title: Whole plant sRNA

city: Guangzhou

first: Rui

last: Xia

state: Guangdong

address: 483 Wushan Rd, Tianhe

department: Horticulture

institute: South China Agricultural University

data_processing:
trim adaptor using fastx-toolkit
collpase reads using fastx-toolkit
map trimmed and collapsed reads to reference gene using bowtie
Supplementary_files_format_and_content: sRNAs in tag_count format

organism: Phylloglossum drummondii

source_name: Whole plant

extract_protocol:
RNA was extracted using PureLink Plant RNA Reagent.
A sRNA library was constructed using the Illumina TruSseq sRNA kit, and sequenced on the Illumina HiSeq platform at the University of Delaware.

value: Whole plant


title: 07_Pang_WGS_RN4220_0.5hPC19

status: Public on Aug 31 2017

type: SRA

city: Boston

first: Ting

last: Pang

state: MA

address: 4 Blackfan Circle

department: MBIB

country: USA

institute: Harvard Medical School

library_source: genomic

data_processing:
Library strategy: WGS-Seq
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
We mapped reads in each FASTQ file back to the genome of Staphylococcus aureus NCTC8325 genome (NCBI Reference Sequence NC_007795.1) independently using CLC genomics workbench 8.0 (Qiagen), and exported .csv file. Three prophage regions(1463618 - 1508580, 1923408 - 1967011, 2031911 - 2074632) were removed manually from samples 1-10, to match the RN4220 genome.
Genome_build: NC_007795.1
Supplementary_files_format_and_content: Files ending with .csv: comma-separated values files of ChIP-seq results. Column1 - genome position, column2 - number of reads at each genome position.

molecule: genomic DNA

organism: Staphylococcus aureus subsp. aureus NCTC 8325

growth_protocol: Cells were grown in tryptic soy broth (TSB)or LB 0.5% NaCl medium  at 37°C with aeration. For the strains harboring a Ptet-noc_his fusion, anhydrotetracycline (aTc, 100 ng/ml) was added >5 generations prior to harvest.

extract_protocol:
Whole genome sequencing was performed according to Baym et al PMID: 26000737.
Standard library construction protocol was used for Illumina Miseq (ChIP-seq). Illumina Truseq indexes were used.

treatment_protocol: Samples 7-10 were treated with 2ug/ml PC190723 at OD600 ~0.13 for 0.5h (samples 7-8) or 1.5h (samples 9-10 ) before harvesting. All cells were harvested at OD600 = 0.4.

tag: derivative strain

tag: growth condition

value: TSB, 37˚C

tag: drug treatment

tag: genotype

value: wild type RN4220


title: 08_Pang_WGS_aTP977_0.5hPC19

source_name: Staphylococcus aureus subsp. aureus NCTC 8325

value: RN4220 {delta}noc::spec


title: WT_gal_glu_3m

first: David

middle: G

last: Hendrickson

address: 725 Parsons

institute: Harvard

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.4
We aligned sequencing reads to SacCer3 assembly and the SGD transcriptome  (Harrow et al. 2012) using TopHat2  (Trapnell, Pachter, and Salzberg 2009)  with options  -p 4    --library-type fr-firststrand  and -M.
We estimated gene abundances per condition using the Cuffllinks CuffNorm option with default options
Genome_build: sacCer3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample at gene level

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: 100 mL cultures were grown in 500 mL baffled flasks overnight in YNB + 2% galactose media to log phase (OD600 between 0.230 and 0.273)

extract_protocol:
total RNA was extracted using a standard yeast RNA extraction protocol (using hot, acidic phenol); briefly, cells are resuspended in a lysis buffer and acidic phenol, then incubated at 65C for 30 minutes to dissolve the proteins/membranes and release the RNA.  Next RNA is purified using alcohol precipitation.
libraries were prepared using Illumina's Tru-seq stranded mRNA prep kit (poly-dT selection of polyA transcripts)(using Invitrogen's SuperScriptIV); fragments ranging from 200-600 bp were selected using a Pippin-HT

treatment_protocol: cultures were sampled at log phase (t=0), then glucose or fructose was added (to a final concentration of 2%) and subsequent time-points were taken

tag: genotype/variation

value: WT

tag: protocol

tag: time point

tag: strain


title: WT_gal_glu_120m


title: WT_gal_glu_10m


title: WT_gal_glu_30m


title: WT_gal_glu_15m


title: 06_Pang_WGS_aTP983_atc100

value: TSB, atc=100ng/ml,37˚C

value: RN4220 {delta}noc::spec geh::pTP069


title: WT_gal_fru_60m


title: 05_Pang_WGS_aTP983_atc0


title: d2diff ATAC cell line 2

city: Coventry

first: Andrew

middle: Christopher

last: Nelson

address: Gibbet Hill Campus

department: School of Life Sciences

country: United Kingdom

institute: University of Warwick

description:
TS cell line #2 d2 diff
d2diff_ATAC.wig.gz
d2diff_ATAC_total_peaks.bed
d2diff_ATAC_DARs.bed

data_processing:
ATAC-seq reads were mapped to mm10 using Stampy with default parameters
Read pairs with identical outer coordinates were removed to give a single unique pair.
To identify total accessible regions at each stage, peaks were called with MACS2.0.10 using default parameters and peaks common to both cell lines identified.  To identify high-confidence differentially accessible regions (DARs) MACS2 was used to call peaks between TS and d2 diff cells for each cell line using a q-value cutoff of 1e-5.  Differentially accessible regions common to both cell lines were then identified.
Genome_build: mm10
Supplementary_files_format_and_content: Wig files for visualization of ATAC-seq peaks, and BED files containing coordinates of total called peaks and differentially accessible regions (DARs) with associated scores.

organism: Mus musculus

source_name: Differentiated trophoblast stem cells

growth_protocol: Trophoblast stem cells were maintained in serum-free conditions exactly as in Kubaczka et al. 2014 (Stem Cell Reports 2:232-42) and differentiated to trophoblast giant cells by withdrawal of FGF4, TGFbeta1 and heparin sulfate.

extract_protocol:
Cells were pelleted, washed once in PBS, resuspended in lysis buffer(10mM Tris.HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% v/v Igepal CA-630) and the nuclei pelleted at 4 degrees celsius.
Transposase reaction and library preparation was then performed using the Illumina Nextera DNA Library prep kit (Cat. No. FC-121-1030) exactly as described in Buenrostro et al. 2015 (Curr. Protoc. Mol. Biol.  109:21.29.1-21.29.9) and four libraries were multiplexed per lane on a HiSeq 4000.

tag: cell type

value: Day 2 differentiated trophoblast stem cells


title: ChIP-seq H3K27Ac BmalKO KLA0h

city: Bunkyo

first: Yumiko

last: Oishi

state: Tokyo

address: 1-5-45, Yushima

department: Department of Cellular and Molecular Medicine

country: Japan

institute: Tokyo Medical and Dental University

description: formaldehyde cross-linked

data_processing:
For ChIP-Seq and RNA-Seq samples, reads were aligned to the mm9 genome using  RNA-Star. Aligned read files were analyzed with HOMER (http://homer.salk.edu/homer/) to find peaks, calculate RPKM from the gene bodies of RefSeq genes, perform motif-  and  other analyses in the study.
Genome_build: mm9

source_name: mouse BMDM

growth_protocol: Mouse thioglycollate-elicited macrophages and bone marrow-derived macrophages were isolated from male 6- to 9-weeks old C57BL/6J (Charles River laboratories) and Arntl-/- mice. Cells are cultured in RPMI-1640 medium containing 10% FCS. M-CSF (20ug/ml) was added for BMDM culture medium for 6 days.

extract_protocol:
ChIP-Seq: Sequencing libraries were prepared from collected DNA by using NEB next Ultra DNA library prep kit for Illumina. Libraries were PCR-amplified for 12-15 cycles and sequenced on a Hi-Seq 1500 (Illumina) for 51 cycles.
RNA-Seq: PolyA-tagged RNA was pulled down with oligo-dT magnetic beads from total RNA.  RNA-seq libraries were multiplexed and prepared according to the manufacturer's protocol (NEB cat#E7530, Ipswich, MA).  Libraries were paired-ended sequenced on a HiSeq 2000 sequencer (Illumina, San Diego, CA)
Reads were aligned to mm9 genome using default parameter for RNA-star.  Aligned reads read files were analyzed with HOMER (http://homer.salk.edu/homer/) to calculate RPKM from the gene bodies of RefSeq genes, perform motif analysis in the study. Reads counts were normalized using DESeq2.

treatment_protocol: Mouse macrophages are treated with bacterial lipopolysaccharide (LPS) or Kdo2-Lipid A,chemically defined substructure of  LPS specifically recognized by Toll-like receptor 4  for indicated time.

tag: tissue

value: bone marrow-derived macrophage

tag: treatment

value: KLA 0h


title: d2diff ATAC cell line 1

description:
TS cell line #1 d2 diff
d2diff_ATAC.wig.gz
d2diff_ATAC_total_peaks.bed
d2diff_ATAC_DARs.bed


title: WT_gal_glu_60m


title: 03_Pang_WGS_aTP977


title: WT_gal_glu_5m


title: WT_gal_fru_5m


title: WT_gal_fru_3m


title: 02_Pang_WGS_RN4220_2


title: WT_gal_fru_30m


title: 01_Pang_WGS_RN4220_1


title: TS ATAC cell line 1

description:
TS cell line #1 TS
TS_ATAC.wig.gz
TS_ATAC_total_peaks.bed
TS_ATAC_DARs.bed

source_name: Trophoblast stem cells

value: Trophoblast stem cells


title: 12_Pang_input_aTP961_for_Sample6

description:
genomic DNA, input sample (no antibodies)
Sample 12

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
We mapped reads in each FASTQ file back to the genome of Staphylococcus aureus NCTC8325 genome (NCBI Reference Sequence NC_007795.1) independently using CLC genomics workbench 8.0 (Qiagen), and exported .csv file.
Genome_build: NC_007795.1
Supplementary_files_format_and_content: Files ending with .csv: comma-separated values files of ChIP-seq results. Column1 - genome position, column2 - number of reads at each genome position.

growth_protocol:
Cells were growing in TSB medium at 37˚C, anhydratetracycline was added to a final concentration of 100ng/ml;, fixed by 3% formaldehyde for 30min at room temperature
All strains used for ChIP-seq experiments contained a transposon insertion in the spa gene encoding Surface Protein A. Cells were grown in tryptic soy broth (TSB) at 37°C with aeration. For the strains harboring a Ptet-noc_his fusion, anhydrotetracycline (aTc, 100 ng/ml) was added >5 generations prior to harvest.

extract_protocol:
ChIP-seq experiments were performed using anti-Noc (Bacillus subtilis) or anti-His6 (Genscript) antibodies according to previous publications (Graham et al, 2014 PMID 24829297; Wang et al, 2015 PMID 26253537).
Standard library construction protocol was used for Illumina Miseq (ChIP-seq). Illumina Truseq indexes were used.

treatment_protocol: Cells were grown in TSB medium to OD600 = 0.4 and incubated with 3% formaldehyde for 30 min at room temperature. Formaldehyde was quenched and the cells washed, and lysed

tag: growth protocol

value: TSB, 37˚C, 100ng/ml anhydrotetracycline

value: HG003 {delta}noc::spec geh::pTP171 (Bsnochis) spa::Tn

tag: chip antibody


title: 11_Pang_input_aTP959_for_Sample5

description:
genomic DNA, input sample (no antibodies)
Sample 11

value: HG003 {delta}noc::spec geh::pTP170 (Sanochis) spa::Tn


title: WT_gal_fru_120m


title: 10_Pang_input_aTP403_for_Sample4

description:
genomic DNA, input sample (no antibodies)
Sample 10

growth_protocol:
Cells were growing in TSB medium at 37˚C, fixed by 3% formaldehyde for 30min at room temperature
All strains used for ChIP-seq experiments contained a transposon insertion in the spa gene encoding Surface Protein A. Cells were grown in tryptic soy broth (TSB) at 37°C with aeration. For the strains harboring a Ptet-noc_his fusion, anhydrotetracycline (aTc, 100 ng/ml) was added >5 generations prior to harvest.

value: HG003 {delta}noc::spec spa::Tn


title: WT_gal_glu_0m


title: WT_gal_fru_10m


title: tps1_gal_glu_60m


title: WT_gal_fru_0m


title: tps1_gal_glu_5m


title: 08_Pang_input_aTP403_for_Sample2

description:
genomic DNA, input sample (no antibodies)
Sample 08


title: 07_Pang_input_aTP394_for_Sample1

description:
genomic DNA, input sample (no antibodies)
Sample 07

value: HG003 spa::Tn


title: tps1_gal_glu_3m


title: 20_Pang_input_bTP041

description: genomic DNA, input sample (no antibodies)

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
We mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently using CLC genomics workbench 8.0 (Qiagen), and exported .csv file.
Genome_build: NC_022898.1
Supplementary_files_format_and_content: Files ending with .csv: comma-separated values files of ChIP-seq results. Column1 - genome position, column2 - number of reads at each genome position.

organism: Bacillus subtilis PY79

source_name: Bacillus subtilis PY79

growth_protocol: Cells were grown in defined rich medium (CH) (Harwood and Cutting 1990, Molecular Biological Methods for Bacillus ) at 37°C with aeration. For the strains harboring a Pspank_noc_his fusion, isopropyl ß-d-thiogalactopyranoside  (IPTG, 0.5mM) was added >5 generations prior to harvest.

extract_protocol:
ChIP-seq experiments were performed using anti-His6 (Genscript) antibodies according to previous publications (Graham et al, 2014 PMID 24829297; Wang et al, 2015 PMID 26253537).
Standard library construction protocol was used for Illumina Miseq (ChIP-seq). Illumina Truseq indexes were used.

