAPEI-227

description: GC6 Cohort


title: 140718_I266_FCC4RDRACXX_L8_RHUMdztTAALKRAAPEI-209

description: GC6 Cohort


title: Day20_C01

description: Single Cell RNA-seq data


title: Day15_C87

description: Single Cell RNA-seq data

value: TRA-1-60(+) cells on day 15


title: Day20_C03

description: Single Cell RNA-seq data


title: 140718_I266_FCC4RDRACXX_L7_RHUMdztTAALFRAAPEI-204

description: GC6 Cohort


title: Day20_C07

description: Single Cell RNA-seq data


title: 140718_I266_FCC4RDRACXX_L7_RHUMdztTAALGRAAPEI-205

description: GC6 Cohort


title: Day15_C61

description: Single Cell RNA-seq data


title: Day15_C55

description: Single Cell RNA-seq data


title: 140718_I266_FCC4RDRACXX_L7_RHUMdztTAALHRAAPEI-206

description: GC6 Cohort


title: 140718_I266_FCC4RDRACXX_L6_RHUMdztTAALCRAAPEI-201

description: GC6 Cohort


title: Day15_C49

description: Single Cell RNA-seq data


title: Day15_C67

description: Single Cell RNA-seq data


title: 140718_I266_FCC4RDRACXX_L6_RHUMdztTAALDRAAPEI-202

description: GC6 Cohort


title: 140718_I266_FCC4RDRACXX_L6_RHUMdztTAALERAAPEI-203

description: GC6 Cohort


title: Day15_C43

description: Single Cell RNA-seq data


title: 140724_I272_FCC4NC6ACXX_L1_RHUMdztTAANBRAAPEI-204

description: GC6 Cohort


title: 140718_I266_FCC4RDRACXX_L4_RHUMdztTAAKZRAAPEI-223

description: GC6 Cohort


title: Day15_C38

description: Single Cell RNA-seq data


title: 140718_I266_FCC4RDRACXX_L4_RHUMdztTAALARAAPEI-225

description: GC6 Cohort


title: Day15_C33

description: Single Cell RNA-seq data


title: 140718_I266_FCC4RDRACXX_L4_RHUMdztTAALBRAAPEI-227

description: GC6 Cohort


title: 140718_I266_FCC4RDRACXX_L3_RHUMdztTAAKWRAAPEI-220

description: GC6 Cohort


title: Day15_C32

description: Single Cell RNA-seq data


title: Day15_C37

description: Single Cell RNA-seq data


title: Day15_C31

description: Single Cell RNA-seq data


title: 140718_I266_FCC4RDRACXX_L3_RHUMdztTAAKXRAAPEI-221

description: GC6 Cohort


title: Day15_C27

description: Single Cell RNA-seq data


title: Day15_C25

description: Single Cell RNA-seq data


title: Day15_C21

description: Single Cell RNA-seq data


title: 140718_I266_FCC4RDRACXX_L2_RHUMdztTAAKTRAAPEI-216

description: GC6 Cohort


title: 140718_I266_FCC4RDRACXX_L2_RHUMdztTAAKVRAAPEI-219

description: GC6 Cohort


title: 140718_I266_FCC4RDRACXX_L2_RHUMdztTAAKURAAPEI-218

description: GC6 Cohort


title: Day15_C20

description: Single Cell RNA-seq data


title: Day15_C19

description: Single Cell RNA-seq data


title: 140718_I266_FCC4RDRACXX_L8_RHUMdztTAALIRAAPEI-207

description: GC6 Cohort


title: Day15_C14

description: Single Cell RNA-seq data


title: 140718_I266_FCC4RDRACXX_L1_RHUMdztTAAKSRAAPEI-215

description: GC6 Cohort


title: MITF_OC_ChIP-seq

city: Charleston

first: Michael

middle: C

last: Ostrowski

state: SC

address: 86 Jonathan Lucas street

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8
ChIPseq reads were aligned to mm9 using bowtie2 software
Peaks were called using peak caller algorithm in HOMER suite at default filters
Peaks were annotated using annotatePeaks algorithm and using mouse genome mm9 using Homer suite
Visualization files in bedgraph.gz to mm9 reference genome were prepared within Homer suite
Genome_build: mm9
Supplementary_files_format_and_content: Annotated peaks in txt.gz format, bedgraphs in bedgraph.gz format

molecule: genomic DNA

organism: Mus musculus

source_name: myeloid precursors treated with RANKL for 72h

growth_protocol: Flushed bone marrow cells from 4-6 week old mice were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Gibco, Life Technologies, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS, Sigma-Aldrich), 50 U/ml penicillin/streptomycin (P/S, Gibco) and 50 ng/ml recombinant human CSF1 (Peprotech, Rocky Hill, NJ) on plastic plates for 3 days in 5% CO2 water jacketed incubator.

extract_protocol:
Sonicated soluble chromatin was immunoprecipitated with 5 micrograms of PU.1 or MITF antibodies and pulled down by protein G sepharose beads equillibriated with yeast tRNA and BSA.
Library construction was perfomed by modified Illumina ChIPseq library preparation kit.

treatment_protocol: Mechanically flushed enriched myeloid precursors plated on 10cm plates at a density of 1.5X10^5cells in the growth medium and treated 100 ng/ml RANKL for 36 and 72 hrs.

tag: strain

value: 4-6 weeks

value: Bone marrow myeloid cells

tag: treated with

value: CSF1 and RANKL for 72h

tag: chip antibody

value: MITF antibody; In lab described in PMID:17403683


title: Day15_C09

description: Single Cell RNA-seq data


title: MITF_cOC_ChIP-seq

source_name: myeloid precursors treated with RANKL for 36h

value: CSF1 and RANKL for 36h


title: MITF_MP_ChIP-seq

source_name: Myeloid precursors

value: CSF1 only


title: Day15_C07

description: Single Cell RNA-seq data


title: Day15_C08

description: Single Cell RNA-seq data


title: Day15_C02

description: Single Cell RNA-seq data


title: IgG_M_ChIP-seq

value: Non specific IgG (control) PreImmune Affinity purified.


title: 140718_I266_FCC4RDRACXX_L1_RHUMdztTAAKQRAAPEI-213

description: GC6 Cohort

value: blood

value: MRC


title: PU_cOC_ChIP-seq

value: PU.1 antibody; In lab described in PMID:17403683


title: 140718_I266_FCC4RDRACXX_L3_RHUMdztTAAKYRAAPEI-222

description: GC6 Cohort

value: F


title: Day11_C75

description: Single Cell RNA-seq data

value: TRA-1-60(+) cells on day 11


title: PU_MP_ChIP-seq


title: Day15_C01

description: Single Cell RNA-seq data


title: Day11_C67

description: Single Cell RNA-seq data


title: mutant3

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

data_processing:
Basecalls with RTA v2 (Illumina)
Reaper version 13-100 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses.
Mapping: alignment versus the Ensembl Zebrafish genome version DanRer10 (GRCz10.87) using STAR 2.4.0a with the parameter “--outFilterMismatchNoverLmax 0.1"
The number of reads aligning to genes was counted with featureCounts 1.4.5-p1 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data (release 06.06.2014) based on Ensembl gene identifiers.
Genome_build: DanRer10
Supplementary_files_format_and_content: library size normalized counts per sample

organism: Danio rerio

source_name: larval hearts

extract_protocol:
RNA extraction was performed with Qiagen miRNeasy kit
Clontech Pico Input Mammalian (Takara Clontech). Briefly, 6.5ng of total RNA was used as input for Pico Input Mammalian (Takara Clontech). Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry, resulting in minimum of 30M reads per library with 1x75bp single end setup.

