title: C1-190-2-C8


title: C1-190-2-C7

status: Public on Mar 06 2018

type: SRA

city: New Haven

first: Nenad

last: Sestan

address: 333 Cedar Street, SHM C-316C

department: Neuroscience

country: USA

institute: Yale University School of Medicine

library_source: transcriptomic

data_processing:
Illumina Casava software used for basecalling
FastQC used for reporting the fundamental quality parameters
To avoid adapter contamination and higher error rates in reads boundary, we trimmed 12 nucleotides in 5’-end and 13 nucleotides in 3’-end, leaving 75 nucleotide long reads for sequence alignment. We employed STAR (v2.4.0) to uniquely align the filtered reads to mouse reference genome (mm9) with default parameters.
We used RSEQTools and SAMtools to calculate gene expression. We used HTSeq (v0.6.1) to calculate gene read count values for each annotation entry.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM and count values for each sample

molecule: total RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
Clontech Smart-seq v4
Illumina Nextera
Poly-A capture followed by full-length cDNA reverse transcription

tag: strain

tag: tissue

value: CGE

tag: age

value: Brain


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title: C1-96-G9


title: C1-96-G7


title: C1-96-G5


title: C1-96-G6


title: C1-96-G3


title: C1-96-G1


title: C1-96-G2


title: C1-96-G12


title: C1-97-A10


title: C1-96-G11


title: C1-96-G4


title: C1-96-H7


title: C1-97-B12


title: C1-96-F12


title: C1-96-F9


title: C1-96-E7


title: C1-96-H6


title: C1-96-E4


title: C1-96-F8


title: C1-96-F7


title: C1-96-E1


title: C1-96-D6


title: C1-96-F10


title: C1-96-E6


title: C1-96-E5


title: C1-96-D5


title: C1-96-E3


title: C1-96-E2


title: C1-96-E12


title: C1-96-D3


title: C1-96-E11


title: C1-96-G10


title: C1-96-D8


title: C1-96-D11


title: C1-96-F6


title: C1-96-D2


title: C1-96-D10


title: C1-96-C9


title: C1-96-D1


title: C1-96-C8


title: C1-96-F4


title: C1-96-D12


title: C1-96-C5


title: C1-96-C6


title: C1-96-C4


title: C1-96-C12


title: C1-96-C10


title: C1-96-C2


title: C1-96-B8


title: C1-96-B5


title: C1-96-B7


title: C1-96-B12


title: C1-96-B10


title: C1-96-B11


title: C1-96-A9


title: C1-96-A2


title: C1-96-A6


title: C1-96-A10


title: C1-93-H7


title: C1-93-H9


title: C1-93-H4


title: C1-93-H6


title: C1-93-H3


title: C1-93-H5


title: C1-93-H2


title: C1-93-H11


title: C1-93-H10


title: C1-93-G8


title: C1-93-H12


title: C1-93-G9


title: C1-93-G7


title: C1-93-G5


title: C1-93-G3


title: C1-96-B6


title: C1-93-G6


title: C1-93-H1


title: C1-93-G2


title: C1-93-G11


title: C1-93-G1


title: C1-93-F6


title: C1-93-G4


title: C1-93-F9


title: C1-93-F8


title: C1-93-F11


title: C1-93-F3


title: C1-93-F2


title: C1-93-F12


title: C1-93-F1


title: C1-93-E9


title: C1-93-F5


title: C1-93-E8


title: C1-93-E2


title: C1-93-E5


title: C1-93-E7


title: C1-93-D9


title: C1-93-E10


title: C1-93-D8


title: C1-93-E1


title: C1-93-D6


title: C1-93-D5


title: C1-93-D3


title: C1-93-D4


title: C1-93-D2


title: C1-93-D12


title: C1-93-D1


title: C1-93-D11


title: C1-93-C8


title: C1-93-C9


title: C1-93-C7


title: C1-93-C5


title: C1-93-E6


title: C1-93-C12


title: C1-93-C1


title: C1-93-C3


title: C1-93-C11


title: C1-93-C10


title: C1-93-C2


title: C1-93-D7


title: C1-93-E12


title: C1-93-B9


title: C1-93-B8


title: C1-93-B3


title: C1-93-B6


title: C1-93-B2


title: C1-93-B5


title: C1-93-B10


title: C1-93-B1


title: C1-93-A9


title: C1-93-B7


title: C1-93-A8


title: C1-93-A7


title: C1-93-B12


title: C1-93-A1


title: C1-93-A4


title: C1-93-A2


title: C1-93-A12


title: C1-93-C6


title: C1-93-A11


title: C1-93-A10


title: C1-92-H9


title: C1-92-H6


title: C1-92-H1


title: C1-92-H4


title: C1-92-H3


title: C1-92-H5


title: C1-92-H12


title: C1-92-H10


title: C1-92-G7


title: C1-92-G9


title: C1-92-H11


title: C1-93-A6


title: C1-92-G1


title: C1-92-G3


title: C1-92-G11


title: C1-92-G4


title: C1-92-F9


title: C1-92-F6


title: C1-92-F7


title: C1-92-G12


title: C1-92-F4


title: C1-92-F2


title: C1-92-F1


title: C1-92-F12


title: C1-92-E9


title: C1-92-E6


title: C1-92-E8


title: C1-92-E4


title: C1-92-E7


title: C1-92-E1


title: Rap1 ChIP - Mixed Mnase

city: Jerusalem

first: Nir

last: Friedman

address: Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

library_source: genomic

data_processing:
Base calling was performed with bcl2fastq (2.17).
Paired end reads were mapped to the yeast (sacCer3) and mouse (mm9) genomes using  bowtie2 default parameters except for setting of maximal fragment size of 2,000 bp.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using genomeCoverageBed tool.
Genome_build: sacCer3, mm9
Supplementary_files_format_and_content: Genome coverage bigwig files were generated using bedGraphToBigWig tool. Peak table was generated from MACS output.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: Yeast cells were grown in YPD media at 30ºC with constant shaking to OD 0.6-0.8. Mouse R1 ESCs were grown on Gelatin and maintained in ESC medium.

extract_protocol:
MNase digested chromatin was allowed to bind to antibodies for 2-4 hours. Paramagnetic  protein G dynabeads were added for an additional hour and the beads were extensively  washed. Bound chromatin was ligated to barcoded DNA adapters, and chromatin was reverse  cross linked and pooled.
Barcoded chromatin was amplified with Illumina NGS - compatible  primers and DNA libraries were paired end sequenced by Illumina NextSeq 500.

treatment_protocol: Cells were fixed with 1% formaldehyde for 15 minutes. Yeast cells were treated with zymolyase  to generate spheroplasts prior to lysis and MNase treatment. Lysed spheroplasts or mESCs  were treated with different amounts of MNase to digest chromatin into nucleosomes.

tag: transcription factor

tag: mnase

value: Mix

tag: antibody

value: Anti Flag (M2)


title: C1-92-G10


title: C1-92-E12


title: Abf1 ChIP - Mixed Mnase


title: Reb1 ChIP - Low Mnase - Low input


title: C1-92-F8


title: C1-92-D8


title: Reb1 ChIP - High Mnase - High input


title: C1-92-D6


title: C1-92-F3


title: C1-92-D7


title: C1-92-D5


title: C1-92-D4


title: Reb1 ChIP - Mid Mnase - High input


title: C1-92-D2


title: Reb1 ChIP - Low Mnase - High input


title: C1-92-D1


title: C1-92-D12


title: C1-92-D11


title: C1-92-E3


title: C1-92-E2


title: C1-92-D10


title: C1-92-D9


title: Sample_84-4_ifng

city: Frederick

first: Dennis

last: Klinman

state: Maryland

address: 1050 Boyles St

department: Cancer and Inflammation Program

institute: National Institutes of Health

data_processing:
Basecall by Illumina RTA 1.18.66.3
demultiplex by Illumina Bcl2fastq 2.17
data was aligned to hg19 using CLC genomics workbench v 10
RNA seq analysis and differential expression for RNA-seq preformed by CLC genomics workbench
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with RPKM for each Sample

organism: Homo sapiens

source_name: FACS sorted MDSC cells

extract_protocol:
cells from stimulated mMDSC were stored in RNA protect (Qiagen, Frederick, MD).  Total RNA was isolated using the RNeasy micro kit (Qiagen) and RNA quality was assessed using an Agilent 2200 TapeStation
Clonetech SMART er Ultra Low Input RNA Kit
Illumina TruSeq V4.0

tag: treatment group

value: ifng

tag: donor number


title: Sample_85-4_ifng


title: Sample_82-4_ifng


title: Sample_79-4_ifng


title: C1-92-C12


title: C1-92-C1


title: C1-92-C9


title: C1-92-C5


title: C1-92-C4


title: C1-92-C7


title: C1-92-C2


title: C1-92-C3


title: C1-92-C11


title: C1-92-B9


title: CTCF ChIP - Mixed Mnase

source_name: Mouse R1 ESCs

value: CTCF

value: Anti CTCF


title: C1-92-B7


title: CTCF ChIP - 100U Mnase


title: C1-92-B3


title: C1-92-B2


title: Reb1 ChIP - Low Mnase - Mid input


title: C1-92-B11


title: C1-92-A9


title: CTCF ChIP - 25U Mnase


title: O5

city: Los Angeles

first: Caroline

last: Keegan

state: CA

address: 615 Charles E. Young Drive South 246 OHRC

institute: UCLA

data_processing:
Sequenced reads were aligned to the human reference genome (build hg19 UCSC) using TopHat and Bowtie2.
Raw counts were calculated with HTseq using the hg19 Ensembl annotation.
Genome_build: hg19
Supplementary_files_format_and_content: comma-separated values file containing raw counts of mapped reads

source_name: PBMC_M.tb tRNA_24h

growth_protocol: PBMC were isolated from whole blood by Ficoll-hypaque (GE Healthcare) density gradient centrifugation and cultured in RPMI (Gibco) supplemented with 10% FCS (Hyclone) and 1% Pen/Strep glutamine (Gibco) at a density of 2x106/ml in 96-well flat bottomed plates (Corning) at 37 °C with 4% CO2.

extract_protocol:
RNA was harvested at 1, 6 and 24 h and isolated with RNeasy micro kit (Qiagen) according to manufacturer’s directions, including on-column DNase digestion. RNA was quantified by Nanodrop and quality assessed by Agilent 2100 Bioanalyzer.
Libraries were created from high quality RNA using TruSeq RNA Library Prep Kit v2 (Illumina). Libraries were quantified by Qubit, pooled by donor in groups of 12, and sequenced in duplicate on a HiSeq 2500 Sequencing System (Illumina).

treatment_protocol: PBMC were stimulated on the same day as isolation. Nucleic acid ligands were complexed with DOTAP (Roche) to facilitate delivery to the endosome.