treatment_protocol:
Cells were growing in CH medium at 37˚C, IPTG was added to a final concentration of 0.5 mM;, fixed by 3% formaldehyde for 30min at room temperature
Cells were grown to OD600 = 0.25 and incubated with 3% formaldehyde for 30 min at room temperature. Formaldehyde was quenched and the cells washed, and lysed

value: CH, 37˚C

value: PY79 {delta}noc::tet ycgO::Pspank-Sanochis (spec)


title: tps1_gal_glu_30m


title: tps1_gal_glu_15m


title: 05_Pang_ChIPHis6_aTP959

description:
ChIP using anti-His6 (Genscript) antibodies
Sample 05

value: anti-6xHis (Genscript, catalog number A00186-100 )


title: TS ATAC cell line 2

description:
TS cell line #2 TS
TS_ATAC.wig.gz
TS_ATAC_total_peaks.bed
TS_ATAC_DARs.bed


title: 06_Pang_ChIPHis6_aTP961

description:
ChIP using anti-His6 (Genscript) antibodies
Sample 06


title: 04_Pang_ChIPHis6_aTP403

description:
ChIP using anti-His6 (Genscript) antibodies
Sample 04

value: TSB, 37˚C


title: 03_Pang_ChIPHis6_aTP394

description:
ChIP using anti-His6 (Genscript) antibodies
Sample 03


title: tps1_gal_glu_10m


title: tps1_gal_glu_120m


title: WT_gal_fru_15m


title: 02_Pang_ChIPBsNoc_aTP403

description:
ChIP using anti-Noc (Bacillus subtilis) antibodies
Sample 02

value: anti-Noc (generated in-house)


title: tps1_gal_glu_0m


title: 01_Pang_ChIPBsNoc_aTP394

description:
ChIP using anti-Noc (Bacillus subtilis) antibodies
Sample 01


title: tps1_gal_fru_60m


title: PckR-_succinate_2

city: Hamilton

first: Turlough

middle: M

last: Finan

state: Ontario

address: 1280 Main St. W.

department: Department of Biology

country: Canada

institute: McMaster University

data_processing:
All data analyses, except for calculation of fold changes, were performed using the Rockhopper v2.03 software using default settings and the following modifications: reverse complement reads and verbose output were selected.
For calculation of fold changes, the normalized reads for each set of duplicate were averaged using Excel, and the averages divided by each other.
Genome_build: Reads were mapped to the S. meliloti Rm1021 reference genome (NC_003047, NC_003037, NC_003078), with the only modification being that the three replicons of the genome were first merged as a single file.
Supplementary_files_format_and_content: Excel, contains a table providing the processed data for each sample.  Each line represents a distinct feature (CDS or RNA) of the genome.  The columns include: transcription start and stop positions (as determined by Rockhopper), translational start and stop positions, strand, gene name, locus tag (synonym), predicted function (product), raw counts for each sample, normalized counts for each sample, RPKM and expression values for each treatment, p-values and adjusted p-values (q-values) for each pairwise comparison of expression of the gene as determined by Rockhopper.

organism: Sinorhizobium meliloti

source_name: Bacterial cells

growth_protocol: S. meliloti strains were grown in LB medium containing 2.5mM MgSO4 and 2.5mM CaCl2 (LBmc).  Cultures were pelleted, washed once and resuspended with carbon free M9 medium.  Each cell suspension was used to inoculate 50 mL cultures of M9 (41 mM Na2HPO4, 22 mM KH2PO4, 8.6 mM NaCl, 18.7 mM NH4Cl, 4.1 mM biotin, 42 nM CoCl2, 1 mM MgSO4, 0.25 mM CaCl2, 38 mM FeCl3, and 15 mM of either glucose or succinate as the carbon source as indicated in the sample characteristics).  Cultures were grown with shaking at 30°C and cells harvested when cultures reached an OD600 ~ 0.4 (0.35 to 0.45).

extract_protocol:
Samples were kept on ice or at 4°C throughout the process except where indicated.  Each cell pellet was resuspended in 480 µL of resuspension solution (10 µL of 14.26 M β-mercaptoethanol per 1 mL of nuclease-free ddH2O) and transferred to a nuclease-free 1.5 mL centrifuge tube.  Cell suspensions were then mixed with 480 µL of room temperature hot phenol solution (per 6 mL: 5 mL of hot phenol buffer [20 mM Tris-HCl pH 7.5, 400 mM NaCl, 40 mM EDTA, 1% SDS, in nuclease-free ddH2O] and 1 mL unbuffered phenol), vigorously vortexed for 30 seconds, and incubated in a water bath at 95°C for 1 minute.  Samples were centrifuged at 16,000 g for 10 minutes at 4°C, and the supernatant was transferred to a fresh 1.5 mL nuclease-free centrifuge tube.  The supernatants were treated with two rounds of unbuffered-phenol:chloroform (1:1) extraction, followed by one round of chloroform extraction.  The nucleic acids were then precipitated by mixing the supernatant with one-tenth sample volume of 3 M sodium acetate and 2x sample volume of isopropanol, mixing, and the mixture was incubated on ice for 30 minutes.  The nucleic acids were pelleted by centrifugation at 16,000 g for 10 minutes, the pellet washed with ice cold 70% ethanol, and air dried.  The pellet was resuspended in 80 µL of nuclease-free ddH2O, mixed with 10 µL DNase I buffer and 10 µL DNase I (20 units; NEB catalog # M0303S), and incubated for 20 minutes at room temperature.  The 100 µL sample was then transferred to a fresh 1.5 mL nuclease-free centrifuge tube, extracted once with unbuffered-phenol:chloroform (1:1) and once with chloroform, and the RNA precipitated as before.  The RNA pellet was resuspended in 100 µL water, the integrity of the RNA confirmed as described below, and the remainder of the sample stored at -80°C until further use.
RNA libraries were prepared for sequencing using standard Illumina protocols by the Farncombe Family Digestive Health Research Institute located at McMaster University (Hamilton, Ontario, Canada).

treatment_protocol: Cells were grown with either 15 mM glucose or with 15 mM succinate, as indicated in the sample characteristics.

value: pckR-

tag: culture carbon source

value: 15 mM succinate


title: Ms_pH4.84 1

city: Karlsruhe

first: Andreas

last: Doetsch

address: Haid-und-Neu-Str. 9

department: Physiology and Biochemistry of Nutrition

country: Germany

institute: Max Rubner-Institute

data_processing:
Cluster detection and base calling were performed using RTA v1.13 (Illumina), and the quality of the reads was assessed with CASAVA v1.8.1 (Illumina).
The two RNA-seq data sets were mapped to the 5 contigs that were assembled from the genomic sequencing data using bowtie2 (Langmead & Salzberg, 2012, doi: 10.1038/nmeth.1923).
The mapped sequence reads were processed with samtools (Li, 2011, doi: 10.1093/bioinformatics/btr509) and sequence reads overlapping the annotated genes were counted using HTSeq (Anders et al, 2015, doi: 10.1093/bioinformatics/btu638) with the ‘intersection-nonempty’ option.
Average gene expression was determined as the arithmetic mean value of both samples using read counts that were normalized using DESeq2 (Love et al., 2014, doi: 10.1186/s13059-014-0550-8) and divided by the gene length (in kilobasepairs, kbp), yielding RPK  values (normalized reads per kilobase).
Genome_build: LDOS01000000
Supplementary_files_format_and_content: RPG (reads per gene) files were created using HTSeq, mapping raw reads (fastq format) against the genomic contigs and corresponding annotation prepared in this study.

organism: Metallibacterium scheffleri

source_name: bacterial culture

growth_protocol: Cells were grown at 30°C and 150 rpm in 21 mL medium, containing 132 mg/L (NH4)2SO4, 53 mg/L MgCl2 x 6 H2O, 27 mg/L KH2PO4, 147 mg/L CaCl2 x 2 H2O, 0.5 mg/L VOSO4 x 5 H2O, 10 mg/L FeSO4 x 7 H2O, 10 mg/L casitone, 1 mL/L Wolfe's mineral elixier (DSMZ medium 792) and 10 mL/L vitamin solution (DSMZ medium 141), buffered with 50 mL 0.2 M Na2HPO4 and 47 mL 0.1 M citrate to pH 4.5.

extract_protocol:
Cells were harvested in exponential growth phase and samples were pooled in triplicates, resulting in two independent replicates that were used for RNA extraction. Cell suspension were immediately treated with RNA protect (Qiagen) and RNA was isolated using the RNeasy Mini Kit (Qiagen). Genomic DNA was depleted using the DNA-free kit (Ambion, life technologies) and rRNA was depleted using the MICROBExpress kit (Ambion, life technologies)
Strand-specific cDNA libraries were prepared from 50 ng of rRNA-depleted samples following the TruSeq RNA protocol (Illumina, San Diego, CA, USA, without purification) with modification of the 2nd strand cDNA synthesis as previously described (Parkhomchuk et al, 2009, doi: 10.1093/nar/gkp596). The libraries were prepared using multiplex primers to allow simultaneous sequencing in a single lane.


title: Ms_pH4.84 2


title: 09_Pang_input_aTP394_for_Sample3

description:
genomic DNA, input sample (no antibodies)
Sample 09


title: tps1_gal_fru_5m


title: PckR+_succinate_2

value: pckR+


title: PckR-_succinate_1


title: tps1_gal_fru_30m


title: tps1_gal_fru_15m


title: tps1_gal_fru_120m


title: PckR-_glucose_2

value: 15 mM glucose


title: 3_Pang_Tn_aTP315_1

data_processing:
Reads from transposon-junctions of each sample were represented in each FASTQ file generated by Illumina sequencing.
The sequencing reads were mapped to S. aureus NCTC8325 genome (NCBI NC_007795.1) using Bowtie. Reads that mapped to the genome at a TA site (Transposon insertion site) were designated as mapped insertions. For each library, the number of reads mapped to each TA site was counted.
Genome_build: NC_007795.1
Supplementary_files_format_and_content: Files ending with .csv: comma-separated values files of Tn-seq results. Column information: genome position, reads = number of mapped transposon insertions at each genome position

source_name: Staphylococcus aureus NCTC8325

growth_protocol: Transposon library of each strain was grown in TSB medium at 30°C with aeration. Biological replicates were used. Cells were harvested at OD600 = 0.4.

extract_protocol:
Genomic DNA was extracted.
Transposon-sequencing (Tn-seq) was adapted from Zhang et al (PMID: 23028335). Briefly, genomic DNA isolated from each library was sonicated to 200-400 bp fragments. Nicked ends were repaired (Quick Blunt kit, NEB), and dA-tails were added with Taq polymerase (NEB), followed by ligation of adapters using T4 ligase (NEB). Transposon-junctions were PCR-amplified using primers binding to adapter and transposon individually. PCR products were purified and incubated with the endonuclease NotI (NEB) to remove any contaminating DNA derived from the transposon plasmid. Finally, a second round of PCR was performed on 100 ng of each sample, using primers that contain barcode and illumina P5/P7 and sequencing primers. A 200-400 bp product was gel-purified.

value: TSB, 30˚C

value: RN4220 delta_attBphi11::Orf5 Dnoc::spec

tag: restriction enzyme


title: PckR+_succinate_1


title: tps1_gal_fru_10m


title: tps1_gal_fru_0m


title: 2_Pang_Tn_TM18_2

value: RN4220 delta_attBphi11::Orf5


title: PckR+_glucose_2


title: 1_Pang_Tn_TM18_1


title: 11KT+Amh_5

status: Public on Aug 30 2017

city: Bergen

first: Diego

last: Crespo

address: Nordnesgaten 50

department: Reproduction and Developmental Biology

country: Norway

institute: Institute of Marine Research

data_processing:
Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite (v0.10.1; default parameters)
Reads were aligned to the zebrafish genome using TopHat v2.0.5 (standard parameters for single-end reads)
Data were filtered using SAMtools (v0.1.18)
The read counts were extracted using the Python package HTSeq
Differential expression analysis was performed using the R/Bioconductor package DESeq
Genome_build: Zv9
Supplementary_files_format_and_content: Tab-delimited text files include gene ID and raw counts for each sample

organism: Danio rerio

source_name: Testis

extract_protocol:
Total RNA was isolated from testis tissue using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio-analyzer 2100 total RNA Nano series II chip (Agilent)
Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 (Illumina, Inc.) according to the manufacturer’s instructions

tag: age

value: Adult

value: Wild type

tag: incubation

value: 3 days

value: Amh


title: 11KT+Amh_4


title: PckR+_glucose_1


title: 11KT+Amh_1


title: 11KT_5

value: control


title: 11KT+Amh_3


title: 11KT+Amh_2


title: 11KT_4


title: 11KT_3


title: 04_Pang_WGS_aTP979

tag: derivative strain

value: RN4220 {delta}noc::spec {delta}naAsup1


title: 11KT_2


title: 11KT_1


title: Glis3-WT RNA Rep3

city: RTP

first: Raja

last: Jothi

state: NC

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

description: Glis3-WT mouse RNA rep3

data_processing:
Sequenced 51bp reads were aligned to the reference genome (mouse mm9 assembly) using Bowtie algorithm. Those reads that mapped to unique genomic locations with at most two mismatches were retained for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing reads mapped to mm9 assembly; TEXT files containing the list of binding sites as defined by SISSRs [PMID: 18684996]
Genome Build:
NS50388_161215_NS500489_AHJKCKBGXY.WT3.single.sanger.bw: mm9

source_name: Glis3-WT RNA

growth_protocol: Thyroid gland was taken from WT and Glis3-EGFP mice fed Low iodine diet and processed for ChIP. WT mice were used as negative control. For RNA-seq analysis, thyroid gland  total RNAs were extracted from WT and Glis3-KO mice fed low iodine diet.

extract_protocol:
For ChIP-Seq, Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with agarose crosslinked with a GFP-binding peptide. For RNA-Seq, total RNAs from thyroid gland were extracted using a RNAqueous-Micro kit (ThermoFisher Scientific)
ChIPed DNA was amplified using a TruSeq RNA Library prep kit. For RNA-Seq, extracted RNA was amplified using a TruSeq RNA Library preparation kit

treatment_protocol: WT and Glis3-KO mice were fed low iodine diet.