tag: developmental stage

value: whole hearts


title: mutant1


title: mutant2


title: WT3


title: WT2


title: Day11_C63

description: Single Cell RNA-seq data


title: Day11_C56

description: Single Cell RNA-seq data


title: Day15_C15

description: Single Cell RNA-seq data


title: Day11_C57

description: Single Cell RNA-seq data


title: Day11_C55

description: Single Cell RNA-seq data


title: Day15_C13

description: Single Cell RNA-seq data


title: Day11_C61

description: Single Cell RNA-seq data


title: WT1


title: Day11_C44

description: Single Cell RNA-seq data


title: Day11_C51

description: Single Cell RNA-seq data


title: PU_OC_ChIP-seq


title: Day11_C39

description: Single Cell RNA-seq data


title: Day11_C26

description: Single Cell RNA-seq data


title: Day11_C37

description: Single Cell RNA-seq data


title: Day11_C33

description: Single Cell RNA-seq data


title: Day11_C25

description: Single Cell RNA-seq data


title: Day11_C32

description: Single Cell RNA-seq data


title: Day11_C21

description: Single Cell RNA-seq data


title: Day11_C20

description: Single Cell RNA-seq data


title: Day11_C15

description: Single Cell RNA-seq data


title: Day11_C50

description: Single Cell RNA-seq data


title: Day11_C13

description: Single Cell RNA-seq data


title: Day11_C19

description: Single Cell RNA-seq data


title: Day11_C08

description: Single Cell RNA-seq data


title: Day11_C09

description: Single Cell RNA-seq data


title: Day7_C67

description: Single Cell RNA-seq data

value: TRA-1-60(+) cells on day 7


title: Day7_C75

description: Single Cell RNA-seq data


title: Day7_C45

description: Single Cell RNA-seq data


title: Day7_C61

description: Single Cell RNA-seq data


title: Day7_C55

description: Single Cell RNA-seq data


title: Day7_C43

description: Single Cell RNA-seq data


title: Day7_C25

description: Single Cell RNA-seq data


title: Day7_C31

description: Single Cell RNA-seq data


title: Day7_C21

description: Single Cell RNA-seq data


title: Day7_C32

description: Single Cell RNA-seq data


title: Day7_C26

description: Single Cell RNA-seq data


title: Day7_C14

description: Single Cell RNA-seq data


title: Day7_C19

description: Single Cell RNA-seq data


title: Day7_C15

description: Single Cell RNA-seq data


title: Day7_C13

description: Single Cell RNA-seq data


title: Day7_C09

description: Single Cell RNA-seq data


title: Day7_C03

description: Single Cell RNA-seq data


title: Day11_C03

description: Single Cell RNA-seq data


title: Day7_C01

description: Single Cell RNA-seq data


title: Day3_C92

description: Single Cell RNA-seq data

value: SOX2-EGFP (+) cells on day 3


title: Day3_C85

description: Single Cell RNA-seq data


title: Day7_C02

description: Single Cell RNA-seq data


title: Day3_C80

description: Single Cell RNA-seq data


title: Day3_C75

description: Single Cell RNA-seq data


title: Day3_C69

description: Single Cell RNA-seq data


title: Day7_C37

description: Single Cell RNA-seq data


title: Day3_C63

description: Single Cell RNA-seq data


title: Day3_C62

description: Single Cell RNA-seq data


title: Day7_C08

description: Single Cell RNA-seq data


title: Day3_C61

description: Single Cell RNA-seq data


title: Day7_C20

description: Single Cell RNA-seq data


title: Day3_C57

description: Single Cell RNA-seq data


title: Day3_C56

description: Single Cell RNA-seq data


title: Day3_C55

description: Single Cell RNA-seq data


title: Day3_C37

description: Single Cell RNA-seq data


title: Day3_C51

description: Single Cell RNA-seq data


title: Day7_C49

description: Single Cell RNA-seq data


title: Day7_C07

description: Single Cell RNA-seq data


title: Day3_C25

description: Single Cell RNA-seq data


title: Day3_C14

description: Single Cell RNA-seq data


title: Day3_C18

description: Single Cell RNA-seq data


title: Day3_C11

description: Single Cell RNA-seq data


title: Day3_C08

description: Single Cell RNA-seq data


title: Day3_C13

description: Single Cell RNA-seq data


title: Day3_C16

description: Single Cell RNA-seq data


title: Day3_C07

description: Single Cell RNA-seq data


title: Day3_C06

description: Single Cell RNA-seq data


title: Hdac2lox/lox 4oht 1

city: Manchester

first: Roshana

middle: S

last: Thambyrajah

address: Wilmslow Road

department: Stem Cell Biology

country: United Kingdom

institute: CRUK Manchester

data_processing:
Basecall files generated from HiSeq sequencing run were converted to FASTQ format with Illumina’s bcl2fastq (v2.17.1.14). Lane-wise alignment was performed by bowtie2 (version 2.2.1) to mouse reference genome mm10 with default parameters. Generated SAM files from bowtie2 alignment were converted to BAM files by samtools v0.1.19. Parameters for samtools SAM to BAM conversion: -q 10 -f 2 -F 268. Resulting lane-wise BAM files from the same sequence library was merged into one BAM file used for downstream analysis. Read counts from BAM files were extracted under the R environment (R v3.1.0) with the package Rsubread version 1.13.13. Only genes with at least 1 count per million in at least two samples were retained for differential expression analysis. Count table was loaded to edgeR v3.8.5 and differentially expressed genes between groups were identified by exact test function.
Genome_build: mm10
Supplementary_files_format_and_content: rawReadCounts

source_name: haemogenic endothelium

growth_protocol: ES cell lines grown and differentiated as in Sroczynska et al, 2009

extract_protocol:
RNA was extracted using the Qiagen RNAeasy micro kit.
200ng of total RNA was processed with SureSelect Strand-Specific RNA Library Prep for Illumina (Catalog Code: G9691A, Agilent) with 15 amplification cycles.

value: haemogenic endothelium

tag: genotype/variation

tag: agent


title: Hdac2lox/lox ETOH 2

value: ETOH


title: Day3_C15

description: Single Cell RNA-seq data


title: Hdac2lox/lox ETOH 1


title: Hdac1lox/lox 4oht 2


title: Hdac2lox/lox 4oht 2


title: Day0_C95

description: Single Cell RNA-seq data

source_name: Human dermal fibroblasts

value: Human dermal fibroblasts


title: Day0_C73

description: Single Cell RNA-seq data


title: Day0_C72

description: Single Cell RNA-seq data


title: Day0_C71

description: Single Cell RNA-seq data


title: Hdac1lox/lox ETOH 2


title: Hdac1lox/lox ETOH 1


title: Day0_C60

description: Single Cell RNA-seq data


title: Hdac1lox/lox 4oht 1


title: Day0_C59

description: Single Cell RNA-seq data


title: Day0_C54

description: Single Cell RNA-seq data


title: input DNA

city: Chicago

first: Benayahu

last: Elbaz

state: IL

address: Department of Neurology 5841 S. Maryland Ave

department: Neurology

institute: University of chicago

description: Input DNA

data_processing:
75-nt sequence reads generated by Illumina sequencing (NextSeq 500) were trimmed for quality>20 and adapters removed using Trimgalorte.
Reads were aligned to the mouse genome (mm10) using the BWA algorithm (default settings).
Peak calling was done with HOMER v4.8.3 (Heinz,  Mol Cell 2010). For this purpose bam files were converted to Tag directories using makeTagDirectory with default parameters and "-tbp 1". (http://homer.ucsd.edu/homer/ngs/tagDir.html).
Peak calling with Homer: findPeaks with default parameters, "-style factor" and control file "-i" once input and once KO.
the peak calling output of Homer was converted to .bed file by pos2bed.pl default parameters
Final peak calls were filtered by intersecting peaks called against ko control with peaks called against input control. Only regiones that were called with both controles were accepted (Intersect the intervals of two datasets (Galaxy Version 1.0.0) with Overlapping Intervals parameter) of peak calling output converted to Bed file with input as conrol file and KO as control file.
Genome_build: mm10
Supplementary_files_format_and_content: bed files containing list of called peaks location for OPC and OLG, with mm10 coordinates

source_name: pooled wt and Zfp191 null oligodendrocyte and oligodendrocyte progenitor cells

growth_protocol: Mouse oligodendrocyte progenitor cells were isolated from C56BL/6J mice and from Zfp191-null mice (Howng et al., 2010) by immunopanning as described by (Emery and Dugas, 2013). To differentiate OPC into oligodendrocytes, cells were  cultured for 5 days in differentiative conditions (−PDGF, +40 ng/ml triiodothyronine; Sigma).

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation.  For ChIP (done by ActiveMotif), the equivalent of 22 microgram DNA was precleared with protein A agarose beads (Invitrogen). and incubated with 20 ul of an antibody against ZNF24 (Sigma, HPA024062, Lot. A71676, 0.16 ug/ul). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and bound fraction was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs using  standard Illumina PE adaptors (Bentley et al., Nature 2008) by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina NextSeq 500 (75 nt reads, single end). Reads were aligned to the mouse genome (mm10).

value: postnatal day (P) 7,

tag: genotype

value: pooled wildtype and Zfp191- null

value: brain

value: pooled OPC and OLG

tag: antibody

value: none (input)


title: Day0_C53

description: Single Cell RNA-seq data


title: oligodendrocyte progenitor cells derived from Zfp191- null mouse

description:
Zfp191 null OPC
processed data file: ZFP191(Zfp24)_peaks_OPC_mm10.bed

source_name: isolated oligodendrocyte progenitor cells

value: Zfp191- null

value: oligodendrocyte progenitor

value: anti-ZFP191 (sigma) [Cat # HPA024062)]


title: Day0_C45

description: Single Cell RNA-seq data


title: oligodendrocyte progenitor cells derived from wt mouse

description:
wt OPC
processed data file: ZFP191(Zfp24)_peaks_OPC_mm10.bed

value: wildtype


title: Day0_C47

description: Single Cell RNA-seq data


title: oligodendrocyte derived from wt

description:
wt OLG
processed data file: ZFP191(Zfp24)_peaks_OLG_mm10.bed

source_name: Differentiated oligodendrocyte

value: oligodendrocyte


title: Day3_C03

description: Single Cell RNA-seq data


title: Day0_C30

description: Single Cell RNA-seq data


title: Day0_C20

description: Single Cell RNA-seq data


title: Ovariectomized Female Dexamethasone 3

city: Research Triangle Park

first: Matthew

middle: Allan

last: Quinn

state: North Carolina

address: 111 T.W. Alexander Dr.

department: Signal Transduction Laboratory

institute: National Institute of Environmental Health Sciences

description:
FemaleDex_Ecto3
Processed data file: Female_Sex_Dex_htseq_count_DESeq_exp_log2_normalized.txt

data_processing:
Raw reads were first cleaned for adapter sequences using Trim Galore with default parameters.
RNA-SEQ reads (~45M per sample) were aligned to the UCSC mm9 reference genome using TopHat2.
The quantification results from htseq-count were then analyzed with the Bioconductor package DESeq2, which fits a negative binomial distribution to estimate technical and biological variability.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Female_Sex_Dex_htseq_count_DESeq_exp_log2_normalized.txt: Tab-delimited text file; log2 transformed and normalized abundance measurements by DESeq2.

source_name: Liver, ovariectomized, dexamethasone

extract_protocol:
Livers were collected after treatment and RNA extracted with Trizol and purified with Qiagen RNeasy Kit.
Libraries were constructed with the use of the Illumina TruSeq library construction kit V2 (Cat #RS-122-2001) according to manufacturer's protocol. Libraries were pooled and sequenced on the Illumina NextSeq500 sequencer.

treatment_protocol: Mice were treated with either PBS or Dexamethasone (1mg/kg) for 6 hours.