tag: donor id

value: donor 3

tag: cell type

value: PBMC

tag: treatment

value: M.tb tRNA

tag: timepoint


title: C1-92-A7


title: CTCF ChIP - 6.25U Mnase


title: C1-92-A4


title: M3

value: ssRNA


title: C1-92-A1


title: C1-92-A6


title: CTCF ChIP - 1.55U Mnase


title: M5

source_name: PBMC_M.tb tRNA_6h


title: C1-92-A2


title: C1-92-A10


title: C1-92-B1


title: C1-91-H8


title: C1-91-H9


title: O3


title: M2


title: K5

source_name: PBMC_M.tb tRNA_1h


title: O2


title: C1-91-H5


title: M1

value: Media


title: C1-91-H6


title: C1-91-H3


title: K3


title: C1-92-A11


title: C1-91-H1


title: C1-91-H12


title: O1


title: K2


title: C1-91-H2


title: C1-91-H11


title: C1-91-H10


title: C1-91-G9


title: C1-91-H7


title: N5

value: donor 2


title: K1


title: C1-91-G7


title: C1-91-G6


title: C1-91-G5


title: C1-91-G3


title: N2


title: Sample_76_4-ifng


title: N3


title: L5


title: C1-91-G2


title: C1-91-F9


title: C1-91-G4


title: C1-91-G12


title: C1-91-F8


title: L2


title: C1-91-F5


title: C1-91-F6


title: L3


title: C1-91-F3


title: C1-91-F11


title: L1


title: N1


title: C1-91-E7


title: C1-91-G1


title: J5


title: C1-91-F1


title: J3


title: C1-91-E4


title: C1-91-E6


title: C1-91-G11


title: C1-91-E12


title: J2


title: C1-91-G10


title: C1-91-E11


title: C1-91-D9


title: J1


title: C1-91-E10


title: H5

value: donor 1


title: C1-91-D8


title: C1-91-D7


title: H2


title: H3


title: C1-91-D6


title: C1-91-D4


title: C1-91-D3


title: C1-91-D5


title: H1


title: C1-91-D1


title: C1-91-C9


title: C1-91-E2


title: E3


title: E5


title: C1-91-D12


title: C1-91-D11


title: E2


title: C1-91-C8


title: C1-91-C7


title: C1-91-C6


title: C1-91-C5


title: C1-91-C3


title: C1-91-C4


title: B5


title: C1-91-C2


title: C1-91-C11


title: C1-91-C1


title: C1-91-C12


title: C1-91-B9


title: C1-91-C10


title: B1


title: B2


title: C1-91-B7


title: C1-91-B4


title: C1-91-B2


title: C1-91-B6


title: C1-91-B12


title: C1-91-B5


title: E1


title: C1-91-A7


title: NS134muscle

city: Boston

first: Sowmya

last: Iyer

state: MA

department: Pathology

institute: Massachusetts General Hospital

description: Normal muscle

data_processing:
STAR was used to align reads; featureCounts was used to count reads against genes
Genome_build: hg19
Supplementary_files_format_and_content: counts matrix and patient metadata provided as supplementary files

molecule: polyA RNA

source_name: muscle

extract_protocol:
As per Shern et al(Cancer Discov February 1 2014 (4) (2) 216-231; DOI: 10.1158/2159-8290.CD-13-0639), "RNA extraction was accomplished with the Qiagen RNeasy Micro Kits according to the manufacturer's protocol (Qiagen)."
RNA libraries were prepared for sequencing using standard Illumina protocols as per Shern et al(Cancer Discov February 1 2014 (4) (2) 216-231; DOI: 10.1158/2159-8290.CD-13-0639)

value: Normal


title: NS127muscle

description: Normal muscle


title: C1-91-B10


title: C1-91-A9


title: B3


title: C1-91-A5


title: C1-91-A4


title: C1-91-A3


title: NCI0082

description: PAX7-FOXO1+ ARMS

source_name: rhabdomyosarcoma

value: tumor


title: NCI0075

description: Fusion Negative RMS


title: C1-91-A12

value: Brain


title: C1-90-H9

value: dMGE


title: NS132muscle

description: Normal muscle


title: C1-90-H8


title: NCI0003

description: Fusion Negative RMS


title: NS129muscle

description: Normal muscle


title: C1-90-H7


title: C1-91-B1

value: vMGE


title: RMS228

description: Fusion Negative RMS


title: C1-90-H5


title: C1-90-H6


title: RMS222.1

description: Fusion Negative RMS


title: NS128muscle

description: Normal muscle


title: C1-90-H3


title: RMS212

description: Fusion Negative RMS


title: RMS2119

description: Fusion Negative RMS


title: C1-90-H2


title: C1-90-H11


title: C1-90-G9


title: RMS2117

description: Fusion Negative RMS


title: C1-90-G6


title: C1-90-H12


title: C1-90-G8


title: RMS2104

description: PAX3-FOXO1+ ARMS


title: C1-90-G7


title: C1-90-G5


title: C1-91-A2


title: RMS2103

description: PAX3-FOXO1+ ARMS


title: C1-90-G4


title: C1-90-G2


title: C1-90-G1


title: C1-90-G12


title: RMS2096

description: PAX7-FOXO1+ ARMS


title: C1-90-G11


title: C1-90-G10


title: RMS2093

description: PAX3-FOXO1+ ARMS


title: C1-90-F5


title: C1-90-F9


title: RMS2094

description: Fusion Negative RMS


title: RMS2090

description: Fusion Negative RMS


title: C1-90-F3


title: C1-90-F4


title: RMS2085

description: Fusion Negative RMS


title: C1-90-F12


title: RMS209.1

description: PAX3-FOXO1+ ARMS


title: C1-90-F10


title: C1-90-E9


title: C1-90-F6


title: C1-90-E8


title: RMS2083

description: Fusion Negative RMS


title: C1-90-E2


title: C1-90-E3


title: C1-90-E5


title: RMS2081

description: Fusion Negative RMS


title: C1-90-E7


title: RMS2084

description: Fusion Negative RMS


title: C1-90-E1


title: C1-90-F11


title: RMS2079

description: PAX3-FOXO1+ ARMS


title: C1-90-E12


title: RMS2076

description: PAX3-FOXO1+ ARMS


title: C1-90-E11


title: RMS2075

description: Fusion Negative RMS


title: C1-90-E10


title: C1-90-F1


title: C1-90-D8


title: C1-90-D9


title: C1-90-D6


title: C1-90-D7


title: RMS2074

description: PAX7-FOXO1+ ARMS


title: RMS2072

description: PAX3-FOXO1+ ARMS


title: C1-90-D2


title: C1-90-D12


title: RMS2065

description: Fusion Negative RMS


title: C1-90-D11


title: RMS2071

description: PAX3-FOXO1+ ARMS


title: C1-90-C9


title: C1-90-D10


title: C1-90-C8


title: C1-90-C5


title: RMS2060

description: Fusion Negative RMS


title: C1-90-C3


title: C1-90-C4


title: RMS2061

description: PAX7-FOXO1+ ARMS


title: C1-90-C6


title: RMS206.1

description: Fusion Negative RMS


title: C1-90-C12


title: RMS2059

description: Fusion Negative RMS


title: C1-90-C11


title: C1-90-C10


title: RMS2058

description: Fusion Negative RMS


title: C1-90-D4


title: C1-90-B9


title: C1-90-B6


title: C1-90-D1


title: C1-90-B2


title: RMS2063

description: Fusion Negative RMS


title: C1-90-B1


title: C1-90-B12


title: RMS2054

description: Fusion Negative RMS


title: C1-90-B11


title: C1-90-B10


title: RMS2053

description: Fusion Negative RMS


title: C1-90-A9


title: RMS2052

description: Fusion Negative RMS


title: C1-90-A7


title: C1-90-A8


title: C1-90-A5


title: RMS2051

description: Fusion Negative RMS


title: C1-90-A4


title: C1-90-A3


title: RMS205.1

description: Fusion Negative RMS


title: C1-90-A2


title: RMS2056

description: Fusion Negative RMS


title: C1-90-A12


title: RMS2049

description: PAX7-FOXO1+ ARMS


title: C1-90-A11


title: C1-90-A10


title: RMS2047

description: Fusion Negative RMS


title: liver control

type: RNA

city: Nankoku

first: Katsumi

last: Toda

state: Kochi

address: Oko-cho, Kohasu

department: Biochemistry

country: Japan

institute: Kochi University, School of Medicine

hyb_protocol: Affymetrix® GeneChip® Hybridization Oven 640, Affymetrix® GeneChip® Fluidics Station 450

scan_protocol: Affymetrix® GeneChip® Scanner 3000 7G System

data_processing: Affymetrix® GeneChip® Command Console® Software ver. 3.2, Affymetrix® Expression ConsoleTM Softwere ver.1.3.0, RMA-Sketch (RMA-Gene-Default)

label: biotin

source_name: liver, 60 min after PBS ip injection

label_protocol: Affymetrix GeneChip® WT PLUS Reagent Kit (Part# 902280)

growth_protocol: Mice were given water and rodent chow (CE-2; Oriental Yeast Ltd., Tokyo, Japan).

extract_protocol: Total ovarian RNAs were prepared individually using NucleoSpin® RNAII (Macherey-Nagel GmbH & Co., Düren, Germany).

treatment_protocol: WT mice (C57BL6/j) were injected intraperitoneally (ip) with 0.75 U/kg body weight of recombinant human insulin (Novolin® R from Novo Nordisk Inc New Jersey 08540 USA), or with glucagon 50 ng/g body weight of glucagon (Sigma-Aldrich, St. Louis, MO, USA). After 60 min, livers were dissected.

value: 6 months of age


title: liver with Insulin

source_name: liver , 60 min after ip injection of insulin


title: CAF PDGFCC stimulated 6h, biological rep3

city: Lund

first: Kristian

last: Pietras

address: Medicon Village, Building 404:A3

department: Laboratory Medicine

country: Sweden

institute: Lund University

description: Gene expression data from PDGFCC stimulated CAF2 cell line, 6h

hyb_protocol: Done by SCIBLU genomics, Lund University, Sweden, on HuGene-2_0-st chip

data_processing: RMA normalization and Student’s t-test for differential expression with Bonferroni adjustment for multiple comparisons were performed using the Qlucore Omics Explorer software

source_name: immortalized healthy human fibroblasts conditioned by tumor cells in vivo in mice, cultured in starvation medium supplemented with PDGF-CC

growth_protocol: Cells were cultured in DMEM Glutamax (Invitrogen), supplemented with 1% Penicillin/Streptomycin and 10% fetal bovine serum at 37°C in a 5% CO2/95% air atmosphere

extract_protocol: RNA was isolated following the RNeasy Mini Kit (Qiagen)

treatment_protocol: Cells were starved for 24 h in DMEM + 0,1 % BSA and stimulated with 100 ng/ml of PDGF-CC

tag: cell line

value: mammary fibroblast

value: stimulated, 6h


title: RMS2041

description: Fusion Negative RMS


title: C1-99-H3


title: C1-99-H4


title: CAF unstimulated 6h, biological rep3

description: Gene expression data from unstimulated CAF2 cell line, 6h

scan_protocol: Done by SCIBLU genomics, Lund University, Sweden

source_name: immortalized healthy human fibroblasts conditioned by tumor cells in vivo in mice, cultured in starvation medium

value: unstimulated, 6h


title: C1-99-H7


title: CAF unstimulated 48h, biological rep3

description: Gene expression data from unstimulated CAF2 cell line, 48h

label_protocol: Done by SCIBLU genomics, Lund University, Sweden

value: unstimulated, 48h


title: liver with Glucagon

source_name: liver , 60 min after ip injection of glucagon


title: CAF PDGFCC stimulated 48h, biological rep3

description: Gene expression data from PDGFCC stimulated CAF2 cell line, 48h

value: stimulated, 48h


title: CAF PDGFCC stimulated 6h, biological rep2


title: CAF PDGFCC stimulated 48h, biological rep2


title: CAF unstimulated 48h, biological rep2


title: RMS2040

description: Fusion Negative RMS


title: C1-99-G8


title: RMS2039

description: PAX3-FOXO1+ ARMS


title: C1-99-G4


title: RMS2038

description: PAX3-FOXO1+ ARMS


title: C1-99-G3


title: CAF PDGFCC stimulated 48h, biological rep1


title: RMS2037

description: Fusion Negative RMS


title: C1-99-G9


title: CAF unstimulated 48h, biological rep1


title: RMS2034

description: Fusion Negative RMS


title: CAF unstimulated 6h, biological rep2


title: C1-99-G11


title: CAF PDGFCC stimulated 6h, biological rep1


title: C1-99-G12


title: C1-99-F6


title: C1-99-G10


title: C1-99-G6


title: C1-99-G5


title: RMS2033

description: Fusion Negative RMS


title: C1-99-F4


title: C1-99-F5


title: RMS2032

description: Fusion Negative RMS


title: C1-99-F1


title: C1-99-F3


title: C1-99-G1


title: 8.5wk_VTP_rep3

city: New York

first: Nicholas

middle: D.