tag: strain background

value: wild type

tag: diet

value: low-iodine diet (LID) for 2 weeks

value: thyroid gland


title: 4_Pang_Tn_aTP315_2

tag: growth condition

tag: genotype


title: Glis3-WT RNA Rep2

description: Glis3-WT mouse RNA rep2

data_processing:
Sequenced 51bp reads were aligned to the reference genome (mouse mm9 assembly) using Bowtie algorithm. Those reads that mapped to unique genomic locations with at most two mismatches were retained for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing reads mapped to mm9 assembly; TEXT files containing the list of binding sites as defined by SISSRs [PMID: 18684996]
Genome Build:
NS50388_161215_NS500489_AHJKCKBGXY.WT2.single.sanger.bw: mm9

tag: genotype/variation


title: Glis3-KO RNA Rep2

description: Glis3-KO mouse RNA rep2

data_processing:
Sequenced 51bp reads were aligned to the reference genome (mouse mm9 assembly) using Bowtie algorithm. Those reads that mapped to unique genomic locations with at most two mismatches were retained for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing reads mapped to mm9 assembly; TEXT files containing the list of binding sites as defined by SISSRs [PMID: 18684996]
Genome Build:
NS50388_161215_NS500489_AHJKCKBGXY.KO2.single.sanger.bw: mm9

source_name: Glis3-KO RNA


title: Glis3-WT RNA Rep1

description: Glis3-WT mouse RNA rep1

data_processing:
Sequenced 51bp reads were aligned to the reference genome (mouse mm9 assembly) using Bowtie algorithm. Those reads that mapped to unique genomic locations with at most two mismatches were retained for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing reads mapped to mm9 assembly; TEXT files containing the list of binding sites as defined by SISSRs [PMID: 18684996]
Genome Build:
NS50388_161215_NS500489_AHJKCKBGXY.WT1.single.sanger.bw: mm9


title: Glis3-KO RNA Rep1

description: Glis3-KO mouse RNA rep1

data_processing:
Sequenced 51bp reads were aligned to the reference genome (mouse mm9 assembly) using Bowtie algorithm. Those reads that mapped to unique genomic locations with at most two mismatches were retained for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing reads mapped to mm9 assembly; TEXT files containing the list of binding sites as defined by SISSRs [PMID: 18684996]
Genome Build:
NS50388_161215_NS500489_AHJKCKBGXY.KO1.single.sanger.bw: mm9


title: Glis3-KO RNA Rep3

description: Glis3-KO mouse RNA rep3

data_processing:
Sequenced 51bp reads were aligned to the reference genome (mouse mm9 assembly) using Bowtie algorithm. Those reads that mapped to unique genomic locations with at most two mismatches were retained for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing reads mapped to mm9 assembly; TEXT files containing the list of binding sites as defined by SISSRs [PMID: 18684996]
Genome Build:
NS50388_161215_NS500489_AHJKCKBGXY.KO3.single.sanger.bw: mm9


title: 2yr_Drd2_TS_222

city: Cambridge

first: Peter

last: Sudmant

address: 77 Massachusetts Ave

institute: MIT

description: barcode: TCCTGATACTCC;

data_processing:
Reads were aligned to the mouse genome using STAR version 2.5.1b and gene/transcript abundances were quantified using RSEM v1.2.20. ENSEMBL version 75 gene annotations were used.
Supplementary_files_format_and_content: RSEM expected counts, TPMs and FPMKs for genes and transcripts
Genome_build: mm10

source_name: Brain, striatum

extract_protocol:
translation ribosome affinity purification (TRAP) of cell-type specific ribosome bound mRNA
NuGEN Ovation V2

value: Drd2::EGFP-L10a on C56BL/6J background

value: D2 spiny projection neurons

value: 2 years old

tag: Sex

value: female


title: 2yr_Drd2_TS_223

description: barcode: AGGCAGTACTCC;

tag: strain


title: 2yr_Drd2_TS_241

description: barcode: TAAGGCTACTCC;

tag: cell type


title: 2yr_Drd1a_TS_205

description: barcode: TAAGGCAGGCTT;

value: Drd1::EGFP-L10a on C56BL/6J background

value: D1 spiny projection neurons


title: 2yr_Drd2_TS_240

description: barcode: CGTACTTACTCC;


title: 2yr_Drd1a_TS_184

description: barcode: TCCTGAAGGCTT;


title: PN42_Drd2_TS_1117

description: barcode: CAGAGATATGCA;

value: 42 days old


title: tps1_gal_fru_3m

tag: protocol

tag: time point


title: 2yr_Drd1a_TS_185

description: barcode: AGGCAGAGGCTT;


title: 2yr_Drd1a_TS_203

description: barcode: CGTACTAGGCTT;


title: PckR-_glucose_1

value: pckR-

value: 15 mM glucose


title: PN42_Drd1a_TS_1414

description: barcode: CAGAGATACTCC;


title: PN42_Drd2_TS_1120

description: barcode: TAGGCATATGCA;


title: PN42_Drd1a_TS_1419

description: barcode: TAGGCATACTCC;


title: PN42_Drd2_TS_1124

description: barcode: GGACTCTATGCA;


title: PN42_Drd1a_TS_1420

description: barcode: GGACTCTACTCC;


title: PN42_Drd1a_TS_1418

description: barcode: TCTCTTACTCC;


title: Cre_rep2

city: Rozzano

first: Simone

last: Serio

state: Milano

address: Via Alessandro Manzoni, 56

department: Cardiovascular Medicine

country: Italy

institute: Humanitas Research Hospital

data_processing:
RNA-seq reads were aligned to the mm10 genome assembly using STAR v2.5 (PMID: 23104886)
Transcript abundance was obtained using the internally  developed RNA read counter of STAR v2.5 (PMID: 23104886)
Differentially expressed genes were identified using R and edgeR (PMID: 19910308)
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig were generated using bam2wig.py module in RSeQC v2.6.3 (PMID: 22743226)

source_name: cardiomyocyte

extract_protocol:
RNA was isolated using RNeasy Mini Kit (Qiagen), and treated with DNase according to the manufacture’s protocol.
Total RNA quality was evaluated using the 2100 Agilent Bioanalyzer and the RNA 6000 Nano kit: only samples with RIN score greater than 8 were further processed. RNA-Seq libraries were created using the Epicentre Script-Seq Complete Gold Kit-Low Input (Epicentre) composed of two modules: the Ribo-Zero Magnetic Kit depletion protocol for rRNA removal and the Script-Seq v2 Kit to prepare the libraries. 150 ng of total RNA was depleted and concentrated with RNeasy MinElute Cleanup Kit (Qiagen). Purified RNA was fragmented and first strand cDNA was synthesized using random hexamer with 5’ tagging sequences. After RNase digestion, a 3’ tag was introduced with random terminal tagging oligos. The obtained double tagged strand-specific cDNA was purified using AMPure XP beads (Beckman Coulter).  Libraries were enriched and indexed by 15 cycles of PCR amplification (ABI GeneAmp PCR system 9700) using FailSafe PCR enzyme and ScriptSeq Index PCR Primers for Illumina (Epicentre). After AMPure XP beads purification, library quality and size distribution were checked using an Agilent Bioanalyzer and DNA 1000 chip.  All libraries were quantified with a Qubit 2.0 Fluorometer (Life Technologies) using dsDNA BR Assay Kit (Life Technologies). RNA-Seq libraries were sequenced using TruSeq PE Cluster Kit v3 and TruSeq SBS Kit v3 (Illumina). According to index compatibility, the libraries were grouped into 2 pools and clustered on a TruSeq v3 flow cell at a concentration of 9pM to obtain > 50 million clusters for each sample.
Paired end sequence reads (75-bp in length) were generated on an Illumina NextSeq 500 (Samples 1 to 4)

value: alphaMHC-MerCreMer +/-


title: G9a_KO_rep2

value: G9a flox/flox; alphaMHC-MerCreMer +/-


title: Cre_rep1


title: RNA-seq CC-CR rep1

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

description: processed data file: RNAseq_counts.txt

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using TopHat2
HTSeq was used to count reads in features
Count data was given to edgeR to test for differential expression
small RNA-seq reads were trimmed for adapter sequence of by Cutadpt, then the sequences shorter than 15 bp were excluded from the downstream analysis
Reads were aligned to the human genome hg19 using Bowtie (version 0.12.7)
Mapped reads were annotated and miRNA expressions were quantified using ncPRO-seq (version v1.5.1) based on miRbase v19
Differentially expressed miRNAs were detected by edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

organism: Homo sapiens

source_name: HCA-7 derived CC-CR subline

growth_protocol: 3D collagen cultures were set up using 3 layers of type I collagen. 14-day old colonies from CC and CC-CR embedded in collagen were isolated for RNA extraction.

extract_protocol:
Total RNA from cells embedded in collagen were first isolated by TRIzol (Invitrogen) and then purified using miRNeasy Mini Kit (Qiagen).
RNA and small RNA libraries were prepared for sequencing using standard Illumina protocols

value: human colorectal cancer cell line

tag: culture type

value: 3D culture

tag: cetuximab sensitivity

value: resisitant


title: RNA-seq CC rep1

description: processed data file: RNAseq_counts.txt

source_name: HCA-7 derived CC subline

value: sensitive


title: DB177-P8

city: Birmingham

first: Andre

last: Ballesteros-Tato

state: AL

address: 1825 University Blvd

department: Medicine, Division of Clinical Immunology and Rheumatology

institute: The University of Alabama at Birmingham

data_processing:
Library preparation and RNA sequencing was conducted through Genewiz. Libraries were sequenced using a 1x50bp single end rapid run on the HiSeq2500 platform. Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality (error rate < 0.05) at the end.After trimming, sequence reads shorter than 30 nucleotides were discarded. Remaining sequence reads were mapped to the Mus musculus mm10 reference genome using CLC genomics workbench v. 9.0.1
Differential gene expression was determined using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Microsoft Excel Open XML Format Spreadsheet files showing Sample mapping stats (raw read count,TPM and RPKM).

source_name: mediastinal LN

extract_protocol:
RNA was isolated using the Single Cell RNA Purification kit (Norgen)
RNA libraries were prepared for sequencing using standard Illumina protocols. All samples (Genewiz)

tag: tissue

value: mediastinal lymph node

value: Tfr cells

tag: cell markers

tag: treatment

value: Day 30 post influenza infection


title: RNA-seq CC rep3

description: processed data file: RNAseq_counts.txt


title: RNA-seq CC-CR rep3

description: processed data file: RNAseq_counts.txt


title: DB175-P8


title: RNA-seq CC rep2

description: processed data file: RNAseq_counts.txt


title: Irg1_lung_d16_rep1

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

description:
lane1
Barcode: CCAGTTAG

data_processing:
single-end demultiplexed
Data were sequenced on HiSeq 2500 instrument (Illumina, San Diego, CA) using 50bpX25bp pair-end sequencing on two lanes. Second mate was used for sample demultiplexing, at which point individual single-end fastqs were aligned to mm10 genome using STAR with following options --outFilterMultimapNmax 10 --outFilterMismatchNmax 10 --outReadsUnmapped Fastx --outSAMstrandField All. Gene expression was obtained using in-house scripts bassed on MACS and HTSeq (https://github.com/ctlab/quant3p).
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file that includes raw count data for each sample and tab delimited file with barcode annotations

source_name: Irg1, lung, d16

extract_protocol:
Neutrophil purity was defined by flow cytometry as the percentage of Ly6G+ CD11b+ cells (negatively selected samples) or Gr-1high CD11b+ cells (positively selected samples). RNA was extracted from purified neutrophils using TriZol reagent (Invitrogen). mRNA was extracted with oligo-dT beads (Invitrogen) and cDNA synthesized using custom oligo-dT primer with a barcode and adaptor-linker sequence (CCTACACGACGCTCTTCCGATCT-XXXXXXXX-T15). Samples were pooled based on Actb qPCR values, RNA-DNA hybrids degraded with acid-alkali treatment and a second sequencing linker (AGATCGGAAGAGCACACGTCTG) was ligated with T4 ligase (NEB). After SPRI-beads clean-up (Agencourt AMPure XP, BeckmanCoulter). the mixture was PCR-enriched (12 cycles) and SPRI-purified yielding final strand-specific RNA-seq libraries.
3'end DGE

tag: infection

value: Mycobacterium tuberculosis

tag: day post infection

value: 16 days post infection

value: Lung neutrophils


title: PN42_Drd2_TS_1118

description: barcode: CTCTCTTATGCA;

value: Drd2::EGFP-L10a on C56BL/6J background

value: D2 spiny projection neurons

tag: age

value: female


title: WT_lung_d21_rep3

description:
lane2
Barcode: GTATAACA

source_name: WT, lung, d21

value: WT


title: Irg1_lung_d16_rep3

description:
lane2
Barcode: CACATCCT


title: WT_lung_d21_rep2

description:
lane2
Barcode: AGTTGCTT


title: DB177-P6

value: Treg cells


title: RNA-seq CC-CR rep2

description: processed data file: RNAseq_counts.txt


title: Irg1_lung_d16_rep2

description:
lane1
Barcode: TGCTCGAC


title: WT_lung_d21_rep1

description:
lane2
Barcode: AACTTGAC


title: BM_Irg1_naive_rep3

description:
lane1
Barcode: TTGAATAG

source_name: BM, Irg1, naive

value: uninfected

value: 0 days post infection

value: Bone Marrow neutrophils


title: DB174-P6


title: BM_WT_naive_rep1

description:
lane1
Barcode: AAGACACT

source_name: BM, WT, naive


title: Irg1KO_PMN_6hpi_rep3

description:
Lane: SNL4
Barcode: CACATCCT

data_processing:
single-end demultiplexed
Data were sequenced on HiSeq 2500 instrument (Illumina, San Diego, CA) using 41bpX11bp pair-end sequencing on two lanes. Second mate was used for sample demultiplexing, at which point individual single-end fastqs were aligned to mm10 genome using STAR with following options --outFilterMultimapNmax 10 --outFilterMismatchNmax 10 --outReadsUnmapped Fastx --outSAMstrandField All. Gene expression was obtained using in-house scripts bassed on MACS and HTSeq (https://github.com/ctlab/quant3p).
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file that includes raw count data for each sample