tag: strain/background

value: wild-type

value: Female

tag: gonadal status

value: ovariectomized

value: liver

tag: treatment

value: Dexamethasone

tag: timepoint

value: 6 hour post treatment


title: Ovariectomized Female Dexamethasone 2

description:
FemaleDex_Ecto2
Processed data file: Female_Sex_Dex_htseq_count_DESeq_exp_log2_normalized.txt

tag: tissue


title: Day0_C23

description: Single Cell RNA-seq data

value: Human dermal fibroblasts


title: Ovariectomized Female Vehicle 3

description:
FemaleVeh_Ecto3
Processed data file: Female_Sex_Dex_htseq_count_DESeq_exp_log2_normalized.txt

source_name: Liver, ovariectomized, vehicle

value: PBS


title: Day0_C19

description: Single Cell RNA-seq data


title: Day0_C32

description: Single Cell RNA-seq data


title: Ovariectomized Female Vehicle 2

description:
FemaleVeh_Ecto2
Processed data file: Female_Sex_Dex_htseq_count_DESeq_exp_log2_normalized.txt


title: Day0_C15

description: Single Cell RNA-seq data


title: Ovariectomized Female Vehicle 1

description:
FemaleVeh_Ecto1
Processed data file: Female_Sex_Dex_htseq_count_DESeq_exp_log2_normalized.txt


title: Day0_C14

description: Single Cell RNA-seq data


title: Day0_C12

description: Single Cell RNA-seq data


title: Intact Female Dexamethasone 2

description:
FemaleDex_intact2
Processed data file: Female_Sex_Dex_htseq_count_DESeq_exp_log2_normalized.txt

source_name: Liver, normal, dexamethasone

value: intact


title: Intact Female Dexamethasone 3

description:
FemaleDex_intact3
Processed data file: Female_Sex_Dex_htseq_count_DESeq_exp_log2_normalized.txt


title: Day0_C09

description: Single Cell RNA-seq data


title: oligodendrocyte derived from Zfp191 null

description:
Zfp191 null OLG
processed data file: ZFP191(Zfp24)_peaks_OLG_mm10.bed

value: postnatal day (P) 7,

value: brain


title: Intact Female Dexamethasone 1

description:
FemaleDex_intact1
Processed data file: Female_Sex_Dex_htseq_count_DESeq_exp_log2_normalized.txt


title: Day0_C08

description: Single Cell RNA-seq data


title: Intact Female Vehicle 3

description:
FemaleVeh_intact3
Processed data file: Female_Sex_Dex_htseq_count_DESeq_exp_log2_normalized.txt

source_name: Liver, normal, vehicle


title: U87-ERβ5-2

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina bcl2fastq software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: U87 MG glioblastoma cell line

growth_protocol: U87 cells were cultured in DMEM supplemented with 10% FBS

extract_protocol:
Total RNA was isolated from U87, U87 ERβ-KO, U87 ERβ-KO cells expressing ERβ1 and ERβ5 isoforms using RNeEasy mini kit using manufacturer’s protocol (Qiagen, Valencia, CA).
Total RNA samples about 1-2 µg were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end (SE) sequencing protocol.

treatment_protocol: Total RNA was isolated from U87 control, U87-ERβ-KO, U87-ERβ1 and U87-ERβ5 cells and subjected to RNAseq analysis

tag: cell line

value: U87 MG glioblastoma

tag: genotype/treatment

value: ERbeta5 isoform was reintroduced into U87-ERbeta-KO cells


title: Day0_C07

description: Single Cell RNA-seq data


title: Intact Female Vehicle 2

description:
FemaleVeh_intact2
Processed data file: Female_Sex_Dex_htseq_count_DESeq_exp_log2_normalized.txt

tag: gender


title: Day0_C06

description: Single Cell RNA-seq data

tag: cell type


title: Ovariectomized Female Dexamethasone 1

description:
FemaleDex_Ecto1
Processed data file: Female_Sex_Dex_htseq_count_DESeq_exp_log2_normalized.txt


title: Intact Female Vehicle 1

description:
FemaleVeh_intact1
Processed data file: Female_Sex_Dex_htseq_count_DESeq_exp_log2_normalized.txt


title: U87-ERβ1-2

value: ERbeta1 isoform was reintroduced into U87-ERbeta-KO cells


title: Day0_C03

description: Single Cell RNA-seq data


title: U87-ERβ1-1


title: U87-ERβ-KO-2

value: ERbeta was knocked out in U87 cells using CRISPR/Cas9 system


title: TeraFib_2_S4

data_processing:
Basecalls performed using BCL2FASTQ Conversion Software 1.8.4 in the CASAVA 1.8.2 pipeline.
Sequence reads were aligned to the human genome (hg19) using TopHat2 software.
The sequenced short reads were mapped to the human reference genome hg19 using TopHat 2.0.14 and Bowtie 2.2.5.
RPKM counts for each gene were obtained using the RPKMforgenes software.
Genome_build: hg19
Supplementary_files_format_and_content: Calculation of gene expression value and normalization were performed by RPKMforgenes (10th, Dec, 2012). The processed data file contains Gene name, Refseq ID, RPKM, and Raw counts columns (from left to right), and the expression level was represented by RPKM.

source_name: Teratoma-derived fibroblasts

extract_protocol:
The cells were lysed with Trizol reagent (Life Technologies) and total RNA was purified using a miReasy mini kit (QIAGEN).
100 ng of DNase-treated RNA was used to prepare individually indexed and strand-specific RNA-seq libraries using a TruSeq Stranded Total RNA sample prep kit (Illumina). Briefly, ribosomal RNA was depleted using a Ribo-Zero Gold kit (AR Brown), followed by RNA fragmentation, cDNA synthesis, end repair, A-base addition, and ligation with Illumina-indexed adaptors. Cluster generation was performed using a TruSeq PE cluster Kit v3 on an Illumina cBot instrument. Six indexed libraries were loaded into each lane of flow cells. Sequencing was performed on a Hiseq2000 in multiplexed paired-read run mode with a total of 150 cycles.

value: Teratoma-derived fibroblasts


title: TeraFib_1_S4


title: 2i_veh_3

city: New York

first: Bryan

last: King

state: NY

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

data_processing:
bcl2fastq v2.17 was used for de-mutiplexing
Unique reads were aligned to mm9 using Tophat with default parameters
Gene features were counted using htseq-count
Normalization and differential expression was determined using the 'edgeR' package in Bioconductor
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited TXT file of normalized gene counts per million

molecule: polyA RNA

source_name: 2i_veh, Murine embryonic stem cells V6.5 1A

growth_protocol: ES cells were grown for 5 passages in media containing either serum and leukemia inhibitor factor (LIF) or serum/LIF supplemented with MEK and GSK3b inhibitors ('2i')

extract_protocol:
Total RNA was extracted with Trizol
Libraries were prepared using the TruSeq mRNA Sample Preparation Kit v2 (Illumina, San Diego, CA) in accordance with the manufacturer's instructions.
Adapter ligated DNA was PCR amplified with Illumina primers for 13 cycles, DNA fragments were sequenced using single-end sequencing technology on Illumina NextSeq 500 platform

treatment_protocol: Cells were treated for 72h with either 500nM JQ1 or vehicle control

value: ESC line V6.5 1A

tag: media

value: vehicle


title: 2i_JQ1_3

source_name: 2i_JQ1, Murine embryonic stem cells V6.5 1A


title: 2i_JQ1_1


title: TeraFib_3_S5


title: U87-control-2

value: U87 cells control


title: 2i_veh_1


title: HDF_3_S2


title: HDF_2_S1


title: SL_JQ1_3

source_name: SL_JQ1, Murine embryonic stem cells V6.5 1A

value: serum/LIF


title: HDF_1_S1


title: SL_JQ1_1


title: U87-ERβ5-1


title: SL_veh_2

source_name: SL_veh, Murine embryonic stem cells V6.5 1A


title: SL_veh_1


title: Day0_C01

description: Single Cell RNA-seq data


title: U87-control-1


title: SL_veh_3


title: non-selected strain PM diet liver biological rep10 [T23-8L]

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

data_processing:
Base-calling and demultiplexing were performed in the sequencer and/or using the native Illumina software CASAVA version 1.8.2.
Raw reads were processed for quality control using the Trim Galore! software version 0.4.0. This software was used to trim low-quality ends from reads in addition to Illumina adapter removal. Quality trimming was then specified at phred33.
Sequences after QC were filtered for potential contaminating ribosomal RNAs using the Bowtie2 software version 2.2.5. All Oncorhynchus species rRNAs available in GenBank were used to align against, where unaligned reads were output for further usage. The default Bowtie2 parameters were used.
Bowtie2 version 2.2.5 was used for alignment of reads to the rainbow trout transcriptome using the alignment parameters as recommended by eXpress software version 1.5.1.
Alignment files were piped into the eXpress version 1.5.1 software using the default parameters, but including the strand information, to generate bias-parameters.
Trinity version 2.1.1 was used to cluster reads into transcripts using the default parameters but including strand information.
Annocript pipeline version 1.1.3 was used to generate putative lncRNAs, using the default parameters.
Bowtie2 version 2.2.5 was used for alignment of reads to the lncRNAs using the alignment parameters as recommended by eXpress software version 1.5.1.
Alignment files were piped into the eXpress version 1.5.1 software using the default parameters, but including the strand information and bias-parameters, to generate read-counts.
Effective read counts output from the eXpress version 1.5.1 software were used to calculate fold-change using the DESeq2 package in R-Bioconductor Release 3.2.
Genome_build: The rainbow trout transcriptome sequences published from Salem et.al., PLoS One, 2015.
Supplementary_files_format_and_content: From each associated raw file, one dataset includes a tab-delimited text file of effective read counts, rounded to the nearest whole number. The other dataset includes a FASTA file of long non-coding RNAs identified.