last: Socci

state: NY

address: 1275 York Ave

department: bioinformatics core

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX HT12 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using Illumina iScanner.

data_processing: The data were analyzed with GenomeStudio using Illumina default analysis settings. No normalization and background correction are performed first, then quantile normalization and background correction are done.

source_name: tumor, VTP, 8.5 week

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

extract_protocol: Total RNA was extracted with Trizol reagent, followed by QIAGEN RNeasy MinElute Cleanup kit. RNA was then treated with Ambion TURBO DNA-free DNase Treatment and Removal Reagents.

value: VTP

tag: time point

value: 8.5 week

value: LNCaP-AR

tag: tissue of origin

value: Prostate cancer


title: CAF unstimulated 6h, biological rep1


title: RMS2031

description: PAX3-NCOA1+ ARMS


title: 8.5wk_VTP_rep5


title: 8.5wk_VTP_rep4


title: C1-99-F11


title: RMS2030

description: Fusion Negative RMS


title: C1-99-F10


title: C1-99-E9


title: RMS2029

description: Fusion Negative RMS


title: C1-99-F7


title: 8.5wk_VTP_rep2


title: C1-99-E6


title: RMS2028

description: Fusion Negative RMS


title: C1-99-E8


title: C1-99-E5


title: 8.5wk_VTP_rep1


title: C1-99-E4


title: RMS2026

description: Fusion Negative RMS


title: C1-99-E3


title: C1-99-E2


title: RMS2024

description: Fusion Negative RMS


title: 8.5wk_control_rep5

source_name: tumor, control, 8.5 weeks

value: control

value: 8.5 weeks


title: C1-99-E1


title: RMS2022

description: Fusion Negative RMS


title: 8.5wk_control_rep3


title: C1-99-E12


title: C1-99-E11


title: 8.5wk_control_rep2


title: C1-99-D8


title: C1-99-D6


title: RMS061

description: PAX3-FOXO1+ ARMS


title: RMS2021

description: Fusion Negative RMS


title: RMS057

description: PAX3-FOXO1+ ARMS


title: C1-99-D9


title: C1-99-D7


title: C1-99-D5


title: RMS055

description: Fusion Negative RMS


title: C1-99-D12


title: C1-99-E10


title: C1-99-C9


title: C1-99-D4


title: 6hr_VTP_rep1

source_name: tumor, VTP, 6 hr

value: 6 hr


title: RMS051

description: Fusion Negative RMS

value: tumor


title: C1-99-D11

source_name: Brain

value: Brain


title: C1-99-C8

value: dMGE


title: C1-99-D10


title: RMS202.1

description: Fusion Negative RMS


title: RMS049

description: PAX3-FOXO1+ ARMS


title: 6hr_VTP_rep4


title: 8.5wk_control_rep4


title: 8.5wk_control_rep1


title: 3hr_VTP_rep3

source_name: tumor, VTP, 3 hr

value: 3 hr


title: 6hr_VTP_rep2


title: 6hr_VTP_rep3


title: C1-99-C4


title: 3hr_VTP_rep4


title: C1-99-C3


title: C1-99-C11


title: C1-99-C10


title: C1-99-B9


title: 3hr_VTP_rep2


title: C1-99-C6


title: C1-99-B3


title: C1-99-B2


title: C1-99-B6


title: C1-99-B11


title: 3hr_VTP_rep1


title: 24hr_VTP_rep3

source_name: tumor, VTP, 24 hr

value: 24 hr


title: C1-99-B10


title: C1-99-A5


title: C1-99-A10


title: C1-99-A1


title: RMS008

description: Fusion Negative RMS


title: C1-98-H9

value: vMGE


title: 24hr_VTP_rep2


title: C1-98-H8


title: 24hr_VTP_rep4


title: C1-99-B7


title: RMS007

description: PAX7-FOXO1+ ARMS


title: 24hr_VTP_rep1


title: C1-98-H6


title: C1-98-H2


title: C1-98-G9


title: 1week_VTP_rep4

source_name: tumor, VTP, 1 week

value: 1 week


title: C1-99-B12


title: C1-98-G8


title: 1week_VTP_rep3


title: 1week_VTP_rep1


title: 1week_VTP_rep2


title: 1week_control_rep6

source_name: tumor, control, 1 week


title: C1-98-G7


title: C1-98-G4


title: C1-98-G6


title: C1-98-G5


title: C1-98-G11


title: 1week_control_rep5


title: C1-98-G1


title: C1-98-G10


title: C1-98-F8


title: C1-98-F7


title: C1-98-F6


title: C1-98-F5


title: 1week_control_rep3


title: C1-98-F3


title: C1-98-F2


title: 1week_control_rep2


title: 1week_control_rep4


title: 1week_control_rep1


title: C1-98-F11


title: C1-98-F10


title: C1-98-E9


title: C1-98-E8


title: C1-98-E6


title: C1-98-E4


title: C1-98-E7


title: C1-98-E3


title: C1-98-E5


title: C1-98-G3


title: C1-98-E1


title: C1-98-E2


title: C1-98-E11


title: C1-98-E12


title: C1-98-D9


title: C1-98-F4


title: C1-98-D8


title: C1-98-E10


title: C1-98-D7


title: C1-98-D6


title: C1-98-F1


title: C1-98-D3


title: C1-98-D12


title: C1-98-D10


title: C1-98-D5


title: C1-98-D11


title: C1-98-C9


title: C1-98-C5


title: C1-98-C8


title: C1-98-C4


title: C1-98-D4


title: C1-98-B7


title: C1-98-C3


title: C1-98-C2


title: C1-98-C12


title: C1-98-B6


title: C1-98-B4


title: C1-98-B3


title: C1-98-B12


title: C1-98-B11


title: C1-98-A8


title: C1-98-D2


title: C1-98-A7


title: C1-98-B1


title: C1-98-A6


title: C1-98-A5


title: C1-98-A10


title: C1-98-A3


title: C1-101-H7


title: C1-101-H5


title: C1-101-H1


title: C1-101-H4


title: C1-101-H6


title: C1-98-C11


title: C1-101-H12


title: C1-98-C10


title: single naive H1

city: Hangzhou

first: Haide

last: Chen

address: 866 Yuhangtang road

country: China

institute: Zhejiang University

data_processing:
Basecalls performed using bcl2fastq_2.19.
Sequenced reads were trimmed for adaptor sequence, then mapped to GRCh38 whole genome using STAR v2.5.2a with parameters --runThreadN 2 --genomeDir $Indexpath --readFilesIn $i --outFileNamePrefix $STAROutDIR
The capture efficiency of C1 was measured under microscope. The capture sites without cell or with more than one cell were excluded from further analysis.
scRNA-seq expression  were quantified by counts via featureCounts v1.5.1. Bulk RNA-seq  were quantified by FPKM via RSEM v0.4.6.
scRNA-seq expression data were analyzed with Seurat (filtering, normalization, PCA and t-SNE) and Monocle (pseudotemporal analysis). Bulk RNA-seq data were analyzed with DEseq2 v1.14.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: comma-delimited csv files include DGE values (scRNA-seq data) and FPKM values (Bulk RNA-seq data) for each sample.

source_name: Naive-like H1

growth_protocol: Primed H9  and H1 were maintained in mTeSR1 media (STEMCELL Technologies) on tissue culture plates coated with Matrigel (BD Bioscience). H9 and H1 were reset into a naïve-like state by RSeT media (STEMCELL Technologies). EBs were differentiated in DMEM/F12 (GIBCO) supplemented with 20% FBS (GIBCO), 50 U/mL penicillin/streptomycin (GIBCO), 2 mM L-Glutamine (GIBCO), 1 x non-essential amino acids, and 100 μM ß-mercaptoethanol (Sigma).

extract_protocol:
C1 system and C1 high-throughput integrated fluidics circuits (HT IFCs) were used to capture single cells. Immediately after cell capture, lysis, reverse transcription and preamplification were performed in the HT IFCs.
Samples harvested from HT IFCs were used to create libraries for Illumina sequencing with Illumina Nextera XT DNA Library kit.

value: Reset HPSCs

tag: culture media

value: RSeTTM media


title: C1-101-H11


title: C1-101-G6


title: single Primed H1

source_name: Primed H1

value: Primed HPSCs

value: mTeSR™1 media


title: C1-101-G5


title: C1-101-G8


title: single EB day 4

source_name: Day 4 embryoid body

value: Primed HPSCs derived EB

value: EB differentiation media


title: C1-98-B10


title: RMS248

description: PAX3-FOXO1+ ARMS

source_name: rhabdomyosarcoma


title: C1-101-F9


title: RMS247

description: PAX3-FOXO1+ ARMS


title: C1-101-H8


title: RMS246

description: PAX3-FOXO1+ ARMS


title: C1-101-F6


title: C1-101-G12


title: RMS244

description: PAX7-FOXO1+ ARMS


title: C1-101-F8


title: C1-101-F4


title: C1-101-G10


title: C1-101-F5


title: C1-101-F3


title: RMS240

description: Fusion Negative RMS


title: C1-101-F2


title: RMS242

description: Fusion Negative RMS


title: C1-101-F1


title: RMS239

description: Fusion Negative RMS


title: C1-101-F11


title: C1-101-E9


title: C1-101-G2


title: RMS235

description: PAX3-NCOA1+ ARMS


title: C1-101-E8


title: RMS232

description: PAX3-FOXO1+ ARMS


title: RMS231

description: Fusion Negative RMS


title: C1-101-E6


title: C1-101-E5


title: RMS230

description: Fusion Negative RMS


title: C1-101-E3


title: C1-101-E4


title: C1-101-E2


title: RMS226

description: Fusion Negative RMS


title: RMS225

description: PAX3-FOXO1+ ARMS


title: C1-101-E12


title: RMS238

description: PAX3-FOXO1+ ARMS


title: RMS227

description: PAX3-FOXO1+ ARMS


title: C1-101-D9


title: RMS224

description: PAX3-FOXO1+ ARMS


title: C1-101-D8


title: RMS223

description: Fusion Negative RMS


title: RMS222

description: Fusion Negative RMS


title: C1-101-D7


title: RMS217

description: Fusion Negative RMS


title: C1-101-D6


title: C1-101-E1


title: RMS216

description: Fusion Negative RMS


title: C1-101-D5


title: C1-101-D3


title: RMS214

description: Fusion Negative RMS


title: RMS2114

description: PAX3-FOXO1+ ARMS


title: C1-101-D2


title: RMS2111

description: Fusion Negative RMS


title: RMS2110

description: Fusion Negative RMS


title: C1-101-D12


title: C1-98-G2


title: C1-101-D1


title: C1-101-D10


title: RMS2107

description: Fusion Negative RMS


title: C1-101-C9


title: parenchymal fibroblasts t05_3278_p4

type: genomic

city: nottingham

first: Rachel

last: Clifford

address: Biodiscovery Institute 3

country: United Kingdom

institute: University of Nottingham

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: fun2norm normalized average beta

label: Cy5 and Cy3

source_name: Parenchymal Fibroblasts

label_protocol: Standard Illumina Protocol

growth_protocol: Grown to confluence, serum starved or 24 hours and then collected