source_name: Irg1KO, PMN, 6hpi

tag: time

value: 6 hours post infection


title: BM_Irg1_naive_rep1

description:
lane1
Barcode: GTCTGATG


title: BM_WT_naive_rep2

description:
lane1
Barcode: TCGCCTTG


title: G9a_KO_rep1

value: G9a flox/flox; alphaMHC-MerCreMer +/-


title: Irg1KO_PMN_6hpi_rep1

description:
Lane: SNL3
Barcode: TGCTCGAC


title: Irg1KO_PMN_2hpi_rep2

description:
Lane: SNL3
Barcode: TCCTTGGT

source_name: Irg1KO, PMN, 2hpi

value: 2 hours post infection


title: Irg1KO_PMN_2hpi_rep3

description:
Lane: SNL4
Barcode: CCAGAGCT


title: DB174-P8

value: mediastinal lymph node


title: DB175-P6


title: WT_PMN_2hpi_rep1

description:
Lane: SNL2
Barcode: CAGCAAGG

source_name: WT, PMN, 2hpi


title: WT_PMN_6hpi_rep2

description:
Lane: SNL2
Barcode: AAGACACT

source_name: WT, PMN, 6hpi


title: Irg1KO_Naive_PMN_rep3

description:
Lane: SNL1
Barcode: AAGACACT

source_name: Irg1KO, Naive, PMN

value: 0 hours post infection


title: Irg1KO_Naive_PMN_rep2

description:
Lane: SNL1
Barcode: AGGATCTA


title: Irg1KO_Naive_PMN_rep1

description:
Lane: SNL1
Barcode: GTCTGATG


title: WT_PMN_6hpi_rep3

description:
Lane: SNL4
Barcode: TTACGCAC


title: WT_PMN_2hpi_rep3

description:
Lane: SNL4
Barcode: GACAGTAA


title: Pkd1MEK WT cells_ChIP Seq

city: Kansas City,

first: Xiaogang

last: Li

state: KS

address: 3901 Rainbow Boulevard

institute: University of Kansas Medical Center

description:
XL-3
Barcode: TTAGGC

data_processing:
ChIP-seq reads were aligned to GRCm38 genome by CLC Genomic Workbench 8.5.1 (Qiagen) using default parameters.
BAM files imported to Seqmonk  (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/), and the peaks are identified and quantitated by MACX Peak Caller Probe Generator using default parameters.
Genome_build: GRCm38
Supplementary_files_format_and_content: peak files

source_name: epithelial cells

growth_protocol: Pkd1 wild type and Pkd1 null MEK cells were cultured in Dulbecco's modified Eagle medium containing 2% fetal bovine serum, 0.75 mug l-1 interferon-gamma, 1.0 gl-1 insulin, 0.67 mg l-1 sodium selenite, 0.55 g l-1 transferrin, 0.2 g l-1 ethanolamine, 36 ng ml-1 hydrocortisone, 0.10 muM 2,3,5-triido-l-thyronine, 100 units penicillin-G (base) in combination with 0.30 mg ml-1 additional glutamine, 100 mug streptomycin sulfate and 0.1 mM citrate to maintain penicillin potency at 33°C.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with Smyd2 antibody.
DNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney

value: renal epithelial cells

tag: chip antibody

value: anti-Smyd2 (Santa Cruz, Catalog# sc-79084, Lot# H2014)

tag: developmental stage

value: Embryo

value: Pkd1 wild-type


title: WT_PMN_2hpi_rep2

description:
Lane: SNL3
Barcode: GTCGCCTT

tag: genotype/variation

value: Mycobacterium tuberculosis


title: Pkd1 MEK null cells_ChIP Seq

description:
XL-4
Barcode: TGACCA

tag: genotype


title: BM_Irg1_naive_rep2

description:
lane1
Barcode: TCCAGCAA

tag: strain


title: WT_PMN_6hpi_rep1

description:
Lane: SNL2
Barcode: AGGATCTA

tag: cell type


title: Irg1KO_PMN_2hpi_rep1

description:
Lane: SNL3
Barcode: CCTATGCC


title: Irg1KO_PMN_6hpi_rep2

description:
Lane: SNL4
Barcode: TCGCCTTG


title: WT_Naive_PMN_rep1

description:
Lane: SNL1
Barcode: CGTTACCA

source_name: WT, Naive, PMN


title: WT_Naive_PMN_rep2

description:
Lane: SNL1
Barcode: TCCAGCAA


title: H3K4me1_MC9_shRad21

city: New York

first: Mark

last: Ptashne

state: NY

address: 1275 York Ave

department: Molecular Biology Program

institute: Sloan Kettering Institute

description: H3K4me1 MC9 shRad21

data_processing:
cutadapt-1.9.1  cutadapt -a AGATCGGAAGAGC
bwa-0.7.13  bwa aln
bwa-0.7.13  bwa sampe
all duplicates eliminated
values at all features are calculated by (number of midpoints of tags / bp of feature) / (total number of unique tags / genome length)
above described values are quantile normalized
Genome_build: mm10
Supplementary_files_format_and_content: bed
Supplementary_files_format_and_content: pdf

source_name: MC9 shRad21

growth_protocol: Bone marrow mast cells (BMMCs) were obtained by flushing the femurs and tibias from adult mice with PBS. Primary mast cells, MC9 cell line, and 32D myeloid cells were grown in RPMI 1640 supplemented with 10% fetal calf serum (FCS), IL-3, nonessential amino acids, and sodium pyruvate.

extract_protocol: See ChIP-Endo Protocol.pdf

tag: cell line

value: MC9 shRad21 Mast


title: H3K27ac_MC9_shRad21

description: H3K27ac MC9 shRad21


title: WT_Naive_PMN_rep3

description:
Lane: SNL1
Barcode: TTGAATAG

value: WT


title: H3K27me3_MC9_shRad21

description: H3K27me3 MC9 shRad21


title: H3K4me1_MC9

description: H3K4me1 MC9

value: MC9 Mast


title: H3K4me3_MC9_shRad21

description: H3K4me3 MC9 shRad21


title: H3K4me3_MC9

description: H3K4me3 MC9


title: H3K27ac_MC9

description: H3K27ac MC9


title: H3K27me3_MC9

description: H3K27me3 MC9


title: PolII_MC9

description: PolII MC9

value: Rpb1 CTD (Cell Signaling 2629S Lot:3)


title: PolII_MC9_shRad21

description: PolII MC9 shRad21


title: H3K27ac_Mast_WSH

description: H3K27ac Mast WSH

source_name: Mast WSH

value: Mast WSH (chromosomal inversion) primary cells


title: H3K27me3_Mast_WSH

description: H3K27me3 Mast WSH


title: H3K4me1_Mast_WSH

description: H3K4me1 Mast WSH


title: H3K27me3_32D

description: H3K27me3 32D

value: 32D Myeloid


title: H3K27ac_Mast_wt

description: H3K27ac Mast wt

source_name: Mast wt

value: Mast wt primary cells


title: H3K27me3_Mast_wt

description: H3K27me3 Mast wt


title: PolII_Mast_WSH

description: PolII Mast WSH


title: PolII_Mast_wt

description: PolII Mast wt


title: H3K4me3_Mast_wt

description: H3K4me3 Mast wt


title: H3K4me3_32D

description: H3K4me3 32D


title: TAC_input_DNA

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using bwa mem v0.7.10-r789 (PMID:19451168)
Reads with mapping quality ≤ 10 and not properly paired were removed with samtools (v1.1)
Differential peak calling was detected using THOR v0.1 (PMID: 27484474). The Input DNA signal was subtracted from each ChIP-seq signal. Differential peaks were filtered by adjusted pValue<= 0.01.
Blacklisted regions identified by the ENCODE project (The ENCODE Project Consortium, 2012) were discarded during differential peaks detection and bigwig profile creation.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.bw: the genomic distribution of ChIP-seq signal subtracted from the input DNA. These profiles were obtained using deeptools2 (PMID: 27079975) and these paramaters: -bs 10 --smoothLength 50 --ratio subtract --normalizeUsingRPKM.
Supplementary_files_format_and_content: *.bed: list of the differential peaks called by THOR after filtering

source_name: cardiomyocyte

extract_protocol:
ChIP was performed as described elsewhere (Peters AH, et al. (2003) Mol Cell 12(6):1577–1589).
The Libraries were generated using NuGEN Ovation Ultralow System V2 1–96 kit.
ChIP-seq libraries were produced from as little as 1 ng of double-stranded DNA. The workflow is consisted of three steps: end repair to generate blunt ends, adaptor ligation with optional multiplexing and PCR amplification to produce the final library.

value: transverse aortic constriction (TAC) for 1 week


title: H3K4me3_Mast_WSH

description: H3K4me3 Mast WSH


title: PolII_32D

description: PolII 32D


title: H3K4me1_Mast_wt

description: H3K4me1 Mast wt


title: H3K27ac_32D

description: H3K27ac 32D


title: H3K4me1_32D

description: H3K4me1 32D


title: TAC_H3K27me3_rep2_ChIP-seq

description:
tac_H3K27me3.bw
sham_tac_H3K27me3-diffpeaks-filt.bed

value: anti-H3K27me3; Millipore (07-449)


title: TAC_H3K27me3_rep1_ChIP-seq


title: TAC_G9a_rep2_ChIP-seq

description:
tac_G9a.bw
sham_tac_G9a-diffpeaks-filt.bed

value: anti-G9a; Sigma (G6919)


title: TAC_H3K9me2_rep1_ChIP-seq

description:
tac_H3K9me2.bw
sham_tac_H3K9me2-diffpeaks-filt.bed

value: anti-H3K9me2; Abcam (ab1220)


title: Sham_H3K9me2_rep1_ChIP-seq

description:
sham_H3K9me2.bw
sham_tac_H3K9me2-diffpeaks-filt.bed

value: No treatment


title: Sham_H3K27me3_rep1_ChIP-seq

description:
sham_H3K27me3.bw
sham_tac_H3K27me3-diffpeaks-filt.bed


title: Sham_G9a_rep1_ChIP-seq

description:
sham_G9a.bw
sham_tac_G9a-diffpeaks-filt.bed


title: Sham_H3K9me2_rep2_ChIP-seq


title: Sham_input_DNA


title: TAC_H3K9me2_rep2_ChIP-seq


title: KO_input_DNA

extract_protocol:
ChIP was performed as described elsewhere (Peters AH, et al. (2003) Mol Cell 12(6):1577–1589).
The Libraries were generated using NuGEN Ovation Ultralow System V2 1–96 kit.
ChIP-seq libraries were produced from as little as 1 ng of double-stranded DNA. The workflow consisted of three steps: end repair to generate blunt ends, adaptor ligation with optional multiplexing and PCR amplification to produce the final library.

value: G9a flox/flox; alphaMHC-MerCreMer +/-


title: KO_Mef2c_rep1_ChIP-seq

description:
cre_ko_Mef2c-diffpeaks-filt.bed
ko_Mef2c.bw

value: anti-Mef2c; Abcam (ab43796)


title: KO_H3K27me3_rep2_ChIP-seq

description:
cre_ko_H3K27me3-diffpeaks-filt.bed
ko_H3K27me3.bw


title: KO_Mef2c_rep2_ChIP-seq


title: TAC_G9a_rep1_ChIP-seq


title: KO_G9a_rep1_ChIP-seq

description:
cre_ko_G9a-diffpeaks-filt.bed
ko_G9a.bw


title: Sham_H3K27me3_rep2_ChIP-seq


title: Cre_Mef2c_rep2_ChIP-seq

description:
cre_ko_Mef2c-diffpeaks-filt.bed
cre_Mef2c.bw

value: alphaMHC-MerCreMer +/-


title: Cre_input_DNA


title: Cre_Mef2c_rep1_ChIP-seq


title: KO_H3K9me2_rep2_ChIP-seq

description:
cre_ko_H3K9me2-diffpeaks-filt.bed
ko_H3K9me2.bw


title: KO_H3K9me2_rep1_ChIP-seq


title: Cre_H3K9me2_rep2_ChIP-seq

description:
cre_ko_H3K9me2-diffpeaks-filt.bed
cre_H3K9me2.bw


title: Sham_G9a_rep2_ChIP-seq


title: KO_G9a_rep2_ChIP-seq

description:
cre_ko_G9a-diffpeaks-filt.bed
ko_G9a.bw


title: Cre_H3K27me3_rep2_ChIP-seq

description:
cre_ko_H3K27me3-diffpeaks-filt.bed
cre_H3K27me3.bw


title: Cre_H3K27me3_rep1_ChIP-seq


title: Cre_H3K9me2_rep1_ChIP-seq


title: pLN_iFRC_2

city: Braunschweig

first: Michael

last: Beckstette

state: Lower Saxony

address: Inhoffenstrase 7

department: Molecular Infection Biology

institute: Helmholtz Centre for Infection Research

data_processing:
library quality assessment using FastQC
Libraries were aligned versus the mouse reference genome (assembly: GRCm38) using the splice junction mapper Tophat2 v1.2.0 with default parameterization.
Reads aligned to annotated genes were quantified with the htseq-count program [Anders et al, 2015, Bioinformatics 31, 166-169].
Determined read counts served as input to DESeq2 [Love et al, 2014, Genome Biology 15, 550] for pairwise detection and quantification of differential gene expression.
RPKM (reads per kilobase maximal transcript length per million mapped reads) values were computed for each library from the raw gene counts.
Genome_build: GRCm38
Supplementary_files_format_and_content: htseqcounts*.tab files: CSV format with raw read counts per gene; htseqcounts*.rpkm.txt files: CSV format with RPKM normalized read counts per gene; DESeq2_genes_diffexp*.csv: CSV files with differentially expressed genes

source_name: skin-draining lymph node

extract_protocol:
RNA was isolated from mLN- and pLN-iFRCs via DNA/RNA AllPrep Kit (Qiagen) according to the manufacturer's protocols.
Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer. Purification of poly A-containing mRNA was carried out via poly T oligo attached magnetic beads. Following purification, the mRNA was subjected to library preparation using Script Seq v2 Library preparation kit (Epicentre).

treatment_protocol: For stromal cell isolation, skin-draining pLNs (inguinal and axillary) or mLNs of BALB/c mice were resected and digested in RPMI 1640 medium (Gibco) containing 0.2 mg/ml collagenase P (Roche), 0.15 U/ml dispase (Roche) and 0.2 mg/ml DNase I (Roche). After digestion, cells were kept at 4°C in PBS containing 0.2 % BSA and 5 mM EDTA (Roth). In a first step, CD45- cells were enriched by autoMACS separation after indirect magnetic labeling of CD45+ cells using anti CD45-APC (30-F11, eBioscience) followed by anti APC microbeads (Miltenyi Biotec). Subsequently, the CD45- fraction was stained using fluorescence-coupled antibodies and either analyzed directly by flow cytometry or used to sort CD45-Ter119-CD31-gp38+ FRCs by FACS (Aria II, 100 μm nozzle; purity >91 97 %). 2 x 104 FRCs were plated on 24 well plates (Thermo Fisher Scientific) coated with 0.05 mg/ml fibronectin (Roche). Immortalization was performed via lentiviral transduction of a Tet inducible SV40 T antigen as described previously [May et al, 2004, Nucleic Acid Research, 32, 5529-5538; May et al, 2010, Tissue Eng Part, 16, 441-452]. After 48 hours transfection, cells were selected for resistance against 0.4 mg/ml G418 (Thermo Fisher Scientific). Proliferation of mLN- and pLN iFRCs was controlled by addition of 2 μg/ml doxycyclin (AppliChem).

