title: M2.Wt.sexF.rep3 (srHC-seq)

description:
srHC.M2.hep.Wt.sexF.bw
srHC.M2.hep.Wt.sexMF.bw
het.M2.hep.Wt.domains.bed
int.M2.hep.Wt.domains.bed

data_processing:
Library strategy: srHC-seq
Demultiplexing and merging: Sequences were basecalled and demultiplexed with bcl2fastq2-v2.19.0.316 (--barcode-mismatches 0 --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --ignore-missing-controls --auto-set-to-zero-barcode-mismatches --find-adapters-with-sliding-window --adapter-stringency 0.9 --mask-short-adapter-reads 35 --minimum-trimmed-read-length 35) and technical and sequencing replicates concatenated (FASTQs)
Alignments: Reads were aligned to NCBI v37/mm9 build from the UCSC genome broser with STAR 2.4.2a with the following parameters: --outFilterMultimapNmax 1  --alignIntronMax 1
Quality control: Alignments were filtered for uniqueness to avoid PCR duplication artifacts
Track creation: For individual biolgical replicate bigWigs: RPM-normalized large and small bedGraphs were generated separately with genomeCoverageBed from bedtools, then log2(large/small) bedGraphs were generated (to avoid divide by zero errors: a small addend was added to small bedGraphs region with values=0, equal to the size of the smallest value in that small bedGraph ), then converted to bigWigs (bedgraphToBigWig tool from the UCSC Genome Browser).
Merged track creation: For merged biological replicate BGRs, data was averaged for all the biological replicates (i.e., take the individual biological replicates as BGRs, merge using bedtools unionbedg -filler "N/A" -i BGR1 BGR2 > unionBGR, then take the unionBGR, and average the values. Note:  If the unionBGR has chr start stop BGRvalue1=10 and BGRvalue2=NA, then the averaged value=10, not 5.)
Enriched domain calling: For heterochromatin/intermediate/euchromatin domain calling, enriched heterochromatic and euchromatic domains were called with the  zdomain-caller (Becker et al, Molecular Cell 2017) with the following parameters: 10kb windows, 2kb slide, 40 percentile cutoff, and a pruning value equal to the cutoff.  Intermediate domains are regions not called as heterochromatic or euchromatic, or double positive het/euch domains.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files represent log2(large/small) (If no biological replicate number, then this is the biological replicate merged version).  BED9 files are domain calls (C=closed/heterochromatin, O=open/euchromatin, I=intermediate).

extract_protocol:
Mice are anesthetized using isoflurane (Butler Animal Health Supply, Cat# 029405) and monitored by paw pinch. A V-shaped incision was used to reveal the abdominal cavity, the intestines moved aside, and a 22 or 24 gauge catheter (Midwest Veterinary Supply, 381423; 22 gauge for M2 animals, 24 gauge for P14 animals) was used to cannulate the venae cavae while liver perfusion media pumps into the circulation, and the portal vein is immediately severed. 37°C liver perfusion media (Invitrogen 17701-038) and then liver digest media (Invitrogen 17703-034) are perfused through the liver (45 mL each for 2-month-old animals, 25 mL each for P14 animals). Livers are dissociated with a cutting motion with cell scrapers in William’s E Medium (Sigma W4128) and strained through a 100 μm filter (BD 352360). Isolated hepatocytes were fixed in 25 mL 1% formaldehyde in PBS for 10 min at room temperature with gentle rocking and quenched with 2.3 mL 2.5 M glycine for 5min at room temperature with gentle rocking. Fixed hepatocytes were pelleted in a swinging bucket centrifuge for 5 min at 4˚C at 50g. Fixed hepatocytes were resuspended in 10 mL (age: P14) or 20 mL (age: M2) ice-cold RSB buffer (10 mM Tris pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.5% NP40, protease inhibitor cocktail tablet, 0.1 mM PMSF, 1% Triton-X 100) and dounced 25 times in a Wheaton dounce on ice to lyse cytoplasmic membranes. Fixed and dounced hepatocytes were pelleted for 10 min at 4˚C at 100g and resuspended in 2 mL ice-cold AS sonication-lysis buffer (10 mM Tris-HCl, pH8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1 mM DTT, Roche Protease Inhibitor Cocktail (Sigma 11697498001), 0.1 mM PMSF).  10 μg DNA fragments were resuspended in 50 μL TE. For large fragments: 25 μL beads (0.5 volumes) were added, incubated, and beads were removed and large DNA isolated from them as described by the manufacturer. For medium fragments: 10 μL beads (0.2 volumes) were added to the supernatant from the large beads/DNA slurry, incubated, and beads were removed and medium DNA isolated from them as described by the manufacturer. For small fragments: 35 μL beads (0.7 volumes) were added to the supernatant from the medium beads/DNA slurry, incubated, and beads were removed and small DNA isolated from them as described by the manufacturer. Large fragments further sonicated to a size amenable for Illumina sequencing.  Large and small fragments were prepped for sequencing with the NEBNext Ultra DNA library prep kit (NEB catalog # E7370). Libraries were sequenced as 75 bp, single-end reads on a NextSeq 500.
NEBNext Ultra DNA library prep kit (NEB catalog # E7370)