extract_protocol: Qiagen AllPrep kit

treatment_protocol: Basal

value: Parenchymal Fibroblasts

tag: passage

tag: disease

value: Healthy

tag: smoker

value: Ex

tag: pack years

tag: Sex

value: F


title: parenchymal fibroblasts T05_12043_P4

tag: age


title: parenchymal fibroblasts t04_10167_p4

value: COPD

tag: gold stage

value: M


title: parenchymal fibroblasts t05_547_p4


title: parenchymal fibroblasts T04_2664_P4_F


title: parenchymal fibroblasts t03_4827_p4


title: C1-101-C8

tag: strain

tag: tissue

value: dMGE

value: Brain


title: RMS2105

description: PAX3-FOXO1+ ARMS

value: tumor


title: parenchymal fibroblasts T03_3445_P4


title: parenchymal fibroblasts T00_4758_P4


title: parenchymal fibroblasts T032423_P4


title: RMS210

description: PAX7-FOXO1+ ARMS


title: C1-101-C4


title: RMS208

description: Fusion Negative RMS


title: parenchymal fibroblasts L30


title: C1-101-C6


title: parenchymal fibroblasts L8


title: parenchymal fibroblasts L26


title: RMS209

description: PAX3-FOXO1+ ARMS


title: RMS2078

description: Fusion Negative RMS


title: parenchymal fibroblasts L29


title: C1-101-C5


title: C1-101-C3


title: RMS2080

description: Fusion Negative RMS


title: parenchymal fibroblasts t05_7920_p4


title: parenchymal fibroblasts L6


title: parenchymal fibroblasts L22

value: Current


title: RMS211

description: Fusion Negative RMS


title: RMS206

description: Fusion Negative RMS


title: parenchymal fibroblasts L25


title: C1-101-C2


title: C1-101-C11


title: parenchymal fibroblasts L23L

value: Non


title: EZH2-F145L rescue H3K27me3 ChIP

city: Washington

first: Jia-Ray

last: Yu

state: DC

address: 7144 13th Pl Nw

institute: FBRI at Virginia Tech Carilion

description: E14-EZH2KO-F145L - H3K27me3-ChIP

data_processing:
ChIP-seq reads were mapped to mm9 genome using Bowtie2 (Ver 2.3.0). All reads that failed to be mapped to mm9 were mapped to the fly genome dm6
The sum of the number of reads mapped to both genomes was used as the actual “library size”. The median of the library sizes across all the samples was used as the reference library size, which is about 20,000,000 reads. All samples were scaled to obtain the new library size equal to the reference library size.
The input samples were normalized to the same total reference library size as the ChIP samples. After adjustment of the total library size, the number of reads mapped to the fly genome was used as the spike-in normalization factor.
All samples were then scaled except for input samples in order to have the same total spike-in content. To obtain EZH2 binding sites, only reads with mapping quality greater than 30 were selected and removed as presumptive PCR duplicates with the same mapped coordinates.
MACS2 software package was used (version 2.1.1) for calling significantly enriched peaks at a false discovery rate (FDR) less than 5% relative to the input samples. For H3K27me3 samples, SICER software package was used (version 1.1) to find broad peaks by setting the window size of 500 bp and allowing peaks within a distance of 500 bp to merge together. The significantly enriched peaks were filtered with the same criteria as above, FDR < 0.05.
Genome_build: mm9; dm6 (reference)
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage

source_name: ATCC CRL-2821

growth_protocol: ES cells grown in ATCC-defined ESC medium with 1:10 dilution during subculture every other day.

extract_protocol:
Chromatin was fomaldehyde crosslinked and prepared using standard ChIP procedure
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: chip antibody

tag: background strain

value: E14 mESC

tag: developmental stage

value: embryonic day 14

tag: genotype


title: C1-101-C10


title: RMS205

description: Fusion Negative RMS


title: C1-101-C12


title: RMS2046

description: PAX3-INO80D+ ARMS


title: C1-101-B9


title: RMS202

description: Fusion Negative RMS


title: EZH2-P132S rescue H3K27me3 ChIP

description: E14-EZH2KO-P132S - H3K27me3-ChIP

tag: cell line


title: EZH2-WT rescue H3K27me3 ChIP

description: E14-EZH2KO-WT - H3K27me3-ChIP


title: RMS2015

description: Fusion Negative RMS


title: C1-101-B8


title: C1-101-B6


title: EZH2-KO empty vector H3K27me3 ChIP

description: E14-EZH2KO-EV - H3K27me3-ChIP


title: parenchymal fibroblasts L21

tag: cell type


title: parenchymal fibroblasts L18


title: parenchymal fibroblasts L17


title: parenchymal fibroblasts L2


title: C1-101-B4


title: parenchymal fibroblasts L15


title: EZH2 knockout H3K27me3 ChIP

description: E14-EZH2KO - H3K27me3-ChIP


title: C1-101-B3


title: C1-101-B2


title: WT H3K27me3 ChIP

description: E14 - H3K27me3-ChIP

value: wild type


title: EZH2-F145L rescue EZH2 ChIP

description: E14-EZH2KO-F145L - EZH2-ChIP


title: EZH2-P132S rescue EZH2 ChIP

description: E14-EZH2KO-P132S - EZH2-ChIP


title: C1-101-B11


title: C1-101-B10


title: EZH2-KO empty vector EZH2 ChIP

description: E14-EZH2KO-EV - EZH2-ChIP


title: EZH2 knockout EZH2 ChIP

description: E14-EZH2KO - EZH2-ChIP


title: parenchymal fibroblasts L16


title: parenchymal fibroblasts L13


title: C1-101-A7


title: C1-101-A9


title: parenchymal fibroblasts L12


title: parenchymal fibroblasts L11


title: C1-101-A8


title: C1-101-B12


title: parenchymal fibroblasts L14


title: parenchymal fibroblasts HAM020_lg


title: WT EZH2 ChIP

description: E14 - EZH2-ChIP


title: parenchymal fibroblasts L1


title: C1-101-A6


title: C1-101-A4


title: C1-101-A5


title: parenchymal fibroblasts ham014_p4


title: parenchymal fibroblasts ham007_p4


title: parenchymal fibroblasts ham006_p4_29_1


title: arr-13-047 Blood

city: Wuerzburg

first: Barbara

last: Vona

state: Bavaria

address: Biozentrum, Am Hubland

department: Institute of Human Genetics

country: Germany

institute: University of Wuerzburg

description: Genomic DNA extracted from whole blood was genotyped using Infinium Omni1-Quad Genotyping BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChip arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Te-Flow Flow-Through Chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader and iScan System (Illumina).

data_processing: Genomic DNA extracted from whole blood was genotyped using Infinium HumanOmni1-Quad BeadChips (Illumina).

source_name: Blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using multi-sample amplification mix 1 and 2 (MA1 and MA2) and multi-sample amplification master mix (WG-MSM). After incubation the amplified DNA was fragmented with fragmentation solution (WG-FMS), precipitated with isopropanol and precipitation solution (PM1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from fresh whole blood was performed using a standard salt extraction.

value: Female

tag: status

value: Affected


title: arr-13-048 Blood

value: Male


title: C1-101-A10


title: parenchymal fibroblasts ham006_p4

value: Parenchymal Fibroblasts


title: Dnmt2-/- normal diet sperm rep2

city: Riverside

first: Junchao

last: Shi

address: 900 University Ave

department: Division of Biomedical Sciences, School of Medicine

institute: University of California, Riverside

data_processing:
For each RNA library, more Than 10 million reads (raw data) were generated by Illumina Hi-Seq 2000. Sequence reads that fit any of the following parameters were removed with following standard quality control criteria: 1) The reads with N; more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score is lower than 13. 2) The reads with 5’ primer contaminants or without 3’ primer. 3) The reads without the insert tag. 4) The reads with ploy A. 5) The reads shorter than 18nt. The clean reads were obtained after data filtration.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include reads length, reads counts and reads sequence.

source_name: Mouse mature sperm

growth_protocol: All animal experiments obey the rules and guidelines of the local animal ethical committee and the Institutional Animal Care and Use Committee of the Institute of Zoology, Chinese Academy of Sciences. For experiments performed, 6 weeks old male C57BL/6NCrl mice were purchased from Charles River Laboratories China Inc. Dnmt2 homozygote knock out mice was imported from The Jackson Laboratory (Dnmt2 KO, B6;129-Dnmt2tm1Bes/J) and was backcrossed for more than five generations onto the C57BL/6NCrl genetic background (Charles River Laboratories China Inc) before we start the experiments. These male mice with the genotypes of Dnmt2+/+ and Dnmt2-/- were housed in cages at a temperature of 22-24 °C and randomly divided into two diet groups of each genotype, one group receiving a high-fat diet (HFD, D12492; Research Diets Inc., New Brunswick, NJ) and the other group received a normal diet (Diet 1415, BEIJING HFK BIOSCIENCE CO.,LTD).

extract_protocol:
Sperm total RNAs are extracted by Trizol (Invitrogen).
Small RNA libraries were constructed according to TruSeq Small RNA Sample Pre Kit (Illumina).

treatment_protocol: Briefly, mature sperm were collected in physiological saline at 37 degrees from adult mouse cadua epididymis. Sperm suspension was then centrifuged by 600g to pellet the sperm.Briefly, mature sperm were collected in physiological saline at 37 degrees from adult mouse cauda epididymis. Sperm suspension was then centrifuged by 600g to collect sperm.

value: mature sperm

tag: genotype/variation

tag: treatment

value: normal diet


title: Dnmt2+/+ high fat diet sperm rep2

value: high fat diet


title: arr-13-046 Blood


title: parenchymal fibroblasts ham001_p4

tag: passage

tag: disease

value: Healthy

value: F


title: airway fibroblasts HAF147

source_name: Airway Fibroblasts

value: Airway Fibroblasts

tag: smoker

value: Ex

tag: pack years


title: parenchymal fibroblasts HAM011

tag: Sex

value: M

tag: age


title: Dnmt2-/- high fat diet sperm rep2

tag: strain


title: arr-13-045 Blood


title: arr-13-044 Blood


title: arr-13-043 Blood


title: arr-13-042 Blood


title: arr-13-041 Blood


title: airway fibroblasts HAF146


title: EZH2-WT rescue EZH2 ChIP

description: E14-EZH2KO-WT - EZH2-ChIP


title: arr-13-040 Blood


title: arr-13-039 Blood


title: arr-13-038 Blood


title: airway fibroblasts HAF118_R

value: COPD

tag: gold stage

value: Current


title: arr-13-037 Blood


title: airway fibroblasts HAF090


title: arr-13-036 Blood


title: airway fibroblasts HAF112


title: Dnmt2+/+ normal diet sperm rep2

tag: tissue


title: airway fibroblasts HAF074


title: arr-13-035 Blood


title: airway fibroblasts HAF084


title: airway fibroblasts HAF126


title: airway fibroblasts HAF091


title: airway fibroblasts HAF079


title: arr-13-034 Blood


title: airway fibroblasts HAF077


title: arr-13-033 Blood


title: airway fibroblasts HAF073


title: airway fibroblasts HAF068


title: airway fibroblasts HAF071


title: arr-13-032 Blood


title: Reprogramming cells induced by O(5R)SK at d7

city: Shanghai

first: BING

last: LIAO

address: 227，South Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

description: Gene expression data from cells at reprogramming day 7, induced by factor combination of OCT4 (5R), SOX2 and KLF4.