value: skin-draining lymph node

value: fibroblastic reticular cell

value: skin

tag: organ

value: lymph node

tag: housing

value: specific-pathogen-free

value: Balb/c


title: pLN_iFRC_3


title: Cre_G9a_rep1_ChIP-seq

description:
cre_ko_G9a-diffpeaks-filt.bed
cre_G9a.bw


title: mLN_iFRC_2

source_name: mesenteric lymph node

value: mesenteric lymph node

value: mesenteries


title: mLN_iFRC_1


title: mLN_iFRC_3


title: pLN_iFRC_1


title: Glis3-EGFP-Fusion GFP-ChIP

description: Glis3-EGFP-Fusion GFP ChIP

data_processing:
Sequenced 51bp reads were aligned to the reference genome (mouse mm9 assembly) using Bowtie algorithm. Those reads that mapped to unique genomic locations with at most two mismatches were retained for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing reads mapped to mm9 assembly; TEXT files containing the list of binding sites as defined by SISSRs [PMID: 18684996]
Genome Build:
MES1113_161003_M02338_ATYKA.IP-GFP.single.sanger.bw: mm9

source_name: Glis3-EGFP-Fusion GFP-ChIP

tag: strain background

tag: diet

value: low-iodine diet (LID) for 2 weeks

value: thyroid gland

value: agarose crosslinked with a GFP-binding peptide


title: Glis3-EGFP-Fusion Input

description: Glis3-EGFP-Fusion Input Control

data_processing:
Sequenced 51bp reads were aligned to the reference genome (mouse mm9 assembly) using Bowtie algorithm. Those reads that mapped to unique genomic locations with at most two mismatches were retained for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing reads mapped to mm9 assembly; TEXT files containing the list of binding sites as defined by SISSRs [PMID: 18684996]
Genome Build:
MES1113_161003_M02338_ATYKA.InputGFP.single.sanger.bw: mm9

source_name: Glis3-EGFP-Fusion Input

tag: tissue


title: KO_H3K27me3_rep1_ChIP-seq

value: anti-H3K27me3; Millipore (07-449)


title: MOFwt_CD2_2B

first: Scott

last: Armstrong

address: 1275 York Avenue

department: Center for Epigenetics

institute: MSKCC

description: Mof excised, 72 hours post Cre transduction

data_processing:
The reads were aligned to genome assembly mm9 using STAR
Number of reads on each transcript was counted using featurecounts
Differentially expressed genes were determined using DESeq2
Genome_build: mm9
Supplementary_files_format_and_content: Transcript read counts. 1st column is NCBI accession id, 2nd column is gene symbol, 3rd column is number of reads

source_name: Transformed bone marrow LSKs

extract_protocol:
Trizol extraction
RNA libraries were prepared for sequencing using standard Illumina protocols, Poly-A tail selection

value: Mof WT

tag: treatment

value: dTomato-Cre+


title: MOFwt_CD2_2A


title: MOFwt_CD2_1


title: MOFff_CD2_2B

value: Mof f/f


title: WT GFP-ChIP

description: WT GFP ChIP Control

data_processing:
Sequenced 51bp reads were aligned to the reference genome (mouse mm9 assembly) using Bowtie algorithm. Those reads that mapped to unique genomic locations with at most two mismatches were retained for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing reads mapped to mm9 assembly; TEXT files containing the list of binding sites as defined by SISSRs [PMID: 18684996]
Genome Build:
MES1113_161003_M02338_ATYKA.IP-WT.single.sanger.bw: mm9

source_name: WT GFP-ChIP

value: wild type


title: Cre_G9a_rep2_ChIP-seq

value: anti-G9a; Sigma (G6919)

value: alphaMHC-MerCreMer +/-


title: WT Input

description: WT Input Control

data_processing:
Sequenced 51bp reads were aligned to the reference genome (mouse mm9 assembly) using Bowtie algorithm. Those reads that mapped to unique genomic locations with at most two mismatches were retained for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing reads mapped to mm9 assembly; TEXT files containing the list of binding sites as defined by SISSRs [PMID: 18684996]
Genome Build:
MES1113_161003_M02338_ATYKA.InputWT.single.sanger.bw: mm9

source_name: WT Input


title: adipose_replicate_23 [intravenous LPS]

first: Chenyi

last: Xue

institute: Columbia University

description: adipose_low_pre_vs_post_gene_exp.diff.gz

data_processing:
Base calling was done by RTA v1.13.48.0
Sequence reads were aligned to hg19 genome using STAR with default options.
Alignment was filtered using the following specifications: 1) read was uniquely mapped, 2) reads from the same pair were mapped to the same chromosome with expected orientations and mapping distance between the read pair was < 500,000 bp
Fragments Per Kilobase of exon per Million reads mapped (FPKM) was estimated by Cufflinks 2.1.1. Differential expression was tested by Cuffdiff with options "-u --max-bundle-frags 50000000". Annotation included mRNAs from RefSeq, stringent set of lincRNAs from Cabili et al. 2011 and lincRNAs from GENCODE v19.
genome build: hg19
processed data files format and content: DIFF files were obtained from Cuffdiff output.
processed data files format and content: adipose_AA_Cau_BodyMap_gene_exp.diff contains differential expression result from African Americans and Caucasians. Annotation included mRNAs from RefSeq and stringent set of lincRNAs from Cabili et al. 2011. sample_1 = African American, sample_2 = Caucasian
processed data files format and content: adipose_AA_Cau_GENCODE_gene_exp.diff contains differential expression result from African Americans and Caucasians. Annotation included mRNAs from RefSeq and lincRNAs from GENCODE v19. sample_1 = African American, sample_2 = Caucasian
processed data files format and content: adipose_male_female_BodyMap_gene_exp.diff contains differential expression result from males and females. Annotation included mRNAs from RefSeq and stringent set of lincRNAs from Cabili et al. 2011. sample_1 = male, sample_2 = female
processed data files format and content: adipose_male_female_GENCODE_gene_exp.diff contains differential expression result from males and females. Annotation included mRNAs from RefSeq and lincRNAs from GENCODE v19. sample_1 = male, sample_2 = female
processed data files format and content: adipose_high_pre_vs_post_gene_exp.diff contains differential expression result from adipose high responders. Annotation included mRNAs from GENCODE, lincRNAs from GENCODE and stringent set of lincRNAs form Cabili et al. sample_1 = baseline, sample_2 = post-LPS
processed data files format and content: adipose_low_pre_vs_post_gene_exp.diff contains differential expression result from adipose low responders. Annotation included mRNAs from GENCODE, lincRNAs from GENCODE and stringent set of lincRNAs form Cabili et al. sample_1 = baseline, sample_2 = post-LPS
processed data files format and content: BigWig files were created from BAM files for each sample.

molecule: polyA RNA

source_name: adipose

extract_protocol:
RNA samples were extracted using RNeasy Lipid Tissue total RNA mini kit  (Qiagen, Valencia, CA). Extracted RNA samples underwent quality control (QC) assessment using the Agilent Bioanalyzer (Agilent, Santa Clara, CA)
With a minimum of 1 µg input RNA, we generated first-strand cDNA using random hexamer-primed reverse transcription, followed by second-strand cDNA synthesis using RNase H and DNA polymerase, and ligation of sequencing adapters using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA). Fragments of ~350 bp were selected by gel electrophoresis, followed by 15 cycles of PCR amplification. The prepared  libraries were then sequenced using Illumina’s HiSeq 2000 with two lanes per sample which generated 2×101 bp or 2x100 bp paired-end reads in ~200 to 500 million unfiltered reads per sample.

value: adipose

tag: Sex

value: Female

tag: race

value: African American

value: intravenous LPS

tag: inflammatory response

value: low


title: adipose_replicate_25 [intravenous LPS]


title: adipose_replicate_24 [intravenous LPS]

value: Male


title: adipose_replicate_22 [intravenous LPS]

value: Caucasian


title: adipose_replicate_19 [intravenous LPS]


title: adipose_replicate_18 [intravenous LPS]


title: adipose_replicate_20 [intravenous LPS]


title: adipose_replicate_17 [intravenous LPS]


title: adipose_replicate_14 [intravenous LPS]


title: adipose_replicate_15 [intravenous LPS]


title: adipose_replicate_21 [intravenous LPS]


title: adipose_replicate_13 [intravenous LPS]

description: adipose_high_pre_vs_post_gene_exp.diff.gz

value: high


title: adipose_replicate_11 [intravenous LPS]


title: adipose_replicate_10 [intravenous LPS]


title: MOFff_CD2_1


title: adipose_replicate_7 [intravenous LPS]


title: adipose_replicate_8 [intravenous LPS]


title: adipose_replicate_5 [intravenous LPS]


title: adipose_replicate_6 [intravenous LPS]


title: adipose_replicate_4 [intravenous LPS]


title: adipose_replicate_2 [intravenous LPS]


title: adipose_replicate_1 [intravenous LPS]


title: miRNA-seq CC-CR rep3

description:
small RNA
processed data file: miRNA_counts.txt

source_name: HCA-7 derived CC-CR subline

value: human colorectal cancer cell line

tag: culture type

value: 3D culture

tag: cetuximab sensitivity

value: resisitant


title: miRNA-seq CC-CR rep1


title: miRNA-seq CC-CR rep2


title: miRNA-seq CC rep3

source_name: HCA-7 derived CC subline

value: sensitive


title: miRNA-seq CC rep2


title: adipose_replicate_16 [intravenous LPS]


title: miRNA-seq CC rep1


title: TAC_HiC

city: Los Angeles

first: Tom

last: Vondriska

state: CA

address: 650 Charles E Young Dr, BH553

institute: UCLA

description: Transverse Aortic Constriction, combined samples.

data_processing:
library strategy: HiC-seq
Raw paired-end 50bp reads were mapped to mm10 using BWA-MEM (Li and Durbin, 2009) as recently described (Schmitt et al., 2016). Raw genome-wide contact matrices were generated using a custom Perl script. To normalize genome-wide raw contact matrices, we first removed bin pairs that fell outside the 5th and 99.5th percentiles (that had abnormally low or high coverage, respectively). We then used a custom Perl script to perform iterative correction and eigenvalue decomposition (ICE) on the filtered matrices for 50 iterations (Imakaev et al., 2012). We then divided all entries in each genome-wide contact matrix by the corresponding matrix sum, and then multiplied them by the arbitrary value of 1 billion for 5kb resolution or 1 million for 40kb and 50kb resolution (Crane et al., 2015). For the main analyses in this study, all biological replicates were combined.
To call and visualize chromatin loops, we used Juicer (Durand et al., 2016b) and Juicebox (Durand et al., 2016a). We first ran juicebox_tools_7.0 pre to generate .hic files for each condition, using reads with mapping quality  10. We then used juicebox_tools_7.0 hiccups, a functionality of Juicer, to call loops on the .hic files, using default parameters. Juicebox v1.5 was used to visualize the data.
Genome_build: mm10
Supplementary_files_format_and_content: .hic files (output from Juicer)

source_name: Isolated cardiac myocytes

extract_protocol:
For each replicate, one million isolated adult cardiomyocytes were fixed in 1% formaldehyde and underwent in situ Hi-C as described (Rao et al., 2014), using MboI as the restriction enzyme. Hi-C libraries were sequenced on an Illumina HiSeq 4000 instrument. Please see Figure S1 for detailed data on read counts, cis/trans interactions, and mappability.
For each replicate, one million isolated adult cardiomyocytes were fixed in 1% formaldehyde and underwent in situ Hi-C as described (Rao et al., 2014), using MboI as the restriction enzyme. Hi-C libraries were sequenced on an Illumina HiSeq 4000 instrument. Please see Figure S1 for detailed data on read counts, cis/trans interactions, and mappability.

tag: genotype/phenotype

value: Transverse Aortic Constriction

value: Left ventricle


title: adipose_replicate_24 [baseline]

description:
adipose_AA_Cau_BodyMap_gene_exp.diff.gz
adipose_AA_Cau_GENCODE_gene_exp.diff.gz
adipose_male_female_BodyMap_gene_exp.diff.gz
adipose_male_female_GENCODE_gene_exp.diff.gz
adipose_low_pre_vs_post_gene_exp.diff.gz

value: baseline


title: adipose_replicate_25 [baseline]


title: adipose_replicate_9 [intravenous LPS]


title: adipose_replicate_12 [intravenous LPS]


title: Control_HiC

description: Control, combined samples. These samples were not given tamoxifen.

value: control


title: adipose_replicate_20 [baseline]


title: adipose_replicate_22 [baseline]


title: adipose_replicate_18 [baseline]


title: adipose_replicate_16 [baseline]


title: adipose_replicate_17 [baseline]


title: adipose_replicate_3 [intravenous LPS]


title: OSvK_rep1_Sox2

description:
Sample 1942
fibroblast 5 days after OSvK addition
[Processed data files]:
Sox2_100_OSvK_avg_Sox2_381.bedGraph.gz
Sox2_100_OSvK_rep1_Sox2_1942.bedGraph.gz

data_processing:
cutadapt-1.9.1  cutadapt -a AGATCGGAAGAGC
bwa-0.7.13  bwa aln
bwa-0.7.13  bwa sampe
all duplicates eliminated
values at all features are calculated by (number of midpoints of tags / bp of feature) / (total number of unique tags / genome length)
above described values are quantile normalized
Genome_build: hg19
Supplementary_files_format_and_content: bed, bedGraph, and wig.