organism: Oncorhynchus mykiss

source_name: section from whole liver

extract_protocol:
Tissue samples were excised, flash-frozen in liquid nitrogen and stored at -80°C until usage. Samples were homogenized using a bead-beater with TRIzol reagent per the manufacturer's recommendation for total RNA isolation.
Total RNA was standardized to 1 µg each sample. DNA was removed using Amplification-grade DNase I from Invitrogen. Ribosomal RNAs were reduced using the Ribo-Zero Gold rRNA Removal Kit from Illumina. Sequencing libraries were then prepared using the ScriptSeq v2 RNA-Seq Library Preparation Kit from Illumina. Barcodes used were Illumina TruSeq indexes 1-12.

tag: strain

value: House Creek

value: liver

tag: diet

value: PM


title: non-selected strain PM diet liver biological rep8 [T23-6L]


title: 2i_JQ1_2


title: non-selected strain PM diet liver biological rep9 [T23-7L]


title: non-selected strain PM diet liver biological rep6 [T23-4L]


title: U87-ERβ-KO-1


title: 2i_veh_2


title: non-selected strain PM diet liver biological rep5 [T17-8L]


title: non-selected strain PM diet liver biological rep7 [T23-5L]


title: selected strain PM diet liver biological rep9 [T11-7L]

value: ARS-KO


title: non-selected strain PM diet liver biological rep1 [T17-4L]


title: selected strain PM diet liver biological rep8 [T11-6L]


title: SL_JQ1_2


title: non-selected strain PM diet liver biological rep2 [T17-5L]


title: selected strain PM diet liver biological rep7 [T11-5L]


title: selected strain PM diet liver biological rep10 [T11-8L]


title: selected strain PM diet liver biological rep5 [T9-8L]


title: selected strain PM diet liver biological rep3 [T9-6L]


title: selected strain PM diet liver biological rep4 [T9-7L]


title: selected strain PM diet liver biological rep6 [T11-4L]


title: 59L3 [miRNA-seq]

status: Public on Apr 09 2018

city: London

first: Amy

middle: Frances

last: Danson

state: Greater London

address: 2 Newark St

department: Centre for Genomics and Child Health

institute: The Blizard Institute

data_processing:
alignment and annotation, SPORTS 1.0 pipeline (https://github.com/junchaoshi/sports1.0.git)
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Tab delimited text file of read counts

extract_protocol:
For RNA extraction, ¾ of the extracted sperm was incubated at 60 °C for 15 mins with slow rotation in 33.3 µl sperm lysis buffer (6.4 M Guanidine HCl, 5% Tween 20, 5% Triton, 120 mM EDTA, 120 mM Tris pH 8.0) with 3.3 µl Proteinase K (19 mg/ml) and 3.3 µl 0.1 M DTT. After the incubation, one volume (100 µl) of ultra-pure water was added. 700 µl Qiazol Lysis reagent (QIAGEN, Cat. 79306) was added and samples were vortexed for 5 mins. 140 µl chloroform was added and samples were shaken vigorously for 30 seconds before 3 mins incubation at RT. Samples were centrifuged at 12,000 x g at 4 °C for 15 mins then the upper aqueous phase was transferred to a new reaction tube. One volume of 70% EtOH was added and mixed thoroughly. Samples were transferred to a RNeasy mini spin column and the protocol from the miRNeasy Mini Kit (Qiagen, Cat. 217004) was then followed, including the separation of the small RNA and large RNA fractions using an RNA MinElute spin column (Qiagen, Cat. 74204). The small RNA fraction was eluted in 14 µl RNase-free water and quantified using the microRNA kit from Qubit® (Cat. Q32880).
6 µl of the small RNA fraction was used for small RNA library preparation using the NEBNext® Small RNA library prep set for Illumina (Cat. E7330S) as per the protocol. Each sample was uniquely barcoded using one of the NEBNext® Index Primers for Illumina (Cat. E7300S, E7580S, E7710S, E7730S). For PCR amplification, 15 cycles were used. Libraries were purified using the QIAQuick PCR purification kit (Qiagen, Cat. 28104) and DNA was eluted into 32 µl nuclease-free water. An aliquot of each library was diluted and 1 µl was run on an Agilent 2100 Bioanalyzer using the Agilent High Sensitivity DNA kit (Cat. 5067-4626) to assess the size distribution of the library. The libraries were pooled using equal volumes and size selected for between 140-200 bp (corresponding to an insert size of 13-73 bp) using a BluePippin machine (Sage Science) with 3% agarose cassettes (Sage Science, Cat. BDF3010).

treatment_protocol: After one week of acclimatisation in the mouse facility on standard chow (control diet, 20% protein), matings were set up by transferring one, or sometimes two, females into a male’s cage in the late afternoon. On the discovery of a vaginal plug the next morning (designated 0.5 days post coitum), pregnant females were singly housed and given ad libitum access to either a protein restricted diet (8% protein) or maintained on the control diet. Breeding males were housed individually for the duration of the breeding period. Females were maintained on the respective diet until offspring were weaned. Whole litters were weighed at 7 and 14 days. Upon weaning at 21 days, male offspring from each litter were put on either a control (CT) or protein restricted (PR) diet until death. Only litters with 5-10 pups were included. Male offspring were housed in cages of 3-5 from weaning and weighed individually every week from weaning until they were killed at 11-13 weeks of age.

tag: diet group

value: PRPR

value: sperm


title: 49K2 [BisPCRseq]

description:
processed data file:
BisPCRSeq_MiSeq_counts2.txt

data_processing:
alignment to the adjusted consensus rDNA reference using Bismark (v0.7.12) and Bowtie2 (v2.1.0)
SNP and methylation state calling using RSamtools
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited txt files containing the number of reads that were found to be methylated at position -133 and to have an A at position -104 (ma), were unmethylated and have an A at -104 (ua), methylated and have a C at -104 (mc) and were unmethylated and have a C at position -104 (uc) in each sample

extract_protocol:
For DNA extraction, 1/4 of the extracted sperm was incubated overnight in 600 µl PK buffer (10 mM Tris-HCl, 100 mM NaCl, 25 mM EDTA, 1% SDS) with 2 µl Proteinase K enzyme (19 mg/ml) and 0.1M DTT at 55 °C with slow rotation. 750 µl phenol was added to the samples and agitated for several minutes before spinning at 17,000 x g for 5 mins at 4 °C. The upper aqueous phase was transferred to a new tube and the process repeated with phenol:chloroform, then chloroform alone. After the final spin, 5 µl Rnase was added and samples were incubated at 37 °C for 60 mins. 0.1 volumes of 3 M sodium acetate (pH 5.2) and 2.5 volumes of 100% EtOH were added and samples incubated at -20 °C for 1 hour. Samples were spun at 17,000 x g for 10 mins at 4 °C and the pellet washed with 75% EtOH. Finally, the pellet was air-dried at 37 °C, resuspended in 200 µl TE buffer and incubated at 50 °C for 3 hours before storage at 4 °C.
DNA from sperm was diluted to a concentration of 11 ng/µl and 45 µl of each sample was sent for sequencing to the Genome Centre Facility at Charterhouse Square, QMUL. Bis-PCR-Seq was performed using the 48.48 layout on the Fluidigm® C1 system (Fluidigm®, USA), coupled with Illumina MiSeq sequencing using version2 chemistry (150 bp, paired-end).

value: CTCT


title: selected strain PM diet liver biological rep2 [T9-5L]


title: 51O3 [miRNA-seq]


title: 59L1 [miRNA-seq]

value: PRCT


title: non-selected strain PM diet liver biological rep4 [T17-7L]


title: 46I3 [miRNA-seq]


title: 46I1 [miRNA-seq]


title: 36K3 [miRNA-seq]


title: 51O1 [miRNA-seq]


title: 31A3 [miRNA-seq]


title: 40H3 [miRNA-seq]


title: 31A6 [miRNA-seq]


title: 39F6 [miRNA-seq]


title: 39F5 [miRNA-seq]


title: 23F6 [miRNA-seq]


title: 40H1 [miRNA-seq]


title: 23F4 [miRNA-seq]


title: 14A4 [miRNA-seq]


title: selected strain PM diet liver biological rep1 [T9-4L]


title: 14A5 [miRNA-seq]


title: 08G3 [miRNA-seq]


title: 08G5 [miRNA-seq]


title: 57P1 [miRNA-seq]

value: CTPR


title: 57P3 [miRNA-seq]


title: 49K1 [miRNA-seq]


title: 49K3 [miRNA-seq]


title: 47I1 [miRNA-seq]


title: 56I1 [miRNA-seq]


title: 53M1 [miRNA-seq]


title: 53M4 [miRNA-seq]


title: 45L1 [miRNA-seq]


title: 45L3 [miRNA-seq]


title: non-selected strain PM diet liver biological rep3 [T17-6L]


title: 35F1 [miRNA-seq]


title: 09H7 [miRNA-seq]


title: 35F2 [miRNA-seq]


title: 29L6 [miRNA-seq]


title: 02A8 [miRNA-seq]


title: 07C3 [miRNA-seq]


title: 02A6 [miRNA-seq]


title: 09H5 [miRNA-seq]


title: P6_JRGC_A

city: Singapore

first: Jinyue

last: Liu

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

description: single-end RNAseq

data_processing:
Reads with poor quality were trimmed with Trimmomatic v0.32
Trimmed reads were aligned to mm9 using tophat v2.0.10
Aligned reads were counted using Htseq v0.6.1
Genome_build: mm9
Supplementary_files_format_and_content: raw counts