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645(Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079,Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000. Raw data was generated by Affymetrix Command Console Software 3.1.

data_processing: The data were analyzed on R system using affy package.

source_name: Cells at reprogramming day 7

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were maintained in standard complete ESC culture medium. The medium was supplemented with 15% fetal bovine serum, 1000U/ml recombinant leukemia inhibitory (Millipore), 0.1mM MEM nonessential amino acid (Gibico), 2mM Glutamax (Gibico), 1mM MEM pyruvate sodium (Gibico), 0.1% β-mercaptoethanol (Sigma).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells at the indicated time points were harvested, rinsed with PBS  and placed on ice in the Trizol solution (GibcoBRL).

value: embryonic fibroblasts

tag: protocol


title: airway fibroblasts HAF082

value: Non


title: parenchymal fibroblasts FHN029


title: arr-13-031 Blood


title: arr-13-030 Blood


title: Reprogramming cells induced by O(WT)SK at d7

description: Gene expression data from cells at reprogramming day 7, induced by factor combination of OCT4 (WT), SOX2 and KLF4.

value: O(WT)SK


title: Reprogramming cells induced by O(WT)SK at d5

description: Gene expression data from cells at reprogramming day 5, induced by factor combination of OCT4 (WT), SOX2 and KLF4.

source_name: Cells at reprogramming day 5


title: Reprogramming cells induced by O(5R)SK at d5

description: Gene expression data from cells at reprogramming day 5, induced by factor combination of OCT4 (5R), SOX2 and KLF4.


title: arr-13-029 Blood


title: parenchymal fibroblasts FHN022


title: parenchymal fibroblasts FHN068


title: C1-101-A1

value: dMGE

value: Brain


title: arr-13-026 Blood

value: Female

value: Affected


title: arr-13-027 Blood


title: parenchymal fibroblasts FHN002

value: Parenchymal Fibroblasts


title: parenchymal fibroblasts FHN003


title: parenchymal fibroblasts 4008_p4


title: parenchymal fibroblasts 7297_lg_p4


title: parenchymal fibroblasts 11691_P4


title: Reprogramming cells induced by O(5R)SK at d3

description: Gene expression data from cells at reprogramming day 3, induced by factor combination of OCT4 (5R), SOX2 and KLF4.

source_name: Cells at reprogramming day 3


title: CDX35: MGH1514-1

first: Benjamin

middle: Jacob

last: Drapkin

state: MASSACHUSETTS

address: 149 13th Street, room 7330-M

department: Cancer Center

data_processing:
Illumina NextSeq Control Software was used for basecalling
Reads were mapped to human (hg19) and mouse (mm9) genome assemblies with BBsplit and only reads mapping to the human reference model were retained for further analysis
Reads were re-mapped to hg19 using STAR and annotated transcripts (Gencode V19) were estimated with Kallisto and parameters "--fragment-length 200 --sd 20"
Gene expression was quantified by as transcripts per million (TPM) by combining TPM values of all transcript isoforms.
Genome_build: hg19
Supplementary_files_format_and_content: TPM matrix (gene expression)

source_name: NSG mouse (Nod Scid IL2-gamma)

growth_protocol: Subcutaneous PDX models were grown to ~1 cm in NSG mice, resected, diced by scalpel and snap-frozen within 5 minutes of animal euthanasia.

extract_protocol:
Total RNA from tissue was extracted using 1ml if TRIzol reagent (Life technologies) and homogenization by rotor. Hereafter, 0.2 ml Chloroform was added to allow for phase-separation by centrifugation. RNA was precipitated using isopropanol, washed with 80% Ethanol and re-suspended in nuclease-free water. DNAse treatment (Qiagen) was performed on RNA with subsequent clean-up using RNeasy mini kit (Qiagen). RNA amount and quality was assessed using Agilent 2100 Bioanalyzer.
RNA was processed into cDNA libraries by the Kapa Stranded RNA-seq kit with RiboErase HMR method and was sequenced on NextSeq 500 (18 pooled barcoded samples) for single-end 75 bp sequencing.

value: Patient Derived Xenograft

value: N

tag: resp

tag: resp rank

tag: ttp

tag: ttp rank

tag: t_dbl rank

tag: ttp/t_dbl rank


title: CDX34: MGH1543-1

value: R


title: CDX38: MGH1545-1A


title: Reprogramming cells induced by O(WT)SK at d3

description: Gene expression data from cells at reprogramming day 3, induced by factor combination of OCT4 (WT), SOX2 and KLF4.


title: arr-13-025 Blood

value: Male

tag: status


title: CDX33: MGH1522-1


title: parenchymal fibroblasts 1873_p4

tag: cell type

tag: passage


title: arr-13-028 Blood


title: arr-13-024 Blood


title: CDX32: MGH1538-1B


title: parenchymal fibroblasts 1226_p4

tag: disease

tag: smoker

value: F


title: CDX29: MGH1534-2


title: arr-13-022 Blood

tag: Sex


title: arr-13-021 Blood


title: arr-13-023 Blood


title: CDX26: MGH1514-2B


title: CDX30: MGH1534-3


title: CDX20: MGH1518-3


title: CDX28: MGH1534-1


title: arr-13-019 Blood


title: arr-13-018 Blood


title: arr-13-020 Blood


title: CDX19: MGH1518-1C


title: arr-13-017 Blood


title: CDX17: MGH1512-1B


title: CDX18: MGH1518-1B


title: CDX16: MGH1512-1A


title: subject HD274 central memory Th1 cells [methylation]

city: Gosselies

first: Martin

last: Bizet

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

hyb_protocol: genomic DNA was bisulfite-converted using an EZ DNA methylation Kit (ZYMO research). DNA methylation level was measured using the Illumina Infinium HD Methylation Assay. Bisulfite converted DNA was hybridized with the Illumina HumanMethylation450 BeadChip 450K array (12 samples/chip), as described previously. (Dedeurwaerder et al, Epigenomics 2011).

scan_protocol: Arrays were imaged using HiScan Reader using standard recommended Illumina scanner setting.

data_processing: Raw data were first filtered using a detection p-value <0.05. Cross-reactive probes (i.e. targeting several genomic locations) were filtered out using the extended annotation provided by Price et al (Epigenetics chromatin, 2013) while probes containing SNPs, which do not introduce an important confounder in intra-individual studies, were kept in the analysis (see Dedeurwaerder et al, Brief.Bioinformatics 2014 for a detailed description). β-values were computed using the following formula: β-value = M/[U+M] where M and U are the raw “methylated” and “unmethylated” signals, respectively. The β-values were corrected for type I and type II bias using the peak-based correction.32,37 The differential analyzes were applied according to the recommendations of Dedeurwaerder et al, Brief.Bioinformatics 2014 : first the methylation values were converted to M-values using the following formula: M-value = log2 (β-value/ (1 – β-value)). The statistical significance of the differential methylation was assessed using a paired t-test applied on these M-values. In parallel a delta-β  was computed as the absolute difference between the median β-values. Cytosine showing a p-value <1e-4 together with an absolute delta-β>0.1 were reported as differentially methylated.

label: Cy3 and Cy5

source_name: central memory Th1 cells

growth_protocol: direct ex-vivo analysis

extract_protocol: Total DNA was extracted using the Qiagen AllPrep DNA/RNA micro or mini kit according to the manufacturer's instructions.Nucleic acid concentration and purity was 1.81 (1.73-1.91).

treatment_protocol: Isolation of PBMC from fresh blood using Ficoll. Enrichement of target populations by negative selection using Miltenyi Automacs technology. FACS-staining and sorting by positive selection on a BD FACS Aria III sorter.

tag: subject id

tag: subject status

value: CMV-seropositive healthy adult

tag: age (yrs)

tag: gender

value: female

value: peripheral blood

value: blood lymphocytes

tag: sorted population

value: central memory Th1 cells

tag: sorted population markers


title: subject HD240 central memory Th1 cells [methylation]

tag: tissue


title: arr-13-014 Blood


title: CDX10: MGH1514-2A

tag: resp

tag: resp rank

tag: ttp


title: arr-13-013 Blood


title: arr-13-015 Blood


title: subject HD361 central memory Th1 cells [methylation]

value: male


title: LU3

city: Daegu

first: Myung-Sook

last: Choi

address: 1370, Sankyuk-Dong, Buk-gu

department: Food and Nutrition

country: South Korea

institute: Kyungpook National University

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Luteolin added high-fat dietr, rep3

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, USA) to yield biotinylated cRNA

growth_protocol: Thirty male C57BL/6J mice were obtained from the Jackson Laboratory (Bar Harbor, ME) at 4 weeks of age. All the mice were individually housed under a constant temperature (24°C) and 12-hour light/dark cycle, fed the AIN-76 semi-purified diet for a one-week acclimation period after arrival

extract_protocol: Total RNA was extracted from the adipose tissue and liver using TRIZOL reagent (Invitrogen Life Technologies, NY) according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: The mice were fed a normal diet (ND, n=10), high-fat diet consisting of 20% fat and 1% cholesterol (HFD, n=10) or HFD with 0.005% (w/w) luteolin (Sigma Chemical, MO) (LU, n=10) for 16 weeks

tag: strain

value: Mouse Epididymal adipose tissue


title: arr-13-012 Blood

tag: status


title: subject HD194 central memory Th1 cells [methylation]

tag: cell type


title: CDX08: MGH1524-1

tag: ttp rank

tag: t_dbl rank

tag: ttp/t_dbl rank


title: arr-13-011 Blood

tag: Sex


title: CDX09: MGH1525-1


title: CDX06: MGH1504-1


title: subject HD274_naive CD4 T cells [methylation]

label: Cy3, Cy5

source_name: naive CD4 T cells

tag: subject id

value: naive CD4 T cells


title: LU1

description: replicate 1

source_name: Luteolin added high-fat diet, rep1


title: arr-13-010 Blood


title: HFD3

description: replicate 3

source_name: High-fat diet, rep3


title: subject HD274_naive CD8 T cells [methylation]

source_name: naive CD8 T cells

tag: subject status

value: naive CD8 T cells


title: subject HD274_cytotoxic CD4 T cells [methylation]

source_name: cytotoxic CD4 T cells

tag: age (yrs)

value: cytotoxic CD4 T cells


title: CDX05: MGH1515-1


title: LU2

description: replicate 2

source_name: Luteolin added high-fat diet, rep2


title: subject HD189 central memory Th1 cells [methylation]

tag: gender


title: arr-13-009 Blood

value: Affected


title: Foxl1 negative rep3

city: Philadelphia

first: Michal

last: Shoshkes-Carmel

state: PA

address: 3400 Civic Center Blvd, 12-161

department: Genetics

institute: University of Pennsylvania

description:
FGC1689_s_6_GCTCATGAGTAAGGAG
2158T

data_processing:
Illumina Casava-1.8.2 software was used for basecalling.
RNA-Seq - Low quality reads as well as ribosomal and other repeat sequences were filtered out before alignment. RUM software was used for aligning reads to mouse genome mm9 and Refseq transcriptome and for transcript quantitation. Differential expression analysis was carried out using a custom script implementing EdgeR software.
Genome_build: mm9
Supplementary_files_format_and_content: Excel format file of transcript raw or FPKM read counts of each sample

source_name: Foxl1 negative

extract_protocol:
Intestine mesenchyme was dissociated to single cells by 7mg/ml DispaseII/0.05% trypsin solution 15 minutes 37℃. Cells were sorted lysed and total RNA was isolated by column purification (Absolutely RNA Nanoprep kit; Agilent Technologies)
NEB Next RNA library prep kit (New England BioLabs, Inc)

tag: strain background

value: mixed

tag: genotype

value: Foxl1Cre; Rosa-mTmG

value: intestine mesenchyme


title: HFD1

description: replicate 1

source_name: High-fat diet, rep1

tag: tissue


title: arr-13-007 Blood

source_name: Blood

value: Female


title: Foxl1 negative rep1

description:
FGC1689_s_6_TAGGCATGCTAAGCCT
2316T


title: arr-13-008 Blood


title: HFD2

description: replicate 2

source_name: High-fat diet, rep2


title: subject HD274_cytotoxic CD8 T cells [methylation]

source_name: cytotoxic CD8 T cells

tag: sorted population

value: cytotoxic CD8 T cells


title: subject HD194_cytotoxic CD4 T cells [methylation]


title: arr-13-006 Blood


title: arr-13-005 Blood

value: Male


title: subject HD189_naive CD4 T cells [methylation]

value: CMV-seropositive healthy adult


title: ND1

description: replicate 1

source_name: Normal diet, rep1


title: ND3

description: replicate 3

source_name: Normal diet, rep3


title: subject HD240_cytotoxic CD4 T cells [methylation]

value: female


title: subject HD240_naive CD8 T cells [methylation]

value: peripheral blood


title: arr-13-004 Blood


title: arr-13-003 Blood


title: subject HD189_naive CD8 T cells [methylation]

value: blood lymphocytes


title: subject HD189_cytotoxic CD4 T cells [methylation]


title: arr-13-002 Blood


title: arr-13-001 Blood


title: ND2

description: replicate 2

source_name: Normal diet, rep2


title: subject HD240_naive CD4 T cells [methylation]


title: thalamus_P-group4

city: Bunkyo-ku

first: Tomiko

last: Asakura

state: Tokyo

department: Graduate School of Agricultural and Life Sciences

institute: University of Tokyo

hyb_protocol: cRNA 15µg were flagmentated, and hybridized for 16hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained with Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were normalized using the statistical software R, and the qFARMS method.