value: hepatocytes


title: L-MEP_2_AntiFlag1

status: Public on Mar 01 2019

type: SRA

city: Houston

first: Daisuke

last: Nakada

state: Texas

address: One Baylor Plaza

department: Molecular and Human Genetics

country: USA

institute: Baylor College of Medicine

library_source: genomic

data_processing:
Library strategy: Cut&Run
Basecalling and fastq generation were performed using Illumina’s software (Casava, bcl2fastq)
Mapping (to mm10) and spike-in normalization were performed using the CutAndRun python scripts available at https://github.com/peteskene
Peaks were called using HOMER (version 4.10)
Motif analysis was performed using HOMER
Genome_build: mm10
Supplementary_files_format_and_content: UCSC formatted bedGraph files, generated using deepTools (bamCoverage); scores are CPM normalized.

molecule: genomic DNA

organism: Mus musculus

source_name: Prdm16s Leukemic-MEP cells

extract_protocol:
200,000 L-MEP were sorted and isolated with antibody for the construction of library using the Cut & Run protocol.
Cut & Run DNA was purified for end repair, adaptor ligation and amplification using KAPA Hyper Prep Kit (Roche, Penzberg, Germany) according to the manufacturer's instructions.

treatment_protocol: We transduced wild-type murine MEP cells with retroviral vectors encoding Prdm16s and transplanted them into syngeneic recipient mice. For library preparation, L-MEPs were sorted from mice that developed leukemia.

tag: strain

tag: chip antibody

value: FLAG antibody (#14793S from Cell Signaling Technologies, Danvers, MA)

tag: genotype

tag: cell type

value: leukemic megakaryocyte-erythroid progenitor (MEP) cells


title: L-MEP_1_AntiFlag1


title: L-MEP_1_AntiFlag2

value: FLAG antibody (F9291 from Sigma Aldrich, St. Louis, MO)


title: M2.Wt.sexF.rep2 (srHC-seq)

city: Philadelphia

first: Jessica

middle: Mae

last: Grindheim

state: PA

address: 3400 Civic Center Blvd SCTR 9-169

department: Cell and Developmental Biology

institute: UNIVERSITY OF PENNSYLVANIA

description:
srHC.M2.hep.Wt.sexF.bw
srHC.M2.hep.Wt.sexMF.bw
het.M2.hep.Wt.domains.bed
int.M2.hep.Wt.domains.bed
euch.M2.hep.Wt.domains.bed

value: Wt

tag: age

tag: Sex

value: female


title: M2.Wt.sexM.rep1 (srHC-seq)

description:
srHC.M2.hep.Wt.sexM.bw
srHC.M2.hep.Wt.sexMF.bw
het.M2.hep.Wt.domains.bed
int.M2.hep.Wt.domains.bed
euch.M2.hep.Wt.domains.bed