source_name: Postnatal day 6 mus musculus retina

extract_protocol:
J-RGCs were purified by flow cytometry and collected in cell lysis buffer for RNA extraction and purification (PicoPure RNA isolation kit, Invitrogen). Extracted RNA was concentrated (RNA Clean & ConcentratorTM-5 kit, Zymo). cDNA libraries were prepared from the RNA using the Ovation Ultralow system V2 1-16 (Nugen).
cDNA libraries were prepared for RNAseq using ultralow system V2 kit (Nugen)

value: retinal ganglion cell type J-RGC


title: 59L3 [BisPCRseq]

description:
processed data file:
BisPCRSeq_MiSeq_counts.txt


title: 51O3 [BisPCRseq]


title: 51O1 [BisPCRseq]


title: 59L2 [BisPCRseq]


title: P6_JRGC_B

description: single-end RNAseq


title: ES_Mtf2GT_H3K4me3_Rep2

city: Nijmegen

first: Gert

middle: Jan

last: Veenstra

state: Not US or Canada

address: Geert Grooteplein 28

department: Molecular Developmental Biology

country: Netherlands

institute: Radboud University

description:
ChIP seq for H3K4me3 in E14 mESC
ES_Mtf2GT_H3K4me3_MAnorm_unbiased.bed

data_processing:
Base-calling was performed by the Illumina CASAVA software.
Reads were aligned to the mouse genome (mm10) using bwa 0.7.10-r789 with default settings.
Peaks were called with macs2-2.7 using the --no-model and manual shift provided with the –extsize parameter. The extent of shifting was calculated with spp R library (https://github.com/hms-dbmi/spp). A q value threshold of 0.001 was applied in all cases and either the --call-summits (Mtf2 and Ezh2) or the --broad (H3K27me3 and H3K4me3) parameters was used.
Reproducible peaks among ChIPseq replicates were identified using MAnorm.
Coverage files in bigWig format were created using bam2bw (https://bitbucket.org/simonvh/bam2bw/) with the -e auto and -c parameters.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Common peaks identified with Manorm in BED format.
Supplementary_files_format_and_content: Coverage files in bigWig format.

source_name: embryonic stem cells

growth_protocol: mESC were grown in serum+LIF medium as described in Marks, H. et al. (doi:10.1016/j.cell.2012.03.026).

extract_protocol:
Chromatin extraction and ChIP were performed as described in Kloet, S. L. et al. (doi:10.1038/nsmb.3248).
Five ng/sample of ChIP were prepared for sequencing with the Kapa Hyper-prep Kit (Kapa Biosystems) using NEXTflex adapters (Bio Scientific) and amplified with ten cycles of PCR. Libraries were size-selected to obtain 300bp fragments using E-gel (Invitrogen) and sequenced on an Illumina NextSeq machine to obtain 75bp reads.

value: Mtf2 GT/GT

value: Gene trapping cassette disrupting Mtf CDS

tag: antibody vendor/catalog#

value: Abicam Ab858, lot GR240214-4


title: ES_Mtf2GT_H3K4me3_Rep1


title: 47I2 [miRNA-seq]


title: 59L1 [BisPCRseq]


title: 46I4 [BisPCRseq]


title: 46I1 [BisPCRseq]


title: 57P1 [BisPCRseq]


title: 49K3 [BisPCRseq]


title: 57P2 [BisPCRseq]


title: 57P3 [BisPCRseq]


title: 46I2 [BisPCRseq]


title: 46I3 [BisPCRseq]


title: 47I2 [BisPCRseq]


title: 49K1 [BisPCRseq]


title: 47I1 [BisPCRseq]


title: 53M5 [BisPCRseq]


title: 56I1 [BisPCRseq]


title: 53M4 [BisPCRseq]


title: 53M3 [BisPCRseq]


title: 53M2 [BisPCRseq]


title: 45L2 [BisPCRseq]


title: 45L4 [BisPCRseq]


title: 51O2 [BisPCRseq]


title: 36K3 [BisPCRseq]


title: 39F6 [BisPCRseq]


title: 31A5 [BisPCRseq]


title: 39F5 [BisPCRseq]


title: 40H3 [BisPCRseq]


title: 31A3 [BisPCRseq]


title: 40H2 [BisPCRseq]


title: 31A6 [BisPCRseq]


title: 23F5 [BisPCRseq]


title: 23F6 [BisPCRseq]


title: 29L6 [BisPCRseq]


title: 29L5 [BisPCRseq]


title: 35F2 [BisPCRseq]


title: 35F1 [BisPCRseq]


title: 23F7 [BisPCRseq]


title: 45L3 [BisPCRseq]


title: 29L4 [BisPCRseq]


title: 08G6 [BisPCRseq]


title: 08G5 [BisPCRseq]


title: 53M1 [BisPCRseq]


title: 08G3 [BisPCRseq]


title: 45L1 [BisPCRseq]


title: 14A5 [BisPCRseq]


title: 14A4 [BisPCRseq]


title: 31A4 [BisPCRseq]


title: 09H6 [BisPCRseq]


title: 40H1 [BisPCRseq]


title: 02A6 [BisPCRseq]


title: 08G4 [BisPCRseq]


title: 07C6 [BisPCRseq]


title: 09H5 [BisPCRseq]


title: 07C5 [BisPCRseq]


title: 07C3 [BisPCRseq]


title: 02A8 [BisPCRseq]


title: PBMC before treatment, 3rd series

city: Kuopio

first: Carsten

last: Carlberg

address: Yliopistonranta 1D

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description:
before 2000 μg of vitamin D3
FAIRE-seq

data_processing:
Alignment to hg19 using Bowtie v1.1 Parameters -n 1 -k 1 -m 1 -l 32 -t -q best
Peak calling using Zinba v 2.02 Parameters -f 200
Genome_build: hg19
Supplementary_files_format_and_content: tdf

source_name: blood

extract_protocol:
PBMCs were isolated within one hour after blood draw from 8 ml of peripheral blood in a Vacutainer CPT Cell Preparation Tube with sodium citrate (Becton Dickinson, Franklin Lakes, NJ, USA) according to the manufacturer’s instructions. FAIRE analysis was performed according to the protocol published by Giresi et al with some modifications (crosslinking with formaldehyde, cell lysis, phenol-chloroform extraction, reverse-crosslinking, purification).
FAIRE-seq library was prepared from 10 ng ChIP DNA with the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) per manufacturer's protocol

treatment_protocol: Subject took 2000 μg of vitamin D3. Blood samples were taken directly before the dose (days 0, 28 and 56), one day (days 1, 29 and 57) and two days (days 2, 30 and 58) after.

tag: series

value: PBMC

tag: treatment protocol

value: before 2000 μg of vitamin D3


title: 02A7 [BisPCRseq]


title: 23F4 [BisPCRseq]


title: 08G7 [BisPCRseq]


title: PBMC 2 day after treatment, 3rd series

description:
two days after 2000 μg of vitamin D3
FAIRE-seq

value: 2000 μg of vitamin D3

tag: time

value: 2 days


title: PBMC 2 day after treatment, 2nd series


title: 09H7 [BisPCRseq]


title: PBMC 1 day after treatment, 1st series

description:
one day after 2000 μg of vitamin D3
FAIRE-seq

value: 1 day


title: 07C4 [BisPCRseq]


title: PBMC before treatment, 1st series

description:
before 2000 μg of vitamin D3
FAIRE-seq


title: PBMC before treatment, 2nd series

description:
before 2000 μg of vitamin D3
FAIRE-seq


title: PBMC 2 day after treatment, 1st series


title: wt replicate 3 for total sample

first: Sonali

last: Arora

address: 1100 Fairview Ave N,

institute: FHCRC

description:
wt replicate  3 total sample
WT-Tot-n3

data_processing:
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and  employed a single-end, 50 base read length (SE50) sequencing strategy.
adaptor was trimmed from raw sequencing files, RRNA was removed from sequencing data using bowtie. Files were then aligned to hg19 using TopHatv2 and counts  per gene were generated using HTSeq.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw values for each Sample.

source_name: WT, Total

extract_protocol:
RNA was extracted from cell cultures every two weeks during the exponential growth phase; RNA was isolated from 0.5-1.0×10^6 cells. Total RNA was prepared using RNeasy Mini Kit with DNase I (Qiagen). RNA concentration and quality (A260/A280) was measured using a NanoDrop 1000 Spectrophotometer (Thermo Scientific)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: stem cell cultures

tag: genotype/variation

value: WT

tag: sample type

value: total sample


title: ko replicate 3 for total sample

description:
ko replicate 3 for total sample
KO-Tot-n3

source_name: KO, Total

value: PUS7 KO


title: ko replicate 1 for total sample

description:
ko replicate 1 for total sample
KO-Tot-n1


title: PBMC 1 day after treatment, 3rd series


title: wt replicate 1 for total sample

description:
wt replicate 1 for total sample
WT-Tot-n1


title: ko replicate 3 for polysome sample

description:
ko replicate 3 for polysome sample
KO-Poly-n3

data_processing:
Library strategy: Polysome-Seq
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and  employed a single-end, 50 base read length (SE50) sequencing strategy.
adaptor was trimmed from raw sequencing files, RRNA was removed from sequencing data using bowtie. Files were then aligned to hg19 using TopHatv2 and counts  per gene were generated using HTSeq.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw values for each Sample.