organism: Rattus norvegicus

source_name: thalamus_Powder diet

label_protocol: Biotin-labeled cRNA was synthesized from 100ng total RNA according to the manufacture's protocol.

growth_protocol: A total of 10, three-week old male Wistar rats (CLEA Japan, Tokyo) were used, which The rats were bred in a room conditioned at 22±1℃ and 50% humidity with 12 hours-12 hours light-dark cycle. As a preparatory phase of the breeding process, the rats were provided with powdered feed and water for two days to get, ad libitum.After that, the rats were divided into two groups in a manner such that the average weight is approximately the same between the groups. One group was fed a powdered feed (powder, P), other group was fed a solid feed (chow, C) for eight days.

extract_protocol: Total RNA was extracted from the brain sample using TRIzol Reagent(Thermo Fisher Scientific) , according to the manufacture's protocol. The extracted total RNA was cleaned up with RNeasy Mini Kit (QIAGEN).

treatment_protocol: A powder diet or a chow diet.

value: Wistar

tag: age

value: 5 weeks old

tag: diet

value: Powder diet


title: subject HD189_cytotoxic CD8 T cells [methylation]


title: arr-12-084 Blood

value: Unaffected


title: thalamus_P-group5

value: male

tag: strain


title: subject HD194_naive CD8 T cells [methylation]

value: naive CD8 T cells


title: subject HD194_naive CD4 T cells [methylation]

value: naive CD4 T cells


title: Foxl1 negative rep2

description:
FGC1689_s_6_CGAGGCTGTCTCTCCG
2093T

value: mixed


title: thalamus_P-group1


title: arr-12-083 Blood

tag: status


title: subject HD361_naive CD8 T cells [methylation]

tag: cell type


title: thalamus_C-group4

source_name: thalamus_Chow diet

value: Chow diet


title: thalamus_P-group3


title: subject HD240_cytotoxic CD8 T cells [methylation]


title: arr-12-082 Blood

value: Affected


title: arr-12-081 Blood


title: arr-12-080 Blood

value: Female


title: subject HD361_cytotoxic CD8 T cells [methylation]

value: cytotoxic CD8 T cells


title: arr-12-079 Blood

value: Male


title: arr-12-078 Blood


title: arr-12-075 Blood


title: arr-12-077 Blood


title: arr-12-076 Blood


title: arr-12-074 Blood


title: arr-12-073 Blood


title: arr-12-072 Blood


title: subject HD361_cytotoxic CD4 T cells [methylation]

value: CMV-seropositive healthy adult

value: cytotoxic CD4 T cells


title: thalamus_P-group2


title: thalamus_C-group2


title: thalamus_C-group3


title: thalamus_C-group1


title: arr-12-070 Blood


title: arr-12-071 Blood


title: arr-11-118 Blood


title: arr-11-119 Blood


title: arr-11-117 Blood


title: subject HD361_naive CD4 T cells [methylation]

value: peripheral blood


title: arr-11-116 Blood


title: arr-11-114 Blood


title: arr-11-115 Blood


title: arr-11-111 Blood


title: arr-11-110 Blood


title: arr-11-112 Blood


title: arr-11-113 Blood


title: arr-11-109 Blood


title: arr-11-108 Blood


title: arr-11-066 Blood


title: arr-11-104 Blood


title: arr-11-105 Blood


title: arr-11-062 Blood


title: arr-11-061 Blood


title: arr-11-064 Blood


title: arr-11-107 Blood


title: arr-11-060 Blood


title: arr-11-059 Blood


title: arr-11-065 Blood


title: arr-11-057 Blood


title: arr-11-056 Blood


title: arr-11-106 Blood


title: arr-11-055 Blood


title: arr-11-063 Blood


title: arr-11-028 Blood


title: arr-11-026 Blood


title: arr-11-025 Blood


title: arr-11-024 Blood


title: arr-11-058 Blood


title: arr-11-022 Blood


title: arr-11-023 Blood


title: arr-11-021 Blood


title: arr-12-085 Blood


title: PCC6803_Light_1100_rep2

city: Suita

first: Kenichi

last: Ogawa

state: Osaka

address: 1-5, Yamadaoka

institute: Osaka University

description: PCC6803 cultured under Light 1100 in replicate 2

hyb_protocol: Gene Expression Hybridization kit (Agilent Technologies)

scan_protocol: Agilent G2565CA microarray scanner (Agilent Technologies), Scan control software (Agilent Technologies), and Feature extraction software (Agilent Technologies)

data_processing: The software program Matlab 2013b (The Mathworks Inc., Natick, MA) was used for data analysis. After removing signal intensities that the Feature extraction software judged unreliable, the median of the probe signal intensities representing each ORF was defined as the gene expression level. Quantile normalization [26] was applied to all data sets to allow comparison of the gene expression profiles.

organism: Synechocystis sp. PCC 6803

source_name: PCC6803, Light1100, replicate 2

label_protocol: Fairplay III microarray labeling kit (Agilent Technologies)

growth_protocol: The glucose-tolerant wild type strain of Synechocystis sp. PCC 6803 was cultivated in modified BG-11 medium. Cells were cultivated in a 1000 ml tubular photo-bioreactor with 400 ml of modiﬁed BG11 medium at 34°C with an agitation rate of 200 rpm, bubbled with 1.0 vvm of air containing 2.5% (v/v) CO2. The light source was a custom LED (CCS, ISL-R100X100-RRRB), with the light intensity of the red and blue lights being 5: 1, and the total light intensity was regulated to adjust the measurements in the center of culture tank to a predetermined value.

extract_protocol: Ambion Ribopure yeast kit (Life Technologies Co., Carlsbad, CA)

treatment_protocol: PCC 6803 was cultivated in tubular photo-bioreactor and harvested at OD730 ≈ 0.6, corresponding to the mid exponential phase. The broth was mixed with an equal volume of 10% (w/v) phenol in ethanol, and cells were collected by centrifugation. The cells were immediately frozen in liquid nitrogen and stored at -80°C.

tag: light intensity


title: PCC6803_Light_1000_rep2

description: PCC6803 cultured under Light 1000 in replicate 2

source_name: PCC6803, Light1000, replicate 2


title: PCC6803_Light_1300_rep2_for check repeatability

description: PCC6803 cultured under Light 1300 in replicate 2 to check repeatability

source_name: PCC6803, Light1300, replicate 2, for check repeatability


title: arr-11-054 Blood


title: arr-11-027 Blood


title: PCC6803_Light_1100_rep3

description: PCC6803 cultured under Light 1100 in replicate 3

source_name: PCC6803, Light1100, replicate 3


title: PCC6803_Light_30_rep3_for check repeatability

description: PCC6803 cultured under Light 30 in replicate 2 to check repeatability

source_name: PCC6803, Light30, replicate 3, for check repeatability


title: PCC6803_Light_1300_rep3

description: PCC6803 cultured under Light 1300 in replicate 3

source_name: PCC6803, Light1300, replicate 3


title: PCC6803_Light_30_rep3

description: PCC6803 cultured under Light 30 in replicate 3

source_name: PCC6803, Light30, replicate 3


title: PCC6803_Light_1000_rep3

description: PCC6803 cultured under Light 1000 in replicate 3

source_name: PCC6803, Light1000, replicate 3


title: PCC6803_Light_300_rep2

description: PCC6803 cultured under Light 300 in replicate 2

source_name: PCC6803, Light300, replicate 2


title: PCC6803_Light_50_rep3

description: PCC6803 cultured under Light 50 in replicate 3

source_name: PCC6803, Light50, replicate 3


title: arr-11-020 Blood

description: Genomic DNA extracted from whole blood was genotyped using Infinium Omni1-Quad Genotyping BeadChips (Illumina).

source_name: Blood


title: PCC6803_Light_1300_rep3_for check repeatability

source_name: PCC6803, Light1300, replicate 3, for check repeatability


title: PCC6803_Light_1300_rep2

description: PCC6803 cultured under Light 1300 in replicate 2

source_name: PCC6803, Light1300, replicate 2


title: arr-11-019 Blood


title: PCC6803_Light_300_rep3

description: PCC6803 cultured under Light 300 in replicate 3

source_name: PCC6803, Light300, replicate 3


title: PCC6803_Light_30_rep2_for check repeatability

source_name: PCC6803, Light30, replicate 2, for check repeatability


title: arr-11-018 Blood


title: arr-11-017 Blood


title: PCC6803_Light_30_rep2

description: PCC6803 cultured under Light 30 in replicate 2

source_name: PCC6803, Light30, replicate 2


title: arr-11-016 Blood


title: arr-11-015 Blood


title: PCC6803_Light_1300_rep1

description: PCC6803 cultured under Light 1300 in replicate 1

source_name: PCC6803, Light1300, replicate 1


title: PCC6803_Light_1000_rep1

description: PCC6803 cultured under Light 1000 in replicate 1

source_name: PCC6803, Light1000, replicate 1


title: arr-11-013 Blood


title: arr-11-014 Blood


title: PCC6803_Light_50_rep2

description: PCC6803 cultured under Light 50 in replicate 2

source_name: PCC6803, Light50, replicate 2


title: PCC6803_Light_300_rep1

description: PCC6803 cultured under Light 300 in replicate 1

source_name: PCC6803, Light300, replicate 1


title: ChIP-seq of Mus musculus: Th2 WT Input

status: Public on Mar 05 2018

city: Bethesda

first: Andrew

middle: J

last: Oler

state: MD

address: 31 Center Drive, Room 3B62E

department: Bioinformatics and Computational Biosciences Branch (BCBB)

institute: NIAID/NIH

data_processing:
Basecalls performed using CASAVA 2.18
RNA-seq reads were mapped to mm10 using TopHat2 v2.0.13 using setting --bowtie-n.
ChIP-seq reads were mapped to mm10 using novoalign (Novocraft), V3.03.00 with adapter trimming (-a option).
Gene expression from RNA-Seq was quantified by RPKM (Mortazavi et al., 2008) with an in-house script based on RefSeq gene annotation.
To identify GATA3- or Bcl11b-binding peaks genome wide from the ChIP-Seq experiments, we used MACS v.1.4.2 (Zhang et al., 2008) with setting keep-dup=1 to call peaks using Input as control.  Peaks were also called in Input sample alone with setting keep-dup=auto.  Peaks were assigned to genes using FindNeighboringGenes (USeq, v.8.8.8; Nix et al., BMC Bioinformatics 2008)
Genome_build: mm10
Supplementary_files_format_and_content: *.rpkm.gz: zipped text file for gene expression. Columns from left to right denote RefSeq ID, RPKM, gene transcript size, number of read mapped to exons, a combination of RefSeq ID, gene symbol, etc, and reserved column for future development.  bed: Columns from left to right are chromosome, start position, end position, peak name,
Supplementary_files_format_and_content: *.xls: chromosome, start of peak, end of peak, name, length, summit, tags, -10*log10(pvalue), fold_enrichment, chromsome, start of peak, stop of peak, name/rank, distance from transcription start site to middle of peak, gene symbol, Refseq id, geneChromosome, geneStart, geneStop, geneStrand, trxnStart

source_name: Late Th2

extract_protocol:
ChIP-Seq experiments were performed following iDeal ChIP-seq Kit for Transcription Factors Kit (C01010055, Diagenode).
ChIP-Seq experiments were performed following iDeal ChIP-seq Kit for Transcription Factors Kit (C01010055, Diagenode) using anti-Bcl11b and anti-GATA3. ChIP DNA was blunt-ended, ligated to the Solexa adaptors, amplified, and sequenced with Illumina HiSeq system.