value: male


title: ChIP_M2.hep.bio2  (re-analysis of GSM3137724) (ChIP-Seq)

description:
ChIP-seq
H3K27me3.M2.hep.bio1and2.bw
H3K27me3.M2.domains.bed

data_processing:
Merging: Technical replicates (FASTQs) were concatenated before alignment
Alignment: Reads were aligned to NCBI v37/mm9 build from the UCSC Genome Browser with STAR 2.4.2a with the following parameters: --outFilterMultimapNmax 1  --alignIntronMax 1
Quality control: Alignments were filtered for uniqueness to avoid PCR duplication artifacts
Track creation: For individual biological replicate bigWigs: RPM-normalized ChIP and Input bedGraphs were generated separately with genomeCoverageBed from bedtools, then ChIP minus Input values calculated for each genomic region, then converted to bigWigs (bedgraphToBigWig tool from the UCSC Genome Browser).
Merged tracks: For merged biological replicate BGRs, data was averaged for all the biological replicates (i.e., take the individual biological replicates as BGRs, merge using bedtools unionbedg -filler "N)
A" -i BGR1 BGR2 > unionBGR, then take the unionBGR, and average the values. Note:  If the unionBGR has chr start stop BGRvalue1=10 and BGRvalue2=NA, then the averaged value=10, not 5.)
Domain calls: To call enriched H3K27me3 broad domains, the genome was divided into 2kb windows with a 1kb slide. ChIP divided by input scores were calculated for each window. The top 30% percent scoring windows for each were defined ?enriched windows?. Overlapping enriched windows were merged, less enriched edges were pruned and merged again, resulting enriched domains. The algorithms for for calling enriched domains was published previously (Becker et al., Mol Cell 2017).
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files represent ChIP minus Input (pooled or separate as described above).  The BED files describe H3K27me3 domains

extract_protocol:
Mice are anesthetized using isoflurane (Butler Animal Health Supply, Cat# 029405) and monitored by paw pinch. A V-shaped incision was used to reveal the abdominal cavity, the intestines moved aside, and a 22 or 24 gauge catheter (Midwest Veterinary Supply, 381423; 22 gauge for M2 animals, 24 gauge for P14 animals) was used to cannulate the venae cavae while liver perfusion media pumps into the circulation, and the portal vein is immediately severed. 37°C liver perfusion media (Invitrogen 17701-038) and then liver digest media (Invitrogen 17703-034) are perfused through the liver (45 mL each for 2-month-old animals, 25 mL each for P14 animals). Livers are dissociated with a cutting motion with cell scrapers in William’s E Medium (Sigma W4128) and strained through a 100 μm filter (BD 352360).  Hepatocytes are pelleted by centrifugation at 50g for 5 min at 4°C.  Isolated hepatocytes were fixed in 25 mL 1% formaldehyde in PBS for 10 min at room temperature with gentle rocking and quenched with 2.3 mL 2.5 M glycine for 5min at room temperature with gentle rocking. Fixed hepatocytes were pelleted in a swinging bucket centrifuge for 5 min at 4˚C at 50g. Fixed hepatocytes were resuspended in 10 mL (age: P14) or 20 mL (age: M2) ice-cold RSB buffer (10 mM Tris pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.5% NP40, protease inhibitor cocktail tablet, 0.1 mM PMSF, 1% Triton-X 100) and dounced 25 times in a Wheaton dounce on ice to lyse cytoplasmic membranes. Fixed and dounced hepatocytes were pelleted for 10 min at 4˚C at 100g and resuspended in 2 mL ice-cold AS sonication-lysis buffer (10 mM Tris-HCl, pH8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1 mM DTT, Roche Protease Inhibitor Cocktail (Sigma 11697498001), 0.1 mM PMSF). Hepatocytes in AS-sonication lysis buffer proceeded to sonication. P14 and M2 hepatocyte H3K27me3 (Millipore 07-449) libraries were then generated using the ThruPlex DNA-seq kit Rubicon Genomics catalog #R400428. The M2 hepatocyte H3K27me3 ChIP was previously submitted for another paper (GEO accession: GSE114198, samples: GSM3137721, GSM3137722, GSM3137723, GSM3137724).
ThruPlex DNA-seq kit Rubicon Genomics catalog #R40042