source_name: MRC5 Day 5 after OSvK rep1

treatment_protocol: About 7-8 x 105 MRC5 fibroblasts were seeded on 10 cm plates on day 0. These cells were grown in EMEM (ATCC) media supplemented with 10% FBS. Twenty-four hours later, two plates were trypsinzed to get an estimate of average number of cells in each 10 cm plate. Cells were then infected with lentiviruses separately encoding either OSKM or OS(v)KM at multiplicities of infections (MOIs) that were determined to be optimal for reprogramming (see Suppl Table 2). Media was changed daily until the time of harvest on day 5. At the time of harvest, cells on plates were washed once with PBS (room temperature) and cross-linked by adding EMEM + 10% FBS containing 1% fomaldehyde. Plates were returned to the incubator and incubated for 10-15 minutes. Cells were washed twice with ice cold PBS containing a cocktail of protease inhibitors (Sigma Cat # P8340; 10ml/ml PBS) and 1mM phenylmethylsulfonyl fluoride (PMSF). Cross-linked cells from each condition (Mock infected MRC5, OSKM or OS(v)KM; all at passage 8) were scraped using a cell scraper, pooled in 15 ml tubes and pelleted. We typically pooled cross-linked cells from at least 4-5, 10cm plates per condition (~ 5 million cells) for each ChIP-Seq assay. As controls, we harvested approximately 5 million cross-linked human ES (H9 hESCs, p. 35) or human iPS cells (an iPSC line derived using OS(v)KM (3S2 hiPSC, p.20) from on 6 cm plates and grown in feeder-free conditions (on vitronectin-coated plates and grown in Essential 8 media).

tag: chip antibody

value: Sox2 (R&D Systems AF2018)

value: MRC5 fibroblast

tag: protocol

value: Oct4, Sox2-VP16 and Klf4 addition

tag: time

value: 5 days

tag: passage


title: OSvK_rep1_Klf4

description:
Sample 1950
fibroblast 5 days after OSvK addition
[Processed data files]:
Klf4_100_OSvK_avg_Klf4_383.bedGraph.gz
Klf4_100_OSvK_rep1_Klf4_1950.bedGraph.gz

value: Klf4 (R&D Systems AF3640)

tag: cell line


title: OSK_rep1_Klf4

description:
Sample 1947
fibroblast 5 days after OSK addition
[Processed data files]:
Klf4_100_OSK_avg_Klf4_370.bedGraph.gz
Klf4_100_OSK_rep1_Klf4_1947.bedGraph.gz

source_name: MRC5 Day 5 after OSK rep1

value: Oct4, Sox2 and Klf4 addition


title: OSK_rep1_Sox2

description:
Sample 1934
fibroblast 5 days after OSK addition
[Processed data files]:
Sox2_100_OSK_avg_Sox2_369.bedGraph.gz
Sox2_100_OSK_rep1_Sox2_1934.bedGraph.gz


title: adipose_replicate_15 [baseline]

value: adipose

value: Female

value: African American

value: low


title: OSvK_rep1_Oct4

description:
Sample 1941
fibroblast 5 days after OSvK addition
[Processed data files]:
Oct4_100_OSvK_avg_Oct4_379.bedGraph.gz
Oct4_100_OSvK_rep1_Oct4_1941.bedGraph.gz


title: CTCF_Knockout_HiC

description: CTCF Knockout, combined samples. These samples were treated with tamoxifen diet to induce CTCF knockout.

tag: strain

value: CTCF Knockout


title: adipose_replicate_14 [baseline]

value: Male

value: Caucasian


title: adipose_replicate_13 [baseline]

description:
adipose_AA_Cau_BodyMap_gene_exp.diff.gz
adipose_AA_Cau_GENCODE_gene_exp.diff.gz
adipose_male_female_BodyMap_gene_exp.diff.gz
adipose_male_female_GENCODE_gene_exp.diff.gz
adipose_high_pre_vs_post_gene_exp.diff.gz

value: high


title: adipose_replicate_23 [baseline]


title: adipose_replicate_21 [baseline]


title: OSK_rep1_Oct4

description:
Sample 1933
fibroblast 5 days after OSK addition
[Processed data files]:
Oct4_100_OSK_avg_Oct4_368.bedGraph.gz
Oct4_100_OSK_rep1_Oct4_1933.bedGraph.gz


title: adipose_replicate_12 [baseline]


title: OSvK_rep1_H3K4me1

description:
Sample 1935
fibroblast 5 days after OSvK addition
[Processed data files]:
OSvK_avg_H3K4me1_Bin_2000_376.bed.gz
OSvK_avg_H3K4me1_Bin_2000_376.wig.gz
OSvK_rep1_H3K4me1_Bin_2000_1935.bed.gz
OSvK_rep1_H3K4me1_Bin_2000_1935.wig.gz


title: adipose_replicate_10 [baseline]


title: OSK_rep1_H3K4me1

description:
Sample 1927
fibroblast 5 days after OSK addition
[Processed data files]:
OSK_avg_H3K4me1_Bin_2000_365.bed.gz
OSK_avg_H3K4me1_Bin_2000_365.wig.gz
OSK_rep1_H3K4me1_Bin_2000_1927.bed.gz
OSK_rep1_H3K4me1_Bin_2000_1927.wig.gz


title: adipose_replicate_19 [baseline]


title: OSK_rep1_H3K27me3

description:
Sample 1929
fibroblast 5 days after OSK addition
[Processed data files]:
OSK_avg_H3K27me3_Bin_2000_366.bed.gz
OSK_avg_H3K27me3_Bin_2000_366.wig.gz
OSK_rep1_H3K27me3_Bin_2000_1929.bed.gz
OSK_rep1_H3K27me3_Bin_2000_1929.wig.gz


title: OSvK_rep1_H3K27me3

description:
Sample 1937
fibroblast 5 days after OSvK addition
[Processed data files]:
OSvK_avg_H3K27me3_Bin_2000_377.bed.gz
OSvK_avg_H3K27me3_Bin_2000_377.wig.gz
OSvK_rep1_H3K27me3_Bin_2000_1937.bed.gz
OSvK_rep1_H3K27me3_Bin_2000_1937.wig.gz


title: OSvK_rep1_H3K27ac

description:
Sample 1938
fibroblast 5 days after OSvK addition
[Processed data files]:
OSvK_avg_H3K27ac_Bin_2000_375.bed.gz
OSvK_avg_H3K27ac_Bin_2000_375.wig.gz
OSvK_rep1_H3K27ac_Bin_2000_1938.bed.gz
OSvK_rep1_H3K27ac_Bin_2000_1938.wig.gz


title: OSK_rep1_H3K27ac

description:
Sample 1930
fibroblast 5 days after OSK addition
[Processed data files]:
OSK_avg_H3K27ac_Bin_2000_364.bed.gz
OSK_avg_H3K27ac_Bin_2000_364.wig.gz
OSK_rep1_H3K27ac_Bin_2000_1930.bed.gz
OSK_rep1_H3K27ac_Bin_2000_1930.wig.gz

value: Oct4, Sox2 andKlf4 addition


title: adipose_replicate_8 [baseline]

value: baseline


title: adipose_replicate_9 [baseline]


title: adipose_replicate_5 [baseline]


title: adipose_replicate_6 [baseline]


title: adipose_replicate_4 [baseline]


title: adipose_replicate_7 [baseline]


title: adipose_replicate_3 [baseline]


title: 585A1-iMeLC#2

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

description: SC3seq amplified from 1 ng total RNA extracted from cells sorted with BTAG

data_processing:
All the reads were surveyed and the adaptor or the poly-A sequences were trimmed by cutadapt-1.3 with options "-c -m 30 -a CTCGAGGGCGCGCCGGATCCATATACGCCTTGGCCGTACAGCAG -g CTCGAGGGCGCGCCGGATCCATATACGCCTTGGCCGTACAGCAG -a AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA". The trimmed reads with less than 30 bp were discarded.
Untrimmed and trimmed reads of 30 bp or longer were mapped onto the genome and the ERCC spike-in RNA sequences with tophat-1.4.1/bowtie1.0.1 with the “—no-coverage-search” option.
Mapped reads on the genome and the ERCC were separated, and the reads on the genome were converted into the expression levels by cufflinks-2.2.0 using the “-compatible-hits-norm”, “-no-length-correction” and “—library-type fr-secondstrand” options and reference gene annotations with extended TTSs. We also set the cufflinks option “-max-mle-iterations” to 50,000, because default iterations (5,000) resulted in “FAILED” when estimating the expression levels of some genes. For the reference gene annotations used in cufflinks, we extended the TTSs of the reference genes up to 10 kb downstream to correctly estimate the expression levels of genes whose transcripts are longer than the reference toward the 3 prime.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

source_name: iMeLC

growth_protocol: hiPSCs were maintained under a feeder-free condition [StemFitTM (Ajinomoto, Tokyo, Japan) medium on recombinant LAMININ511 (rLN511E8) (iMatrix-511, Nippi, Tokyo, Japan)-coated cell culture plates] (Nakagawa et al., 2014).  The iMeLCs were induced by plating 1.0-2.0 × 105 hiPSCs maintained in StemFitTM onto a well of a human plasma fibronectin (Millipore, FC010)-coated 12-well plate in GK15 medium [GMEM (Life Technologies) with 15% KSR, 0.1 mM NEAA, 2 mM L-glutamine, 1 mM sodium pyruvate and 0.1 mM 2-mercaptoethanol] containing 50 ng/ml of Activin A, 3 µM of CHIR99021 and 10 µM of a ROCK inhibitor (Y-27632; Wako Pure Chemical Industries).

extract_protocol:
Total RNA was extracted from hiPSCs and iMeLCs by using an RNeasy Micro Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions.  Synthesis and amplification of cDNAs using 1 ng of purified total RNA, and construction of cDNA libraries for RNA sequencing (ABI SOLiD 5500XL system; Life Technologies) were performed as described in (Nakamura et al., 2015).
cDNA synthesis and amplification from isolated RNAs/single cells were perfomed essentially as reported in [Kurimoto, K.et.al., Nucleic Acids Research, 34(5), e42.]. Library constructions for SOLiD System were performed as reported in [Nakamura et.al., Nuceic Acids Res. (2015)].

tag: cell type

value: iMeLC


title: OSK_rep1_H3K4me3

description:
Sample 1928
fibroblast 5 days after OSK addition
[Processed data files]:
OSK_avg_H3K4me3_Bin_2000_363.bed.gz
OSK_avg_H3K4me3_Bin_2000_363.wig.gz
OSK_rep1_H3K4me3_Bin_2000_1928.bed.gz
OSK_rep1_H3K4me3_Bin_2000_1928.wig.gz


title: adipose_replicate_11 [baseline]


title: adipose_replicate_1 [baseline]


title: 585A1-iMeLC#1


title: 585A1-hiPSC#2

source_name: hiPSC

value: hiPSC


title: OSvK_rep1_PolII

description:
Sample 1940
fibroblast 5 days after OSvK addition
[Processed data files]:
OSvK_avg_PolII_Bin_2000_373.bed.gz
OSvK_avg_PolII_Bin_2000_373.wig.gz
OSvK_rep1_PolII_Bin_2000_1940.bed.gz
OSvK_rep1_PolII_Bin_2000_1940.wig.gz
gene_OSvK_avg_PolII_373.bed.gz
gene_OSvK_avg_PolII_373.bedGraph.gz
gene_OSvK_rep1_PolII_1940.bed.gz
gene_OSvK_rep1_PolII_1940.bedGraph.gz

value: Rpb1 CTD (Cell Signaling 2629S Lot:3)

value: MRC5 fibroblast


title: 585B1-868-iMeLC#1


title: 585B1-868-hiPSC#2


title: 585B1-868-hiPSC#1


title: 201B7-iMeLC#2


title: MM_4

city: Brisbane

first: James

last: Hudson

state: QLD

address: 300 Herston Rd

country: Australia

institute: QIMR Berghofer Medical Research Institute

description:
EdgeR_Normalised_CPM
CountMatrix_Maturation_Ensembl_IDs

data_processing:
FASTQ files were quality trimmed with Trimmomatic
Reads were mapped to hg38 using RNA STAR
Count matrix was calculated with GENCODE v24 annotations using Htseq tools
EdgeR was used for all comparisons
Genome_build: GRCh38/hg38

source_name: human cardiac organoids

growth_protocol: Briefly, HES3 were maintained as TypLE (ThermoFisher Scientific) passaged cultures using mTeSR-1 (Stem Cell Technologies)/Matrigel (Millipore). hPSCs were seeded at 2  104 cells/cm2 in Matrigel-coated flasks and cultured for 4 days using mTeSR-1. They were then differentiated into cardiac mesoderm using RPMI B27- medium (RPMI1640 GlutaMAX+ 2% B27 supplement without insulin, 200   M L-ascorbic acid 2 phosphate sesquimagnesium salt hydrate (Sigma) and 1% Penicillin/Streptomycin (all ThermoFisher Scientific) containing 5 ng/ml BMP-4 (RnD Systems), 9 ng/ml Activin A (RnD Systems), 5 ng/ml FGF-2 (RnD Systems) and 1   M CHIR99021 (Stem Cell Technologies) with daily medium exchange for 3 days. Subsequently, they were specified into a cardiomyocyte/stromal cell mixture using RPMI B27- containing 5   M IWP-4 (Stem Cell Technologies) followed by another 7 days of RPMI B27+ (RPMI1640 GlutaMAX + 2% B27 supplement with insulin, 200   M L-ascorbic acid 2 phosphate sesquimagnesium salt hydrate and 1% Penicillin/Streptomycin) with medium exchange every 2-3 days. The differentiated cells were then cultured in RPMI B27+ until digestion at 15 days using 0.2% collagenase type I (Sigma) in 20% fetal bovine serum (FBS) in PBS (with Ca2+ and Mg2+) for 60 min at 37  C, followed by 0.25% trypsin-EDTA for 10 min. The cells were filtered using a 100 mm mesh cell strainer (BD Biosciences), centrifuged at 300 x g for 3 min, and resuspended at the required density in CTRL medium:   -MEM GlutaMAX, 10% FBS, 200   M L-ascorbic acid 2 phosphate sesquimagnesium salt hydrate and 1% Penicillin/Streptomycin.