tag: genotype/variation

value: Th2 WT

tag: chip antibody


title: Hepatocellular carcinoma SMMC-7721 cells_si-PRMT5-2

status: Public on Mar 11 2018

first: Shengli

last: Li

address: 650 Xinsongjiang Road

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR
HTseq-count was used to calculate read counts for each gene and lncRNA and then counts were normalized into FPKM.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Hepatocyte

growth_protocol: Cells were cultured at 37°C in a humidified incubator with 5% CO2 in Dulbecco’s modified Eagle’s medium supplemented with 10% foetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/ml streptomycin, and 8mg/L antibiotic Tylosin tartrate against mycoplasma.

extract_protocol:
Total RNA of cells was harvested using Trizol reagent. NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (Cat#E7420L) was used with 3 ug of total RNA for the construction of sequencing libraries. RNA-seq libraries were prepared using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (Cat#E7420L) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using RNAseq protocols

treatment_protocol: Treated the cells with small interference RNA (siRNA) oligonucleotides which include si-Negative control-LINC01138, si-LINC01138-1, si-LINC01138-2, si-Negative control-PRMT5, si-PRMT5-1, si-PRMT5-2. Transfections of siRNA (75 nM) were performed with Lipofectamine 2000.

value: liver

tag: cell line

value: human liver cancer


title: PCC6803_Light_30_rep1

description: PCC6803 cultured under Light 30 in replicate 1

source_name: PCC6803, Light30, replicate 1


title: RNA-seq of Mus musculus: Th2 Late Gata3 KO Rep 1

extract_protocol:
RNA was extracted with the RNAeasy Mini Kit (QIAGEN, 74104).
10 ng RNA was amplified with the Ovation RNA-Seq System V2 (7102-08, NuGEN) per manufacture’s instruction. 220 ng double stranded DNA was sonicated into 200–400 bp using Diagenode Bioruptor. cDNA was blunt-ended, ligated to Illumina adaptors, amplified, and sequenced with Illumina HiSeq system.

value: Th2 Late Gata3 KO


title: ChIP-seq of Mus musculus: Th2 WT Gata3

value: anti-GATA3 (L50-823) from BD Biosciences


title: PCC6803_Light_50_rep1

description: PCC6803 cultured under Light 50 in replicate 1

source_name: PCC6803, Light50, replicate 1


title: RNA-seq of Mus musculus: Th2 Late Gata3 WT Rep 2

value: Th2 Late Gata3 WT


title: RNA-seq of Mus musculus: Th2 Late Gata3 KO Rep 2


title: ChIP-seq of Mus musculus: Th2 WT Bcl11b

value: anti-Bcl11b (A300-385A-2) from Bethyl


title: RNA-seq of Mus musculus: Th2 Early Gata3 KO Rep 2

source_name: Early Th2

value: Th2 Early Gata3 KO


title: RNA-seq of Mus musculus: Th2 Late Gata3 WT Rep 1


title: RNA-seq of Mus musculus: Th2 Late Bcl11b KO Rep 1

value: Th2 Late Bcl11b KO


title: RNA-seq of Mus musculus: Th2 Late Bcl11b KO Rep 2


title: RNA-seq of Mus musculus: Th2 Early Gata3 WT Rep 2

value: Th2 Early Gata3 WT


title: RNA-seq of Mus musculus: Th2 Early Bcl11b KO Rep 2

value: Th2 Early Bcl11b KO


title: RNA-seq of Mus musculus: Th2 Early Gata3 WT Rep 1


title: RNA-seq of Mus musculus: Th2 Early Gata3 KO Rep 1


title: RNA-seq of Mus musculus: Th2 Late Bcl11b WT Rep 1

value: Th2 Late Bcl11b WT


title: RNA-seq of Mus musculus: Th2 Early Bcl11b KO Rep 1


title: PCC6803_Light_1100_rep1

description: PCC6803 cultured under Light 1100 in replicate 1

source_name: PCC6803, Light1100, replicate 1


title: RNA-seq of Mus musculus: Th2 Early Bcl11b WT Rep 1

value: Th2 Early Bcl11b WT


title: RNA-seq of Mus musculus: Th2 Early Bcl11b WT Rep 2


title: RNA-seq of Mus musculus: Th2 Late Bcl11b WT Rep 2


title: colon_1662_LibRep_B_SeqRep_A

city: Huntsville

first: Brian

middle: Scott

last: Roberts

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

data_processing:
Fastqs from multiple lanes of the same flowcell were merged with zcat.
Reads were adaptor trimmed for both 5' adaptors (4 separate) and 3' adaptors.  See script "adaptor_trim_example.sh" for help (raw files provided are not trimmed, in accordance with GEO guidelines).
Trimmed reads were aligned to hg19 reference using bowtie2-2.1.0 keeping only perfect alignments.  Reads aligning to mutliple locii were assigned to each locii proportionally to the total number of reads.  Reads were filtered to keep only features with counts in at least 10 samples, and with a count average of at least 1.
Reads as processed above were read into R and sequencing replicates and library replicates were summed.  Reads were normalized and regression analysis were performed with the R package DESeq2.
Classifiers were constructed from normalized reads via LASSO regression using the R package glmnet.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text and Excel files

source_name: blood plasma

extract_protocol:
RNA was isolated from 1 mL of plasma using the Plasma/Serum Circulating and Exosomal RNA Purification Kit (Slurry Format) from Norgen Biotek using manufacturer's protocols.
Libraries were constructed exactly as detailed in "Blocking of targeted microRNAs from next-generation sequencing libraries", Roberts et al, PMID:26209131

treatment_protocol: Blood was drawn from patients prior to undergoing colonoscopy. Plasma was isolated within 30 min using standard centrifugation protocol.

tag: Sex

value: F

tag: self-identified ancestry

value: C

tag: finding

tag: patient id

tag: library id

tag: library replicate

value: B

tag: sequencing replicate

value: A

tag: library bath id


title: colon_1628_LibRep_B_SeqRep_A

value: M

tag: age


title: colon_1634_LibRep_B_SeqRep_A

value: adenoma


title: colon_1559_LibRep_B_SeqRep_A


title: colon_1639_LibRep_A_SeqRep_A


title: colon_1678_LibRep_A_SeqRep_A


title: colon_1590_LibRep_A_SeqRep_A

value: AA


title: colon_1590_LibRep_B_SeqRep_A


title: colon_1634_LibRep_A_SeqRep_A


title: colon_1639_LibRep_B_SeqRep_A


title: colon_1662_LibRep_A_SeqRep_A


title: colon_1559_LibRep_A_SeqRep_A


title: colon_1628_LibRep_A_SeqRep_A


title: colon_1551_LibRep_A_SeqRep_A


title: colon_1691_LibRep_B_SeqRep_B


title: colon_1670_LibRep_B_SeqRep_B


title: Neural Tube part3, biological rep1

city: Boston

first: Jerome

last: Chal

address: 77 ave Louis Pasteur

institute: Brigham and Women's Hospital

description: Gene expression data from mouse E9.5 posterior neural tube

hyb_protocol: Following fragmentation, cRNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse Genome arrays. Each microarray was then washed and stained on a GeneChip® fluidics station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G. Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 3.1.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0)

source_name: Mouse embryo NT at stage E9.5

label_protocol: Biotinylated cRNA targets were prepared from total RNA using a double amplification protocol according to the GeneChip® Expression Analysis Technical Manual: Two-Cycle Target Labeling Assay (P/N 701021 Rev.5, Affymetrix, Santa Clara, USA).

extract_protocol: Total RNA was extracted from PSC populations using Trizol (Invitrogen) or with the RNAeasy plus mini-kit (Qiagen).

treatment_protocol: CD1 mouse embryos (9.5 days post-coitus [dpc]) were dissected in cold PBS prepared in RNAse-free conditions. Embryo is treated by Pancreatin (2mg/ml) at 1 min. The PSM and Neural tube were dissected using tungsten needles to remove the surrounding structures (e.g., the ectoderm, endoderm and lateral plate), then dissected NT  Neural tube were divided into 6 pieces, finally stored in Trizol (Invitrogen) at -80C for RNA extraction.