source_name: KO, Poly

value: polysome sample


title: wt replicate 2 for total sample

description:
wt replicate 2 for total sample
WT-Tot-n2


title: ko replicate 2 for total sample

description:
ko replicate 2 for total sample
KO-Tot-n2


title: ko replicate 2 for polysome sample

description:
ko replicate 2 for polysome sample
KO-Poly-n2


title: ko replicate 1 for polysome sample

description:
ko replicate 1 for polysome sample
KO-Poly-n1


title: wt replicate 2 for polysome sample

description:
wt replicate 2 for polysome sample
WT-Poly-n2

source_name: WT, Poly


title: wt replicate 3 for polysome sample

description:
wt replicate  3 polysome sample
WT-Poly-n3


title: wt replicate 1 for polysome sample

description:
wt replicate 1 for polysome sample
WT-Poly-n1


title: PBMC 1 day after treatment, 2nd series


title: #125

city: Verona

first: Silvia

last: Dal Santo

address: Strada Le Grazie, 15

department: Department of Biotechnology

country: Italy

institute: University of Verona

data_processing:
base-calling ( Illumina Casava v. 1.8.2)
Illumina quality filtering (custom script)
alignment of reads to the reference genome (TopHat v. 2.0.9)
transcripts assembly and generation of normalized abundance measurements (Cufflinks v. 2.1.1)
Genome_build: Vitis vinifera PN40024 reference genome V1 (assembly 12x). Jaillon O, et al. (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449: 463-467
Supplementary_files_format_and_content: [FPKM_table.tab] normalized abundance values (tab-delimited text file)

organism: Vitis vinifera

source_name: berry pericarp

growth_protocol: Grapevine berry samples (2 cultivars) were collected from 3 geographical  areas (Italy), in 2 years at 2 different growth stages, PV (pre-veraison) and MR (mid-ripening)

extract_protocol:
Total RNA was isolated from approximately 400 mg of berry pericarps using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich), with modifications as described in Dal Santo et al. (Jove,2016).
A total of 72 non-directional cDNA libraries were prepared from 2.5 μg total RNA using the Illumina TruSeq RNA Library preparation kit (Illumina Inc., San Diego CA, USA)

tag: cultivar

value: Cabernet Sauvignon

tag: growth stage

value: Mid-ripening, MR, berries developing color, BBCH 83

tag: geographical area

value: Bolgheri

tag: year


title: #121

value: Riccione


title: #126


title: #123


title: #120

value: Montalcino


title: #118


title: #119


title: #116

value: Sangiovese


title: #115


title: #114


title: #113


title: WT Mouse 7

city: La Jolla

first: Heidi

last: Cook-Andersen

state: California

address: 2880 Torrey Pines Scenic Drive, Rm 4811

department: Department of Reproductive Medicine

institute: University of California, San Diego

description:
WT frontal cortex
WL_WT7

data_processing:
RNA-seq reads were mapped with the STAR pipeline against mm10 transcriptome hosted at TSCC.
The python script rpkmforgenes.py was used to quantify counts for each gene and scde was used to calculate differential expression.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes raw read counts for each Sample.

source_name: frontal cortex

growth_protocol: mouse were housed in a pathogen-free facility

extract_protocol:
RNA was isolated with Trizol and the ZYMO Directzol kit, and total RNA quality was assessed using Agilent TapeStation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: frontal cortex was dissected and RNA was then extracted

value: wildtype


title: WT Mouse 5

description:
WT frontal cortex
WL_WT5


title: WT Mouse 6

description:
WT frontal cortex
WL_WT6


title: #112


title: UPF3B KO Mouse 4

description:
UPF3B KO frontal cortex
WL_KO4

value: UPF3B KO


title: WT Mouse 3

description:
WT frontal cortex
WL_WT3


title: #117


title: #111


title: UPF3B KO Mouse 6

description:
UPF3B KO frontal cortex
WL_KO6


title: WT Mouse 1

description:
WT frontal cortex
WL_WT1


title: #124


title: UPF3B KO Mouse 3

description:
UPF3B KO frontal cortex
WL_KO3


title: #122


title: UPF3B KO Mouse 2

description:
UPF3B KO frontal cortex
WL_KO2


title: #109


title: #110


title: UPF3B KO Mouse 1

description:
UPF3B KO frontal cortex
WL_KO1


title: #107

value: Pre-veraison, PV, majority of berries touching, BBCH 79


title: #106


title: even3

city: Beijing

first: Xiaowei

address: 15 Datun Road, Chaoyang District

country: China

institute: Institute of Biophysics, CAS

description:
immortalized line of human T lymphocyte cells
merge3_peaks.corr.txt

data_processing:
Library strategy: ChIRP-Seq
ChIRP-seq data quality evaluation was performed using FastQC. Version 0.11.3
ChIRP-seq reads were mapped to the human (UCSC hg19) genome using bowtie2. Version 2.2.6. parameters: --trim5 3 --trim3 30 -L 25 -N 1 -q.
The process of peak calling was described in (Qu et al., 2011). The scripts and readme were available at http://changlab.stanford.edu/protocols.html
Genome_build: human (UCSC hg19) genome
Supplementary_files_format_and_content: The processed data files are the output files of script peak_correlation.pl in tab-delimited txt format. The files contain header to describe the content of each column.

source_name: Jurkat

growth_protocol: Jurkat cells were cultured in RPMI-1640 (Gibco) media supplemented with 10% fetal bovine serum (Gibco) at 37°C with 5% CO2.

extract_protocol:
Chromatin isolation by RNA purification (ChIRP) assay was carried out as described before (Chu et al., 2012).
ChIRP-ed  DNA was subjected to library preparation using KAPA Hyper Prep Kit (Kapa Biosystems) and sequenced using an Illumina HiSeq 2500 platform.

treatment_protocol: Jurkat cells stablly expressing SLEAR were cultured in RPMI-1640 (Gibco) media supplemented with 10% fetal bovine serum (Gibco) .

tag: cell line

value: Jurkat


title: #108


title: odd3


title: WT Mouse 4

description:
WT frontal cortex
WL_WT4


title: WT Mouse 2

description:
WT frontal cortex
WL_WT2


title: lacZ3


title: #105


title: even2

description:
immortalized line of human T lymphocyte cells
merge2_peaks.corr.txt


title: input3


title: #104


title: lacZ2


title: #102


title: odd2


title: #101


title: input2


title: #103


title: even1

description:
immortalized line of human T lymphocyte cells
merge1_peaks.corr.txt


title: odd1


title: #98


title: lacZ1


title: #100


title: input1


title: #99


title: #96


title: SLEAR shRNA-2

data_processing:
RNA-seq data quality evaluation: RNA-seq data quality evaluation was performed using FastQC. Version 0.11.3
Mapping to genomes: RNA-seq reads were mapped to the human (UCSC hg19) genome using bowtie2. Version 2.2.4. parameters: --trim5 4 --trim3 17 -L 25 -N 1 -q. The output SAM files were sorted and converted into BAM format using samtools. Version 1.2.
Gene expression profiling: maps3end was used to generate the gene expression profile. The souce code and ananlysis pipeline are available at https://code.google.com/archive/p/maps3end/.
Genome_build: human (UCSC hg19) genome
Supplementary_files_format_and_content: The processed data files are in tab-delimited txt format. Column 1 in the processed data file is the transcript ID, column 2-5 are gene expression levels in control, SLEAR sh1, SLEAR sh2 and SLEAR sh3. Column 6 is NM ID from RefSeq. Column 7 is gene symbol.

extract_protocol:
Cells were lysed in Trizol (Invitrogen) for total RNA extraction with DNAs removed by treating samples using RNase-free DNase I (Roche).
RNA-Seq experiments and data analysis were performed as described previously (Fox-Walsh et al., 2011) and sequenced using an Illumina HiSeq 2500 platform.
Multiplex Analysis of PolyA-linked Sequences (MAPS)

treatment_protocol: Short hairpin RNAs (shRNAs) against SLEAR were designed and cloned into pGreenPuro shRNA Cloning and Expression Lentivector (SBI) as described by the manufacturer. Jurkat cells were seeded into 6 well plates at 50-60% confluence and transduced with lentiviral particles in presence of 2 μg/ml polybrene.

tag: tissue

value: immortalized line of human T lymphocyte cells


title: SLEAR shRNA-1


title: SLEAR shRNA-3


title: #92


title: Control


title: #95


title: SCBO-15_tumor

first: Suk Hyung

last: Lee

address: 1130 St. Nicholas Ave, ICRC rm 208A

department: Medicine

institute: Columbia University

description:
urothelial carcinoma
MS038

data_processing:
RNA-seq pipeline description:
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit. Libraries are then sequenced using Illumina HiSeq2000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane.
We use RTA (Illumina) for base calling and CASAVA (version 1.8.2) for converting BCL to fastq format, coupled with adaptor trimming. We map the reads to a reference genome (Human: NCBI/build37.2) using Tophat [1] (version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10). To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.  We estimate the relative abundance (aka expression level) of genes and splice isoforms using cufflinks [2] (version 2.0.2) with default settings. We test for differentially expressed genes under various conditions using DEseq [3]. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Raw RNAseq counts were normalized (variance stabilization) using DESeq2 package in R-studio Version 0.99.484
Genome_build: Human: NCBI/build37.2
Supplementary_files_format_and_content: Tab-delimited text or xls files include DESeq normalized values for each Sample

source_name: bladder tissue

extract_protocol:
RNA was extracted using the MagMAX-96 RNA isolation kit (Ambion). Quality control was performed with Agilent Bioanalyser 2100
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit. Libraries are then sequenced using Illumina HiSeq2000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane.