extract_protocol:
RNA was extracted using trizol and precipitated using glycogen according to manufacturers instructions. Clean-up and DNAse protocols was performed using Rneasy MinElute Cleanup Kit (QIAGEN)
RNA-seq libraries were created with TruSeq Stranded Total RNA kits (Illumina) and read with HiSeq SR Cluster v4 kit (Illumina) on a HiSeq 2500 sequencer. Barcode information:  <sample_name>_<flowcell_ID>_<index >_<lane>_<readNum>_fastq.gz

treatment_protocol: human cardiac organoids were cultured in either CTRL or MM media (DMEM without glucose, glutamine and phenol red (ThermoFisher Scientific) supplemented with 4% B27 (without insulin), 1% GlutaMAX, 200 μM L-ascorbic acid 2 phosphate sesquimagnesium salt hydrate and 1% Penicillin/Streptomycin, 1mM glucose and 100uM palmitatic acid) for 11 days and then harvested

value: ES-cell derived human cardiac organoids


title: 201B7-iMeLC#1


title: MM_1


title: MM_2


title: MM_3


title: iPS_rep1_Myc

description:
Sample 1535
[Processed data files]:
Myc_100_iPS_avg_Myc_346.bedGraph.gz
Myc_100_iPS_rep1_Myc_1535.bedGraph.gz

value: Myc (R&D Systems AF3696)

value: iPS cells

value: iPS 3s2


title: iPS_rep2_Myc

description:
Sample 1772
[Processed data files]:
Myc_100_iPS_avg_Myc_346.bedGraph.gz
Myc_100_iPS_rep2_Myc_1772.bedGraph.gz


title: OSvKM_rep2_Myc

description:
Sample 1731
[Processed data files]:
Myc_100_OSvKM_avg_Myc_345.bedGraph.gz
Myc_100_OSvKM_rep2_Myc_1731.bedGraph.gz

value: MRC5 fibroblasts

value: Oct4, Sox2-VP16, Klf4 and Myc addition

value: 5 days


title: OSvKM_rep1_Myc

description:
Sample 1527
[Processed data files]:
Myc_100_OSvKM_avg_Myc_345.bedGraph.gz
Myc_100_OSvKM_rep1_Myc_1527.bedGraph.gz


title: OSKM_rep2_Myc

description:
Sample 1720
[Processed data files]:
Myc_100_OSKM_avg_Myc_344.bedGraph.gz
Myc_100_OSKM_rep2_Myc_1720.bedGraph.gz

value: Oct4, Sox2, Klf4 and Myc addition


title: adipose_replicate_2 [baseline]

description:
adipose_AA_Cau_BodyMap_gene_exp.diff.gz
adipose_AA_Cau_GENCODE_gene_exp.diff.gz
adipose_male_female_BodyMap_gene_exp.diff.gz
adipose_male_female_GENCODE_gene_exp.diff.gz
adipose_high_pre_vs_post_gene_exp.diff.gz

value: adipose

value: Male

value: African American


title: MRC5_rep1_Myc

description:
Sample 1698
[Processed data files]:
Myc_100_MRC5_avg_Myc_343.bedGraph.gz
Myc_100_MRC5_rep1_Myc_1698.bedGraph.gz


title: 585A1-hiPSC#1


title: OSvKM_rep2_Klf4

description:
Sample 1730
[Processed data files]:
Klf4_100_OSvKM_avg_Klf4_338.bedGraph.gz
Klf4_100_OSvKM_rep2_Klf4_1730.bedGraph.gz

value: Klf4 (R&D Systems AF3640)


title: OSK_rep1_PolII

description:
Sample 1932
fibroblast 5 days after OSK addition
[Processed data files]:
OSK_avg_PolII_Bin_2000_362.bed.gz
OSK_avg_PolII_Bin_2000_362.wig.gz
OSK_rep1_PolII_Bin_2000_1932.bed.gz
OSK_rep1_PolII_Bin_2000_1932.wig.gz
gene_OSK_avg_PolII_362.bed.gz
gene_OSK_avg_PolII_362.bedGraph.gz
gene_OSK_rep1_PolII_1932.bed.gz
gene_OSK_rep1_PolII_1932.bedGraph.gz

value: Oct4, Sox2 and Klf4 addition


title: MRC5_rep2_Myc

description:
Sample 1709
[Processed data files]:
Myc_100_MRC5_avg_Myc_343.bedGraph.gz
Myc_100_MRC5_rep2_Myc_1709.bedGraph.gz


title: iPS_rep1_Klf4

description:
Sample 1534
[Processed data files]:
Klf4_100_iPS_avg_Klf4_339.bedGraph.gz
Klf4_100_iPS_rep1_Klf4_1534.bedGraph.gz


title: iPS_rep2_Klf4

description:
Sample 1771
[Processed data files]:
Klf4_100_iPS_avg_Klf4_339.bedGraph.gz
Klf4_100_iPS_rep2_Klf4_1771.bedGraph.gz


title: 201B7-hiPSC#1


title: OSvKM_rep1_Klf4

description:
Sample 1526
[Processed data files]:
Klf4_100_OSvKM_avg_Klf4_338.bedGraph.gz
Klf4_100_OSvKM_rep1_Klf4_1526.bedGraph.gz


title: OSKM_rep1_Klf4

description:
Sample 1516
[Processed data files]:
Klf4_100_OSKM_avg_Klf4_337.bedGraph.gz
Klf4_100_OSKM_rep1_Klf4_1516.bedGraph.gz


title: OSKM_rep2_Klf4

description:
Sample 1719
[Processed data files]:
Klf4_100_OSKM_avg_Klf4_337.bedGraph.gz
Klf4_100_OSKM_rep2_Klf4_1719.bedGraph.gz


title: MRC5_rep2_Klf4

description:
Sample 1708
[Processed data files]:
Klf4_100_MRC5_avg_Klf4_336.bedGraph.gz
Klf4_100_MRC5_rep2_Klf4_1708.bedGraph.gz


title: OSvKM_rep2_Sox2

description:
Sample 1729
[Processed data files]:
Sox2_100_OSvKM_avg_Sox2_330.bedGraph.gz
Sox2_100_OSvKM_rep2_Sox2_1729.bedGraph.gz

value: Sox2 (R&D Systems AF2018)


title: iPS_rep1_Sox2

description:
Sample 1533
[Processed data files]:
Sox2_100_iPS_avg_Sox2_327.bedGraph.gz
Sox2_100_iPS_rep1_Sox2_1533.bedGraph.gz


title: MRC5_rep1_Klf4

description:
Sample 1697
[Processed data files]:
Klf4_100_MRC5_avg_Klf4_336.bedGraph.gz
Klf4_100_MRC5_rep1_Klf4_1697.bedGraph.gz


title: OSvKM_rep1_Sox2

description:
Sample 1525
[Processed data files]:
Sox2_100_OSvKM_avg_Sox2_330.bedGraph.gz
Sox2_100_OSvKM_rep1_Sox2_1525.bedGraph.gz


title: iPS_rep3_Sox2

description:
Sample 723
[Processed data files]:
Sox2_100_iPS_avg_Sox2_327.bedGraph.gz
Sox2_100_iPS_rep3_Sox2_723.bedGraph.gz

value: iPS R4


title: 201B7-hiPSC#2

description: SC3seq amplified from 1 ng total RNA extracted from cells sorted with BTAG

value: hiPSC


title: MRC5_rep2_Sox2

description:
Sample 1707
[Processed data files]:
Sox2_100_MRC5_avg_Sox2_332.bedGraph.gz
Sox2_100_MRC5_rep2_Sox2_1707.bedGraph.gz


title: OSKM_rep2_Sox2

description:
Sample 1718
[Processed data files]:
Sox2_100_OSKM_avg_Sox2_329.bedGraph.gz
Sox2_100_OSKM_rep2_Sox2_1718.bedGraph.gz


title: OSKM_rep1_Myc

description:
Sample 1517
[Processed data files]:
Myc_100_OSKM_avg_Myc_344.bedGraph.gz
Myc_100_OSKM_rep1_Myc_1517.bedGraph.gz


title: OSKM_rep1_Sox2

description:
Sample 1514
[Processed data files]:
Sox2_100_OSKM_avg_Sox2_329.bedGraph.gz
Sox2_100_OSKM_rep1_Sox2_1514.bedGraph.gz


title: MRC5_rep1_Sox2

description:
Sample 1696
[Processed data files]:
Sox2_100_MRC5_avg_Sox2_332.bedGraph.gz
Sox2_100_MRC5_rep1_Sox2_1696.bedGraph.gz


title: iPS_rep2_Oct4

description:
Sample 1769
[Processed data files]:
Oct4_100_iPS_avg_Oct4_103.bedGraph.gz
Oct4_100_iPS_rep2_Oct4_1769.bedGraph.gz


title: OSvKM_rep1_Oct4

description:
Sample 1524
[Processed data files]:
Oct4_100_OSvKM_avg_Oct4_326.bedGraph.gz
Oct4_100_OSvKM_rep1_Oct4_1524.bedGraph.gz


title: White adipose tissue WATM33

city: Seattle

first: Julia

middle: Yue

last: Cui

state: WA

address: 4225 Rossevelt Way Ne

department: Environmental and Occupational Health Sciences

institute: University of Washington

description:
Germ free
CuffDiff_WAT.zip

data_processing:
Fastq files were demultiplexed and checked with FastQC
reads were mapped to the mouse mm10 geneome using TopHat2
SAM files were convereted to BAM files and then sorted using SAMTools
Transcript differential regulation was determined using CuffDiff
FDR-BH (q value) below 0.05 were considered statistically significant
Genome_build: mm10
Supplementary_files_format_and_content: zipped Cuffdiff output

source_name: White adipose tissue

extract_protocol:
Livers were collected after removing the gallbladder. Intestinal contents were flushed with phosphate buffered saline and intestinal tissues were separated into various sections, namely duodenum, jejunum, ileum, and large intestine (colon).  Brown adipose, white adipose, and muscle were collected. All tissues were snap-frozen in liquid nitrogen and stored at -80˚C.Total RNA was isolated from tissues using RNA Bee reagent and RNA integrity was confirmed using a dual Agilent 2100 Bioanalyzer (RIN>7.0).
The cDNA libraries from total RNA samples were prepared using an Illumina TruSeq RNA sample prep kit. Three micrograms of total RNA were used as the RNA input according to recommendations of the manufacturer’s protocol.
multiplexed, TrueSeq version 3 chemistry

value: White adipose tissue

tag: age

value: 2-3 months

tag: genotype

value: wild type


title: White adipose tissue WATM29

description:
Germ free
CuffDiff_WAT.zip

tag: tissue


title: OSvKM_rep2_Oct4

description:
Sample 1728
[Processed data files]:
Oct4_100_OSvKM_avg_Oct4_326.bedGraph.gz
Oct4_100_OSvKM_rep2_Oct4_1728.bedGraph.gz


title: iPS_rep1_Oct4

description:
Sample 1532
[Processed data files]:
Oct4_100_iPS_avg_Oct4_103.bedGraph.gz
Oct4_100_iPS_rep1_Oct4_1532.bedGraph.gz

value: iPS cells


title: OSKM_rep2_Oct4

description:
Sample 1717
[Processed data files]:
Oct4_100_OSKM_avg_Oct4_325.bedGraph.gz
Oct4_100_OSKM_rep2_Oct4_1717.bedGraph.gz


title: OSKM_rep1_Oct4

description:
Sample 1513
[Processed data files]:
Oct4_100_OSKM_avg_Oct4_325.bedGraph.gz
Oct4_100_OSKM_rep1_Oct4_1513.bedGraph.gz


title: White adipose tissue WATM31

description:
Germ free
CuffDiff_WAT.zip


title: MRC5_rep2_Oct4

description:
Sample 1706
[Processed data files]:
Oct4_100_MRC5_avg_Oct4_101.bedGraph.gz
Oct4_100_MRC5_rep2_Oct4_1706.bedGraph.gz


title: White adipose tissue WATM28

description:
Conventional
CuffDiff_WAT.zip


title: White adipose tissue WATM25

description:
Conventional
CuffDiff_WAT.zip


title: iPS_rep2_H3K4me1

description:
Sample 1743
[Processed data files]:
iPS_avg_H3K4me1_Bin_2000_152.bed.gz
iPS_avg_H3K4me1_Bin_2000_152.wig.gz
iPS_rep2_H3K4me1_Bin_2000_1743.bed.gz
iPS_rep2_H3K4me1_Bin_2000_1743.wig.gz

value: iPS 3s2


title: White adipose tissue WATM26

description:
Conventional
CuffDiff_WAT.zip


title: OSvKM_rep2_H3K4me1

description:
Sample 1722
[Processed data files]:
OSvKM_avg_H3K4me1_Bin_2000_150.bed.gz
OSvKM_avg_H3K4me1_Bin_2000_150.wig.gz
OSvKM_rep2_H3K4me1_Bin_2000_1722.bed.gz
OSvKM_rep2_H3K4me1_Bin_2000_1722.wig.gz

value: MRC5 fibroblasts


title: Muscle MusM29

description:
Germ free
CuffDiff_Mus.zip

source_name: Muscle

value: Muscle


title: Muscle MusM28

description:
Conventional
CuffDiff_Mus.zip


title: iPS_rep3_H3K27me3

description:
Sample 734
[Processed data files]:
iPS_avg_H3K27me3_Bin_2000_144.bed.gz
iPS_avg_H3K27me3_Bin_2000_144.wig.gz
iPS_rep3_H3K27me3_Bin_2000_734.bed.gz
iPS_rep3_H3K27me3_Bin_2000_734.wig.gz


title: OSKM_rep2_H3K4me1

description:
Sample 1711
[Processed data files]:
OSKM_avg_H3K4me1_Bin_2000_149.bed.gz
OSKM_avg_H3K4me1_Bin_2000_149.wig.gz
OSKM_rep2_H3K4me1_Bin_2000_1711.bed.gz
OSKM_rep2_H3K4me1_Bin_2000_1711.wig.gz

value: 5 days


title: MRC5_rep2_H3K4me1

description:
Sample 1700
[Processed data files]:
MRC5_avg_H3K4me1_Bin_2000_148.bed.gz
MRC5_avg_H3K4me1_Bin_2000_148.wig.gz
MRC5_rep2_H3K4me1_Bin_2000_1700.bed.gz
MRC5_rep2_H3K4me1_Bin_2000_1700.wig.gz


title: Muscle MusM26

description:
Conventional
CuffDiff_Mus.zip


title: MRC5_rep1_Oct4

description:
Sample 1695
[Processed data files]:
Oct4_100_MRC5_avg_Oct4_101.bedGraph.gz
Oct4_100_MRC5_rep1_Oct4_1695.bedGraph.gz