tag: dissected section

tag: Stage

value: Neural Tube

tag: developmental stage

tag: treatment


title: colon_1678_LibRep_B_SeqRep_A


title: colon_1551_LibRep_B_SeqRep_A


title: Neural Tube part6, biological rep2

tag: strain


title: Neural Tube part2, biological rep2


title: Neural Tube part4, biological rep1


title: Neural Tube part1, biological rep2


title: Neural Tube part4, biological rep2


title: Neural Tube part3, biological rep2


title: Neural Tube part2, biological rep1


title: colon_1669_LibRep_B_SeqRep_B


title: Neural Tube part6, biological rep1


title: Neural Tube part5, biological rep2


title: Neural Tube part5, biological rep1


title: colon_1613_LibRep_B_SeqRep_B


title: colon_1611_LibRep_B_SeqRep_B


title: colon_1608_LibRep_B_SeqRep_B


title: colon_1599_LibRep_B_SeqRep_B


title: Neural Tube part1, biological rep1


title: colon_1648_LibRep_B_SeqRep_B


title: colon_1592_LibRep_B_SeqRep_B


title: colon_1500_LibRep_B_SeqRep_B


title: colon_1498_LibRep_B_SeqRep_B


title: colon_1546_LibRep_B_SeqRep_B


title: colon_1538_LibRep_B_SeqRep_B


title: colon_1444_LibRep_B_SeqRep_B


title: colon_1542_LibRep_B_SeqRep_B


title: colon_1408_LibRep_B_SeqRep_B


title: colon_1432_LibRep_B_SeqRep_B


title: colon_1405_LibRep_B_SeqRep_B


title: colon_1550_LibRep_B_SeqRep_B


title: colon_1400_LibRep_B_SeqRep_B


title: colon_1397_LibRep_B_SeqRep_B


title: colon_1391_LibRep_B_SeqRep_B


title: colon_1398_LibRep_B_SeqRep_B


title: colon_1383_LibRep_B_SeqRep_B


title: colon_1257_LibRep_B_SeqRep_B


title: colon_1281_LibRep_B_SeqRep_B


title: colon_1691_LibRep_A_SeqRep_B


title: colon_1252_LibRep_B_SeqRep_B


title: colon_1095_LibRep_B_SeqRep_B


title: colon_1292_LibRep_B_SeqRep_B


title: colon_1648_LibRep_A_SeqRep_B


title: colon_1660_LibRep_A_SeqRep_B


title: colon_1630_LibRep_A_SeqRep_B


title: colon_1433_LibRep_B_SeqRep_B


title: colon_1613_LibRep_A_SeqRep_B


title: colon_1599_LibRep_A_SeqRep_B


title: colon_1608_LibRep_A_SeqRep_B


title: colon_1414_LibRep_A_SeqRep_B


title: colon_1550_LibRep_A_SeqRep_B


title: colon_1592_LibRep_A_SeqRep_B


title: colon_1313_LibRep_B_SeqRep_C


title: colon_1611_LibRep_A_SeqRep_B


title: colon_1546_LibRep_A_SeqRep_B


title: colon_1225_LibRep_B_SeqRep_B


title: colon_1215_LibRep_B_SeqRep_C


title: colon_1210_LibRep_B_SeqRep_C


title: colon_1344_LibRep_B_SeqRep_B


title: colon_1414_LibRep_A_SeqRep_A


title: colon_1507_LibRep_C_SeqRep_A


title: colon_1669_LibRep_A_SeqRep_B


title: colon_1670_LibRep_B_SeqRep_A


title: colon_1669_LibRep_B_SeqRep_A


title: colon_1691_LibRep_B_SeqRep_A


title: colon_1648_LibRep_B_SeqRep_A


title: colon_1613_LibRep_B_SeqRep_A


title: colon_1382_LibRep_B_SeqRep_B


title: colon_1630_LibRep_B_SeqRep_A


title: colon_1599_LibRep_B_SeqRep_A


title: colon_1608_LibRep_B_SeqRep_A


title: colon_1550_LibRep_B_SeqRep_A


title: colon_1500_LibRep_B_SeqRep_A


title: colon_1546_LibRep_B_SeqRep_A


title: colon_1444_LibRep_B_SeqRep_A


title: colon_1538_LibRep_B_SeqRep_A


title: colon_1542_LibRep_B_SeqRep_A


title: colon_1611_LibRep_B_SeqRep_A


title: colon_1432_LibRep_B_SeqRep_A


title: colon_1405_LibRep_B_SeqRep_A


title: colon_1400_LibRep_B_SeqRep_A


title: colon_1408_LibRep_B_SeqRep_A


title: colon_1398_LibRep_B_SeqRep_A


title: colon_1397_LibRep_B_SeqRep_A


title: colon_1391_LibRep_B_SeqRep_A


title: colon_1498_LibRep_B_SeqRep_A


title: colon_1385_LibRep_B_SeqRep_A

value: ASIAN


title: colon_1344_LibRep_B_SeqRep_A


title: colon_1383_LibRep_B_SeqRep_A


title: colon_1592_LibRep_B_SeqRep_A


title: colon_1382_LibRep_B_SeqRep_A


title: colon_1313_LibRep_B_SeqRep_B


title: colon_1292_LibRep_B_SeqRep_A


title: colon_1257_LibRep_B_SeqRep_A


title: colon_1225_LibRep_B_SeqRep_A


title: colon_1281_LibRep_B_SeqRep_A


title: colon_1491_LibRep_B_SeqRep_A


title: colon_1210_LibRep_B_SeqRep_B


title: colon_1252_LibRep_B_SeqRep_A


title: colon_1095_LibRep_B_SeqRep_A


title: colon_1433_LibRep_B_SeqRep_A


title: colon_1691_LibRep_A_SeqRep_A


title: colon_1648_LibRep_A_SeqRep_A


title: colon_1630_LibRep_A_SeqRep_A


title: colon_1669_LibRep_A_SeqRep_A


title: colon_1660_LibRep_A_SeqRep_A


title: colon_1613_LibRep_A_SeqRep_A


title: colon_1611_LibRep_A_SeqRep_A


title: colon_1599_LibRep_A_SeqRep_A


title: colon_1546_LibRep_A_SeqRep_A


title: colon_1550_LibRep_A_SeqRep_A


title: colon_1608_LibRep_A_SeqRep_A


title: colon_1151_LibRep_A_SeqRep_B


title: colon_1032_LibRep_B_SeqRep_C


title: colon_1403_LibRep_B_SeqRep_D

value: D


title: colon_1352_LibRep_A_SeqRep_B


title: colon_1346_LibRep_B_SeqRep_C


title: colon_1370_LibRep_B_SeqRep_C


title: colon_1356_LibRep_A_SeqRep_B


title: colon_1346_LibRep_A_SeqRep_B


title: colon_1186_LibRep_A_SeqRep_C


title: colon_1215_LibRep_B_SeqRep_B


title: colon_1191_LibRep_B_SeqRep_C


title: colon_1113_LibRep_B_SeqRep_C


title: colon_1167_LibRep_B_SeqRep_C


title: colon_1057_LibRep_B_SeqRep_B


title: colon_1386_LibRep_B_SeqRep_C


title: colon_1146_LibRep_A_SeqRep_C


title: colon_1196_LibRep_A_SeqRep_C


title: colon_1149_LibRep_A_SeqRep_C


title: colon_1356_LibRep_B_SeqRep_C


title: colon_1168_LibRep_B_SeqRep_C


title: colon_1091_LibRep_B_SeqRep_C


title: colon_1247_LibRep_B_SeqRep_C


title: colon_1332_LibRep_B_SeqRep_F


title: colon_1308_LibRep_B_SeqRep_C


title: colon_1345_LibRep_B_SeqRep_C


title: colon_1592_LibRep_A_SeqRep_A


title: colon_1196_LibRep_B_SeqRep_C


title: colon_1207_LibRep_B_SeqRep_C


title: colon_1286_LibRep_A_SeqRep_C


title: colon_1156_LibRep_A_SeqRep_C


title: colon_1113_LibRep_A_SeqRep_C


title: colon_1530_LibRep_A_SeqRep_C


title: colon_1119_LibRep_C_SeqRep_B


title: colon_1265_LibRep_C_SeqRep_B


title: colon_1219_LibRep_A_SeqRep_C


title: colon_1404_LibRep_C_SeqRep_B


title: colon_1279_LibRep_B_SeqRep_C


title: colon_1143_LibRep_A_SeqRep_C


title: colon_1057_LibRep_C_SeqRep_B


title: colon_1381_LibRep_A_SeqRep_C


title: colon_1082_LibRep_C_SeqRep_B


title: colon_1482_LibRep_B_SeqRep_B


title: colon_1389_LibRep_B_SeqRep_B


title: colon_1390_LibRep_B_SeqRep_B


title: colon_1379_LibRep_B_SeqRep_B


title: colon_1386_LibRep_B_SeqRep_B


title: colon_1523_LibRep_A_SeqRep_C


title: colon_1352_LibRep_B_SeqRep_B


title: colon_1348_LibRep_B_SeqRep_B


title: colon_1345_LibRep_B_SeqRep_B


title: colon_1308_LibRep_B_SeqRep_B


title: colon_1346_LibRep_B_SeqRep_B


title: colon_1291_LibRep_B_SeqRep_B


title: colon_1283_LibRep_B_SeqRep_B


title: colon_1219_LibRep_B_SeqRep_B


title: colon_1218_LibRep_B_SeqRep_B


title: colon_1207_LibRep_B_SeqRep_B


title: colon_1168_LibRep_B_SeqRep_B


title: colon_1186_LibRep_B_SeqRep_B


title: colon_1191_LibRep_B_SeqRep_B


title: colon_1159_LibRep_B_SeqRep_B


title: colon_1003_LibRep_C_SeqRep_B


title: colon_1154_LibRep_B_SeqRep_B


title: colon_1381_LibRep_B_SeqRep_B


title: colon_1146_LibRep_B_SeqRep_B


title: colon_1356_LibRep_B_SeqRep_B


title: colon_1370_LibRep_B_SeqRep_B


title: colon_1032_LibRep_B_SeqRep_B


title: colon_1542_LibRep_A_SeqRep_B


title: colon_1088_LibRep_B_SeqRep_B


title: colon_1670_LibRep_A_SeqRep_B


title: colon_1538_LibRep_A_SeqRep_B


title: colon_1444_LibRep_A_SeqRep_B


title: colon_1344_LibRep_A_SeqRep_B


title: colon_1302_LibRep_A_SeqRep_B


title: colon_1292_LibRep_A_SeqRep_B


title: colon_1252_LibRep_A_SeqRep_B


title: colon_1281_LibRep_A_SeqRep_B


title: colon_1225_LibRep_A_SeqRep_B


title: colon_1156_LibRep_B_SeqRep_B


title: colon_1265_LibRep_C_SeqRep_A


title: colon_1404_LibRep_C_SeqRep_A


title: colon_1182_LibRep_B_SeqRep_B


title: colon_1198_LibRep_B_SeqRep_B


title: colon_1135_LibRep_C_SeqRep_A


title: colon_1119_LibRep_C_SeqRep_A


title: colon_1003_LibRep_C_SeqRep_A


title: colon_1390_LibRep_B_SeqRep_A


title: colon_1386_LibRep_B_SeqRep_A


title: colon_1389_LibRep_B_SeqRep_A


title: colon_1082_LibRep_C_SeqRep_A


title: colon_1381_LibRep_B_SeqRep_A


title: colon_1057_LibRep_C_SeqRep_A


title: colon_1482_LibRep_B_SeqRep_A


title: colon_1348_LibRep_B_SeqRep_A


title: colon_1346_LibRep_B_SeqRep_A


title: colon_1356_LibRep_B_SeqRep_A


title: colon_1370_LibRep_B_SeqRep_A


title: colon_1352_LibRep_B_SeqRep_A


title: colon_1345_LibRep_B_SeqRep_A


title: colon_1379_LibRep_B_SeqRep_A


title: colon_1283_LibRep_B_SeqRep_A


title: colon_1219_LibRep_B_SeqRep_A


title: colon_1218_LibRep_B_SeqRep_A


title: colon_1308_LibRep_B_SeqRep_A


title: colon_1207_LibRep_B_SeqRep_A


title: colon_1186_LibRep_B_SeqRep_A


title: colon_1182_LibRep_B_SeqRep_A


title: colon_1168_LibRep_B_SeqRep_A


title: colon_1159_LibRep_B_SeqRep_A


title: colon_1198_LibRep_B_SeqRep_A


title: colon_1156_LibRep_B_SeqRep_A


title: colon_1154_LibRep_B_SeqRep_A


title: colon_1146_LibRep_B_SeqRep_A


title: colon_1088_LibRep_B_SeqRep_A


title: colon_1670_LibRep_A_SeqRep_A


title: colon_1032_LibRep_B_SeqRep_A


title: colon_1344_LibRep_A_SeqRep_A


title: colon_1444_LibRep_A_SeqRep_A


title: colon_1302_LibRep_A_SeqRep_A


title: colon_1542_LibRep_A_SeqRep_A


title: colon_1292_LibRep_A_SeqRep_A


title: colon_1257_LibRep_A_SeqRep_B


title: colon_1523_LibRep_B_SeqRep_B


title: colon_1530_LibRep_B_SeqRep_B


title: colon_1498_LibRep_A_SeqRep_B


title: colon_1538_LibRep_A_SeqRep_A


title: colon_1506_LibRep_A_SeqRep_B


title: colon_1291_LibRep_B_SeqRep_A


title: colon_1191_LibRep_B_SeqRep_A


title: colon_1491_LibRep_A_SeqRep_B


title: colon_1252_LibRep_A_SeqRep_A


title: colon_1225_LibRep_A_SeqRep_A


title: colon_1281_LibRep_A_SeqRep_A


title: colon_1433_LibRep_A_SeqRep_B


title: colon_1432_LibRep_A_SeqRep_B


title: colon_1405_LibRep_A_SeqRep_B


title: colon_1408_LibRep_A_SeqRep_B


title: colon_1401_LibRep_A_SeqRep_B


title: colon_1400_LibRep_A_SeqRep_B


title: colon_1398_LibRep_A_SeqRep_B


title: colon_1397_LibRep_A_SeqRep_B


title: colon_1095_LibRep_A_SeqRep_B


title: colon_1391_LibRep_A_SeqRep_B


title: colon_1385_LibRep_A_SeqRep_B


title: colon_1500_LibRep_A_SeqRep_B


title: colon_1383_LibRep_A_SeqRep_B


title: colon_1382_LibRep_A_SeqRep_B


title: colon_1374_LibRep_A_SeqRep_B


title: colon_1354_LibRep_B_SeqRep_B


title: colon_1381_LibRep_A_SeqRep_B