tag: cell type

value: bladder tumor

tag: passages

tag: tumor stage

tag: tumor grade

value: Hg


title: #91


title: SCBO-12_tumor

description:
urothelial carcinoma
MS037

value: Ta

value: Lg


title: #69


title: #97


title: SCBO-11_tumor

description:
squamous cell carcinoma
MS036


title: SCBO-9_tumor

description:
urothelial carcinoma
MS035

value: Lg/Hg


title: SCBO-7_tumor

description:
urothelial carcinoma
MS034


title: SCBO-5_tumor

description:
urothelial carcinoma
MS033


title: SCBO-7.2_tumor

description:
urothelial carcinoma
MS048


title: #64


title: #65


title: SCBO-16_tumor

description:
urothelial carcinoma
MS045

value: Ta+CIS


title: #66


title: #57

value: Cabernet Sauvignon


title: SCBO-14_orgP10

description:
urothelial carcinoma
MS050

value: patient-derived bladder cancer organoids

value: bladder


title: #94


title: SCBO-11.3_orgP2

description:
urothelial carcinoma
MS047


title: #54

value: Riccione


title: #93

value: Bolgheri


title: #55

value: Mid-ripening, MR, berries developing color, BBCH 83


title: SCBO-16_orgP4

description:
urothelial carcinoma
MS046


title: #56


title: SCBO-7.2_orgP1

description:
urothelial carcinoma
MS049


title: #52


title: #53


title: #45

value: Sangiovese


title: SCBO-13_orgP7

description:
urothelial carcinoma
MS042


title: SCBO-15_orgP8

description:
urothelial carcinoma
MS043


title: #68


title: #43


title: SCBO-11.2_orgP3

description:
squamous cell carcinoma
MS041


title: #44


title: SMBO-2_orgP2

description:
urothelial carcinoma
MS031


title: #67


title: #41


title: #42


title: SMBO-1_orgP0

description:
urothelial carcinoma
MS030


title: SCBO-15_orgP0

description:
urothelial carcinoma
MS028


title: SCBO-14_orgP2

description:
urothelial carcinoma
MS027


title: #40


title: SCBO-12_orgP7

description:
urothelial carcinoma
MS026


title: #32


title: #33


title: SCBO-11_orgP8

description:
squamous cell carcinoma
MS025


title: SCBO-10_orgP9

description:
urothelial carcinoma
MS024


title: #31


title: #29


title: SCBO-9_orgP9

description:
urothelial carcinoma
MS023


title: SCBO-8_orgP11

description:
urothelial carcinoma
MS022


title: #28


title: #30


title: SCBO-7_orgP7

description:
urothelial carcinoma
MS021


title: SCBO-3.2_orgP14

description:
urothelial carcinoma
MS019


title: #20

value: Montalcino


title: SCBO-11_orgP1

description:
squamous cell carcinoma
MS017


title: SCBO-12_orgP0

description:
urothelial carcinoma
MS018


title: SCBO-3_orgP14

description:
urothelial carcinoma
MS044


title: #18

value: Pre-veraison, PV, majority of berries touching, BBCH 79


title: #17


title: SCBO-10_orgP0

description:
urothelial carcinoma
MS016


title: SCBO-9_orgP0

description:
urothelial carcinoma
MS015


title: #19


title: #16


title: #9


title: SCBO-7_orgP0

description:
urothelial carcinoma
MS013


title: #7


title: SCBO-3.2_orgP1

description:
urothelial carcinoma
MS011


title: #8


title: SCBO-5_orgP3

description:
urothelial carcinoma
MS010


title: #5


title: SCBO-6_orgP4

description:
urothelial carcinoma
MS005


title: SCBO-4_orgP10

description:
urothelial carcinoma
MS009


title: SCBO-3_orgP4

description:
urothelial carcinoma
MS004


title: SCBO-2_orgP5

description:
urothelial carcinoma
MS008


title: #4


title: rdr1/2/6 Inflorescence Rep 1

city: University Park

first: Michael

middle: J

last: Axtell

state: PA

address: 280 Mueller Lab

department: Biology

institute: Pennsylvania State University

data_processing:
Reads were trimmed using ShortStack ver 3.2
Unique sequences were counted from each library using a custom script
Supplementary_files_format_and_content: Frequency counts of inferred small RNAs (after trimming); tab-delimited text with frequencies<tab>sequence, sorted in ascending order by frequency

organism: Arabidopsis thaliana

source_name: rdr1/2/6_Inflorescence tissue

growth_protocol: Plants were grown at 24⁰C with 16 hours day/8 hours night cycle under cool-white fluorescent lighting.  The soil was supplemented with Osmocote®

extract_protocol:
RNA were extracted using Tri-Reagent (Sigma Aldrich, St. Louis, MO)
Small RNA (sRNA) libraries were prepared via TruSeq Small RNA Library Preparation Kit following manufacturer’s protocol.

tag: ecotype

value: Inflorescence

tag: molecule subtype

value: Small RNA


title: SCBO-1_orgP7

description:
urothelial carcinoma
MS003


title: rdr1/2/6 Inflorescence Rep 2


title: rdr1/2/6 Inflorescence Rep 3


title: Wild type Inflorescence Rep 3

source_name: WT_Inflorescence tissue

value: Wild-type


title: Wild type Inflorescence Rep 1


title: SCBO-5_orgP13

description:
urothelial carcinoma
MS002

value: Hg


title: WT_gate17_cult7d_Flt3L_4

city: Freiburg im Breisgau

first: Josip

middle: Stefan

last: Herman

address: Stuebeweg 51

department: Quantitative Single Cell Biology

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
cellbarcodes_cellid_culture_experiment_2.csv
Library of 96 cells

data_processing:
Image acquisition, intensity extraction and basecalling for HiSeq3000 was done unsing HiSeq Control Software-HD 3.4.0.38.
Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction (Baker et al., 2005). Reads mapping to multiple loci were discarded.
The left read contains the barcode information: the first six bases corresponded to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch. The left read was not used for mapping to the murine transcriptome.
For each cell barcode, the number of UMIs per transcript were counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs were converted into transcript counts (Grün et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

source_name: Cultured primary hematopoieitc progenitors

growth_protocol: Hematopoietic progenitors were isolated from C57BL/6J wildtype mice.

extract_protocol:
Bone marrow of 5-week old male C57BL/6J wildtype mice purchased from Charles River or from in house breedings of C57BL/6J wildtype mice was isolated from femora and tibiae by flushing using 1x MojoSort™ Buffer (BioLegend®, 480017). Hematopoietic progenitors were enriched using the MojoSort™ Mouse Hematopoietic Progenitor Cell Isolation Kit (BioLegend®, 480004), stained and sorted according to different surface markers. Hematopoietic progenitors were cultured and sorted after 7d of culturing in media for B cell or plasmacytoid dendritic cell differentiation.
The amplified RNA (aRNA) was reversely transcribed in order to generate libraries for sequencing. 1 µl of custom random hexamer RT primers (GCCTTGGCACCCGAGAATTCCANNNNNN) and 0.5 µl of 10mM dNTP were added to the aRNA. The samples were incubated at 65˚C for 5 min and cooled to 4˚C afterwards. Thereafter 4 µl of First Strand Reaction Mix containing SuperScript™ II Reverse Transcriptase and Buffer (Invitrogen, 18064014) and RnaseOUT™ (Invitrogen, 10777019) was added and samples were first incubated at 25˚C for 10 min followed by incubation at 42˚C for 1 hour. To every sample 2 µl of one uniquely indexed RPI index primer and 2 µl of RP1 primer (TruSeq Library Prep, sequences available from Illumina), 25 µl of Phusion® High-Fidelity PCR Master Mix with HF Buffer (NEB, M0531) and 11 µl of nuclease-free water were added. PCR was performed using 98˚C for 30 s as initial step, followed by 11 cycles of amplification (98˚C for 10 s, 60˚C for 30 s, 72˚C for 30 s) and a final extension at 72˚C for 10 min. To each sample 1 volume (50 µl) of Agencourt® AMPure XP beads (Beckman Coulter, A63881) was added and the samples were incubated at 25˚C for 15 min. The samples were incubated for 5 min on a magnetic stand (96 well format), the supernatant was removed and the beads were washed twice by adding 180 µl of 80 % ethanol and by incubating for 40 s. Ethanol was removed and beads were dried for 10 min at room temperature. DNA was eluted with 25 µl nuclease-free water and the purification was repeated with an adjusted volume of magnetic beads (25 µl). After the final step the samples were eluted in 10 µl nuclease-free water. DNA concentration and fragment size were determined using the Qubit® dsDNA HS Assay Kit (Invitrogen, Q32854) and the Agilent High Sensitivity DNA Kit for Bioanalyzer (Agilent Technologies, 5067-4627), respectively. Libraries were sequenced on an Illumina HiSeq 2500 System in high output run mode at a depth of 150000 to 200000 reads per cell.
CEL-Seq2 (Hashimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8)

treatment_protocol: no treatment

tag: strain

value: bone marrow

tag: surface marker

value: gating on Cells in SSC to FSC plot including only single cells using SSC-W to SSC-H and FSC-W to FSC-H

tag: illumina barcode

tag: barcode sequence

value: CCGTCC


title: #21


title: Wild type Inflorescence Rep 2

tag: genotype/variation


title: SCBO-8_orgP3

description:
urothelial carcinoma
MS014

value: Ta


title: WT_gate17_cult7d_Flt3L_3

value: ATGTCA


title: WT_gate16_cult7d_Flt3L_2

value: TAGCTT


title: WT_gate16_cult7d_Flt3L_1

value: GATCAG


title: #6

tag: cultivar

value: Cabernet Sauvignon


title: LMPP_WT3616_gate7_4

source_name: Bone marrow-derived hematopoietic progenitors

value: Lin neg, Flt3 pos, Sca-1 hi, c-Kit hi

value: ACTTGA


title: WT_3615_3616_mixed_2

value: Lin neg, Flt3pos, Sca-1 int, Kit int

value: GCCAAT


title: WT_3615_3616_mixed_1

value: ACAGTG


title: CLP_WT3616_IL7rpos_gate13_3

value: Lin neg, Flt3pos, Sca-1 int, Kit int, Il7r pos, Cd34 neg


title: CLP_WT3615_Cd34pos_gate15_2

value: Lin neg, Flt3pos, Sca-1 int, Kit int, Il7r neg, Cd34 pos

value: AGTTCC


title: SCBO-5_orgP10

description:
urothelial carcinoma
MS001

value: patient-derived bladder cancer organoids

value: bladder

value: Hg


title: Loop-ES2_replicate2

city: Montpellier

first: Thierry

last: Forné

address: 1919, Route de Mende

country: France

institute: CNRS

data_processing:
Library strategy: HRS-seq
Base calling was performed using the RTA software from Illumina
Trimming of adaptor sequences (remove the following sequence from the 3' end of reads : TCGTATGCCGTCTTCTGCTTG).
Only reads starting by the WWGG motif are kept (presence of a styI cut site)
Reads were aligned to the 129P2 genome assembled from the mm9 genome assembly using the  CASAVA version 1.8.2, script ELAND_standalone.pl) from Illumina.
Reads were counted for each StyI restriction fragment in the 129P2 reference genome assembled from the mm9 assembly.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include read counts for each StyI fragment. Sorted_Count*txt.gz files contain read counts for each class of repeats. Repeat classes were downloaded from Repbase at http://www.girinst.org/repbase/  and are included in the file repbase.fa available on the series record.