title: Brown adipose tissue BATM32

description:
Germ free
CuffDiff_BAT.zip

source_name: Brown adipose tissue

value: Brown adipose tissue


title: OSvKM_rep2_H3K27me3

description:
Sample 1725
[Processed data files]:
OSvKM_avg_H3K27me3_Bin_2000_142.bed.gz
OSvKM_avg_H3K27me3_Bin_2000_142.wig.gz
OSvKM_rep2_H3K27me3_Bin_2000_1725.bed.gz
OSvKM_rep2_H3K27me3_Bin_2000_1725.wig.gz

value: Oct4, Sox2-VP16, Klf4 and Myc addition


title: Brown adipose tissue BATM34

description:
Germ free
CuffDiff_BAT.zip


title: iPS_rep2_H3K27me3

description:
Sample 1746
[Processed data files]:
iPS_avg_H3K27me3_Bin_2000_144.bed.gz
iPS_avg_H3K27me3_Bin_2000_144.wig.gz
iPS_rep2_H3K27me3_Bin_2000_1746.bed.gz
iPS_rep2_H3K27me3_Bin_2000_1746.wig.gz


title: Brown adipose tissue BATM29

description:
Germ free
CuffDiff_BAT.zip


title: Brown adipose tissue BATM27

description:
Conventional
CuffDiff_BAT.zip


title: Brown adipose tissue BATM26

description:
Conventional
CuffDiff_BAT.zip


title: OSvK_rep1_H3K4me3

description:
Sample 1936
fibroblast 5 days after OSvK addition
[Processed data files]:
OSvK_avg_H3K4me3_Bin_2000_374.bed.gz
OSvK_avg_H3K4me3_Bin_2000_374.wig.gz
OSvK_rep1_H3K4me3_Bin_2000_1936.bed.gz
OSvK_rep1_H3K4me3_Bin_2000_1936.wig.gz

value: MRC5 fibroblast

value: Oct4, Sox2-VP16 and Klf4 addition


title: MRC5_rep2_H3K27me3

description:
Sample 1703
[Processed data files]:
MRC5_avg_H3K27me3_Bin_2000_140.bed.gz
MRC5_avg_H3K27me3_Bin_2000_140.wig.gz
MRC5_rep2_H3K27me3_Bin_2000_1703.bed.gz
MRC5_rep2_H3K27me3_Bin_2000_1703.wig.gz


title: iPS_rep2_H3K27ac

description:
Sample 1747
[Processed data files]:
iPS_avg_H3K27ac_Bin_2000_137.bed.gz
iPS_avg_H3K27ac_Bin_2000_137.wig.gz
iPS_rep2_H3K27ac_Bin_2000_1747.bed.gz
iPS_rep2_H3K27ac_Bin_2000_1747.wig.gz


title: Muscle MusM31

description:
Germ free
CuffDiff_Mus.zip


title: Brown adipose tissue BATM24

description:
Conventional
CuffDiff_BAT.zip


title: Liver LivM32

description:
Germ free
CuffDiff_Liv.zip

source_name: Liver

value: Liver


title: OSvKM_rep2_H3K27ac

description:
Sample 1726
[Processed data files]:
OSvKM_avg_H3K27ac_Bin_2000_135.bed.gz
OSvKM_avg_H3K27ac_Bin_2000_135.wig.gz
OSvKM_rep2_H3K27ac_Bin_2000_1726.bed.gz
OSvKM_rep2_H3K27ac_Bin_2000_1726.wig.gz


title: Liver LivM31

description:
Germ free
CuffDiff_Liv.zip


title: MRC5_rep1_H3K4me1

description:
Sample 1689
[Processed data files]:
MRC5_avg_H3K4me1_Bin_2000_148.bed.gz
MRC5_avg_H3K4me1_Bin_2000_148.wig.gz
MRC5_rep1_H3K4me1_Bin_2000_1689.bed.gz
MRC5_rep1_H3K4me1_Bin_2000_1689.wig.gz


title: OSvKM_rep1_H3K27ac

description:
Sample 1521
[Processed data files]:
OSvKM_avg_H3K27ac_Bin_2000_135.bed.gz
OSvKM_avg_H3K27ac_Bin_2000_135.wig.gz
OSvKM_rep1_H3K27ac_Bin_2000_1521.bed.gz
OSvKM_rep1_H3K27ac_Bin_2000_1521.wig.gz


title: Muscle MusM32

description:
Germ free
CuffDiff_Mus.zip


title: iPS_rep1_H3K27ac

description:
Sample 1529
[Processed data files]:
iPS_avg_H3K27ac_Bin_2000_137.bed.gz
iPS_avg_H3K27ac_Bin_2000_137.wig.gz
iPS_rep1_H3K27ac_Bin_2000_1529.bed.gz
iPS_rep1_H3K27ac_Bin_2000_1529.wig.gz


title: OSKM_rep2_H3K27ac

description:
Sample 1715
[Processed data files]:
OSKM_avg_H3K27ac_Bin_2000_134.bed.gz
OSKM_avg_H3K27ac_Bin_2000_134.wig.gz
OSKM_rep2_H3K27ac_Bin_2000_1715.bed.gz
OSKM_rep2_H3K27ac_Bin_2000_1715.wig.gz

value: Oct4, Sox2, Klf4 and Myc addition


title: Jejunum JejM33

description:
Germ free
CuffDiff_Jej.zip

source_name: Jejunum

value: Jejunum


title: Liver LivM29

description:
Germ free
CuffDiff_Liv.zip


title: OSKM_rep1_H3K27ac

description:
Sample 1510
[Processed data files]:
OSKM_avg_H3K27ac_Bin_2000_134.bed.gz
OSKM_avg_H3K27ac_Bin_2000_134.wig.gz
OSKM_rep1_H3K27ac_Bin_2000_1510.bed.gz
OSKM_rep1_H3K27ac_Bin_2000_1510.wig.gz


title: MRC5_rep1_H3K27ac

description:
Sample 1693
[Processed data files]:
MRC5_avg_H3K27ac_Bin_2000_133.bed.gz
MRC5_avg_H3K27ac_Bin_2000_133.wig.gz
MRC5_rep1_H3K27ac_Bin_2000_1693.bed.gz
MRC5_rep1_H3K27ac_Bin_2000_1693.wig.gz


title: MRC5_rep2_H3K27ac

description:
Sample 1704
[Processed data files]:
MRC5_avg_H3K27ac_Bin_2000_133.bed.gz
MRC5_avg_H3K27ac_Bin_2000_133.wig.gz
MRC5_rep2_H3K27ac_Bin_2000_1704.bed.gz
MRC5_rep2_H3K27ac_Bin_2000_1704.wig.gz


title: Muscle MusM24

description:
Conventional
CuffDiff_Mus.zip


title: Jejunum JejM29

description:
Germ free
CuffDiff_Jej.zip


title: OSKM_rep2_H3K27me3

description:
Sample 1714
[Processed data files]:
OSKM_avg_H3K27me3_Bin_2000_141.bed.gz
OSKM_avg_H3K27me3_Bin_2000_141.wig.gz
OSKM_rep2_H3K27me3_Bin_2000_1714.bed.gz
OSKM_rep2_H3K27me3_Bin_2000_1714.wig.gz


title: Ileum IleM33

description:
Germ free
CuffDiff_Ile.zip

source_name: Ileum

value: Ileum


title: iPS_rep3_H3K4me3

description:
Sample 735
[Processed data files]:
iPS_avg_H3K4me3_Bin_2000_129.bed.gz
iPS_avg_H3K4me3_Bin_2000_129.wig.gz
iPS_rep3_H3K4me3_Bin_2000_735.bed.gz
iPS_rep3_H3K4me3_Bin_2000_735.wig.gz

value: iPS R4


title: MRC5_rep1_H3K27me3

description:
Sample 1692
[Processed data files]:
MRC5_avg_H3K27me3_Bin_2000_140.bed.gz
MRC5_avg_H3K27me3_Bin_2000_140.wig.gz
MRC5_rep1_H3K27me3_Bin_2000_1692.bed.gz
MRC5_rep1_H3K27me3_Bin_2000_1692.wig.gz


title: Ileum IleM31

description:
Germ free
CuffDiff_Ile.zip


title: iPS_rep2_H3K4me3

description:
Sample 1744
[Processed data files]:
iPS_avg_H3K4me3_Bin_2000_129.bed.gz
iPS_avg_H3K4me3_Bin_2000_129.wig.gz
iPS_rep2_H3K4me3_Bin_2000_1744.bed.gz
iPS_rep2_H3K4me3_Bin_2000_1744.wig.gz


title: Ileum IleM29

description:
Germ free
CuffDiff_Ile.zip


title: iPS_rep1_H3K4me3

description:
Sample 1530
[Processed data files]:
iPS_avg_H3K4me3_Bin_2000_129.bed.gz
iPS_avg_H3K4me3_Bin_2000_129.wig.gz
iPS_rep1_H3K4me3_Bin_2000_1530.bed.gz
iPS_rep1_H3K4me3_Bin_2000_1530.wig.gz


title: OSvKM_rep2_H3K4me3

description:
Sample 1723
[Processed data files]:
OSvKM_avg_H3K4me3_Bin_2000_127.bed.gz
OSvKM_avg_H3K4me3_Bin_2000_127.wig.gz
OSvKM_rep2_H3K4me3_Bin_2000_1723.bed.gz
OSvKM_rep2_H3K4me3_Bin_2000_1723.wig.gz


title: Duodenum DuodM34

description:
Germ free
CuffDiff_Duod.zip

source_name: Duodenum

value: Duodenum


title: Duodenum DuodM32

description:
Germ free
CuffDiff_Duod.zip

value: 2-3 months


title: OSvKM_rep1_H3K4me3

description:
Sample 1522
[Processed data files]:
OSvKM_avg_H3K4me3_Bin_2000_127.bed.gz
OSvKM_avg_H3K4me3_Bin_2000_127.wig.gz
OSvKM_rep1_H3K4me3_Bin_2000_1522.bed.gz
OSvKM_rep1_H3K4me3_Bin_2000_1522.wig.gz


title: Duodenum DuodM29

description:
Germ free
CuffDiff_Duod.zip

value: wild type


title: MRC5_rep2_H3K4me3

description:
Sample 1701
[Processed data files]:
MRC5_avg_H3K4me3_Bin_2000_125.bed.gz
MRC5_avg_H3K4me3_Bin_2000_125.wig.gz
MRC5_rep2_H3K4me3_Bin_2000_1701.bed.gz
MRC5_rep2_H3K4me3_Bin_2000_1701.wig.gz


title: Colon ColM34

description:
Germ free
CuffDiff_Col.zip

source_name: Colon

value: Colon


title: OSKM_rep2_H3K4me3

description:
Sample 1712
[Processed data files]:
OSKM_avg_H3K4me3_Bin_2000_126.bed.gz
OSKM_avg_H3K4me3_Bin_2000_126.wig.gz
OSKM_rep2_H3K4me3_Bin_2000_1712.bed.gz
OSKM_rep2_H3K4me3_Bin_2000_1712.wig.gz


title: MRC5_rep1_H3K4me3

description:
Sample 1690
[Processed data files]:
MRC5_avg_H3K4me3_Bin_2000_125.bed.gz
MRC5_avg_H3K4me3_Bin_2000_125.wig.gz
MRC5_rep1_H3K4me3_Bin_2000_1690.bed.gz
MRC5_rep1_H3K4me3_Bin_2000_1690.wig.gz


title: Colon ColM33

description:
Germ free
CuffDiff_Col.zip


title: Colon ColM32

description:
Germ free
CuffDiff_Col.zip


title: iPS_rep2_PolII

description:
Sample 1748
[Processed data files]:
iPS_avg_PolII_Bin_2000_121.bed.gz
iPS_avg_PolII_Bin_2000_121.wig.gz
iPS_rep2_PolII_Bin_2000_1748.bed.gz
iPS_rep2_PolII_Bin_2000_1748.wig.gz
gene_iPS_avg_PolII_121.bed.gz
gene_iPS_avg_PolII_121.bedGraph.gz
gene_iPS_rep2_PolII_1748.bed.gz
gene_iPS_rep2_PolII_1748.bedGraph.gz

value: Rpb1 CTD (Cell Signaling 2629S Lot:3)

value: iPS cells

value: iPS 3s2


title: iPS_rep1_PolII

description:
Sample 1531
[Processed data files]:
iPS_avg_PolII_Bin_2000_121.bed.gz
iPS_avg_PolII_Bin_2000_121.wig.gz
iPS_rep1_PolII_Bin_2000_1531.bed.gz
iPS_rep1_PolII_Bin_2000_1531.wig.gz
gene_iPS_avg_PolII_121.bed.gz
gene_iPS_avg_PolII_121.bedGraph.gz
gene_iPS_rep1_PolII_1531.bed.gz
gene_iPS_rep1_PolII_1531.bedGraph.gz


title: Jejunum JejM31

description:
Germ free
CuffDiff_Jej.zip


title: OSvKM_rep2_PolII

description:
Sample 1727
[Processed data files]:
OSvKM_avg_PolII_Bin_2000_119.bed.gz
OSvKM_avg_PolII_Bin_2000_119.wig.gz
OSvKM_rep2_PolII_Bin_2000_1727.bed.gz
OSvKM_rep2_PolII_Bin_2000_1727.wig.gz
gene_OSvKM_avg_PolII_119.bed.gz
gene_OSvKM_avg_PolII_119.bedGraph.gz
gene_OSvKM_rep2_PolII_1727.bed.gz
gene_OSvKM_rep2_PolII_1727.bedGraph.gz

value: MRC5 fibroblasts

value: 5 days


title: OSvKM_rep1_PolII

description:
Sample 1523
[Processed data files]:
OSvKM_avg_PolII_Bin_2000_119.bed.gz
OSvKM_avg_PolII_Bin_2000_119.wig.gz
OSvKM_rep1_PolII_Bin_2000_1523.bed.gz
OSvKM_rep1_PolII_Bin_2000_1523.wig.gz
gene_OSvKM_avg_PolII_119.bed.gz
gene_OSvKM_avg_PolII_119.bedGraph.gz
gene_OSvKM_rep1_PolII_1523.bed.gz
gene_OSvKM_rep1_PolII_1523.bedGraph.gz

value: Oct4, Sox2-VP16, Klf4 and Myc addition