source_name: Embryonic Stem Cells

growth_protocol: Mouse ESC (E14 strain, 129P2 genomic background) were maintained on gelatin in DMEM (Invitrogen) supplemented with 15% ES-certified FBS (Invitrogen), 0.1mM non-essential amino acids (Invitrogen), 1mM sodium pyruvate (Invitrogen), 0.1mM Beta-mercaptoethanol (Sigma), 50U/ml penicillin/streptomycin and 10³ U/ml LIF (Millipore)

extract_protocol:
Nucleus preparations and HRS assays were performed as previously described in (Milligan et al. 2000 Oncogene 19, 5810-16) and (Braem et al. 2008 J. Biol. Chem. 283, 18612-20).
For each sequencing library, 150 ng of genomic DNA issued from the HRS or loop fractions of the assays were used. Briefly, a first biotinylated StyI DNA adaptor, containing a binding site for the MmeI type IIS restriction enzyme, is ligated to the StyI fragments. Ligated products are then captured onto streptavidin beads and digested with MmeI to homogenize the size of the StyI restriction fragments (~18 to 20 nucleotides). A second sequencing adaptor is ligated to MmeI restricted sites and DNA fragments are released from streptavidin beads, purified on an acrylamide gel and sequenced using high-throughput sequencing.

value: E14Tg2a ESC

tag: background strain

value: embryonic stem cells


title: Loop-ES1_replicate1


title: Loop-ES3_replicate3


title: D0_input genomic DNA


title: HRS-ES2_replicate2


title: HRS-ES3_replicate3


title: HRS-ES1_replicate1


title: WT_gate18_cult7d_Flt3L_1

value: bone marrow

value: gating on Cells in SSC to FSC plot including only single cells using SSC-W to SSC-H and FSC-W to FSC-H

value: AGTCAA


title: WT_gate18_cult7d_Flt3L_2


title: oldBPH2J.3

city: Portland

first: Jessica

last: Minnier

state: OR

address: 3181 SW Sam Jackson Park Rd, UHN62

institute: Oregon Health & Science University

data_processing:
Input sequences were 101bp mouse single-end samples.
Illumina Casava 1.8.2 was used to assemble fastq files
Trimming of known adapters and low-quality regions of reads was performed using Fastq-mcf
Sequence quality control was assessed using the program FastQC
Alignment of the provided samples to the mm9 whole genome was performed using Tophat 2.0.13 for spliced reads and Bowtie v2.24 for unspliced reads, with parameters --min-anchor=5 --segment-length=25 --no-coverage-search --segment-mismatches=2 --splice-mismatches=2
Reads were assigned to genes using the program "featureCounts", part of the Subread suite (http://subread.sourceforge.net/); Gene-level counts were arrived at using Ensembl's gene annotation v66 smallRNA annotaiton files were downloaded from miRBase release 19
We calculated differential expression P-values using edgeR
We first filter out any genes where there were not at least two samples with a CPM (counts per million) between 0.5 and 5000.
We then normalize the remaining expression values using "calcNormFactors" in edgeR.
edgeR performs the calculation of P-values for the differential expression between samples, using a negative binomial distribution for gene expression.
Finally we use the built-in R function "p.adjust" to calculating the FDR (false discovery rate) for each P-value, using the Benjamini-Hochberg method.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files includes multiple gene identifiers, transcript length, raw count, and normalized CPM values (edgeR) for each sample along with associated log fold-change, p-value, and FDR adjusted p-value (Benjamini-Hochberg)

source_name: Cardiac Endothelium

extract_protocol:
Endothelium were acutely extracted from cardiac tissue using miltenyi microbeads (Cat# 130-097-418) according to the manufacore instructions. Beads were sorted on an autoMACS instrument using the POSSLD protocol. Positively sorted endothelial cells were spun down and disolved in 500uL of Qiazol and subsequently extracted using a RNAeasy universal mini RNA kit.
PolyA(+) RNA is isolated using oligo-dT bound to magnetic beads.  Recovered RNA is chemically fragmented to about 200-300 bp.  Double stranded cDNA is made from the fragmented RNA using random hexamer priming.  The double stranded cDNA product is treated to “blunt” the ends.  A single “A” base is added to the ends of the fragments.  Proprietary Illumina adaptors are attached to the fragments by ligation. The unique “Y” structure of the adaptors ensures that different oligonucleotides are on the end of each strand.  The library is amplified by a limited number (usually 12) rounds of polymerase chain reaction.  The amplified library is cleaned using AMPure XP beads (Agencourt), then run on the Bioanalyzer (Agilent) to ensure that library preparation has been successful.  Sequenced 100 cycle single read on the HiSeq 2000.  Data was converted to fastq files with CASAVA (Illumina).

tag: age

value: 22 weeks


title: oldBPN3J.1


title: oldBPN3J.2


title: oldBPH2J.2


title: oldBPN3J.3


title: oldBPH2J.1


title: LMPP_WT3615_gate7_3

value: Lin neg, Flt3 pos, Sca-1 hi, c-Kit hi

value: CAGATC


title: youngBPH2J.3

value: 4 weeks


title: youngBPH2J.1


title: CLP_WT3616_Cd34pos_gate15_4

value: CCGTCC


title: G144_M10

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: Liver DNase-I released fragments

data_processing:
27 h data sets were processed as single end reads, by using read1 (R1) only, for consistency with the 3 h data sets. Sequence reads were mapped to the mouse genome (mm9) using Bowtie
Peaks were called using MACS2
Genome_build: mm9
Supplementary_files_format_and_content: Excel spreadhseet; MACS2 output (peaks discovered and statistics per peak)

source_name: DNase of female mouse liver_27 h TCPOBOP_pool2_G144_M10

extract_protocol:
DNA fragments were released from regions hypersensitive to DNase-I cutting and purified using a two step process: 1) sucrose gradient to isolate fragments less than 1-kb; followed by 2) SPRI bead purification isolating DNA fragments 125-400 bp
NEBNext Ultra DNA library prep kit for Illumina
SE50 or PE50 DNase-Seq. Sample from 27 h data sets were processed as single end reads by using read1 (R1) only.

treatment_protocol: Male and female CD1 (ICR) mice were obtained from Charles River Labs (Wilmington, MA) at 7 weeks of age. Mice were injected i.p. with 3 mg/kg TCPOBOP or vehicle alone (1% DMSO in corn oil)  between 8:00-8:45 AM on Day 1 and liver was collected between 11:00-11:45 AM on Day 1 (3 h) or between 11:00-11:45 AM on Day 2 (27 h). Nuclei were isolated and stored at -80C prior to DNase-I digestion.

value: CD-1 (Charles River)

tag: treatment

value: 3 mg/kg TCPOBOP_27 h exposure

tag: Sex

value: female

value: 7 weeks

value: liver


title: G144_M8

description: Liver DNase-I released fragments

source_name: DNase of female mouse liver_27 h vehicle_pool2_G144_M8

value: Vehicle (1% DMSO in corn oil)_27 h exposure

tag: tissue


title: CLP_WT3615_IL7rpos_gate13_1

value: Lin neg, Flt3pos, Sca-1 int, Kit int, Il7r pos, Cd34 neg


title: G115_M3

description: Liver DNase-I released fragments

source_name: DNase of male mouse liver_27 h TCPOBOP_pool1_G115_M3

value: male


title: G144_M9

description: Liver DNase-I released fragments

source_name: DNase of female mouse liver_27 h TCPOBOP_pool1_G144_M9


title: G115_M2

description: Liver DNase-I released fragments

source_name: DNase of male mouse liver_27 h vehicle_pool2_G115_M2


title: G144_M7

description: Liver DNase-I released fragments

source_name: DNase of female mouse liver_27 h vehicle_pool1_G144_M7


title: G115_M1

description: Liver DNase-I released fragments

source_name: DNase of male mouse liver_27 h vehicle_pool1_G115_M1


title: youngBPH2J.2


title: G98_M2

description: Liver DNase-I released fragments

source_name: DNase of male mouse liver_3 h vehicle_pool2_G98_M2

value: Vehicle (1% DMSO in corn oil)_ 3 h exposure


title: G98_M7

description: Liver DNase-I released fragments

source_name: DNase of male mouse liver_3 h TCPOBOP_pool2_G98_M7

value: 3 mg/kg TCPOBOP_ 3 h exposure


title: G91_M3

description: Liver DNase-I released fragments

source_name: DNase of female mouse liver_3 h TCPOBOP_pool1_G91_M3