value: unknown

tag: antibody

value: H3K27me3 (Millipore 07-449)


title: ChIP_M2.hep.bio1 (re-analysis of GSM3137723) (ChIP-Seq)


title: M2.Wt.sexF.rep1 (srHC-seq)


title: P14.Ezh12.sexF.rep3 (srHC-seq)

description:
srHC.P14.hep.Ezh12.sexF.bw
srHC.P14.hep.Ezh12.sexMF.bw
het.P14.hep.Ezh12.domains.bed
int.P14.hep.Ezh12.domains.bed
euch.P14.hep.Ezh12.domains.bed

value: postnatal day 14


title: P14.Ezh12.sexF.rep2 (srHC-seq)


title: P14.Wt.sexM.rep3 (srHC-seq)

description:
srHC.P14.hep.Wt.sexM.bw
srHC.P14.hep.Wt.sexMF.bw
het.P14.hep.Wt.domains.bed
int.P14.hep.Wt.domains.bed
euch.P14.hep.Wt.domains.bed


title: P14.Ezh12.sexF.rep1 (srHC-seq)


title: P14.Ezh12.sexM.rep2 (srHC-seq)

description:
srHC.P14.hep.Ezh12.sexM.bw
srHC.P14.hep.Ezh12.sexMF.bw
het.P14.hep.Ezh12.domains.bed
int.P14.hep.Ezh12.domains.bed
euch.P14.hep.Ezh12.domains.bed


title: Input_P14.hep.sexM.bio2 (ChIP-Seq)

description:
ChIP-seq
H3K27me3.P14.hep.sexMF.bio123and4.bw
H3K27me3.P14.domains.bed

value: none (input)


title: ChIP_P14.hep.sexF.bio1 (ChIP-Seq)


title: Input_P14.hep.sexF.bio1 (ChIP-Seq)


title: Input_P14.hep.sexF.bio2 (ChIP-Seq)


title: ChIP_P14.hep.sexM.bio2 (ChIP-Seq)


title: Input_M2.hep.bio1 (re-analysis of GSM3137721) (ChIP-Seq)


title: Input_M2.hep.bio2 (re-analysis of GSM3137722) (ChIP-Seq)


title: M2.Wt.sexM.rep2 (srHC-seq)


title: Input_P14.hep.sexM.bio1 (ChIP-Seq)


title: P14.Wt.sexM.rep1 (srHC-seq)


title: P14.Wt.sexM.rep2 (srHC-seq)


title: ChIP_P14.hep.sexF.bio2 (ChIP-Seq)


title: P14.Wt.sexF.rep1 (srHC-seq)

description:
srHC.P14.hep.Wt.sexF.bw
srHC.P14.hep.Wt.sexMF.bw
het.P14.hep.Wt.domains.bed
int.P14.hep.Wt.domains.bed
euch.P14.hep.Wt.domains.bed


title: ChIP_P14.hep.sexM.bio1 (ChIP-Seq)


title: P14.Ezh12.sexM.rep1 (srHC-seq)


title: M2.hep.Wt.sexF.bio2 (RNA-Seq)

description:
rawCounts.txt
normCounts.txt
M2.hep.Wt.sexF.Grindheim.SS.2462.4

library_source: transcriptomic

data_processing:
Merging: Sequencing replicates were concatenated before alignment.
Alignment: Reads were aligned to NCBI v37/mm9 build from the UCSC Genome Browser with STAR 2.4.2a with the following parameters: ----outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000
Quantitation: Alignments were assigned to mm9 RefSeq (refFlat, from UCSC genome table browser) transcripts with HTSeq v0.6.1p1 and the following arguments: -f sam -r pos -t exon -i gene_id -s no
Differential testing: The count table from HTSeq was normalized and differential gene expression called with DESeq2 v1.14.1
Track creation: Alignments greater than 75bp (corresponding to splicing events) were filtered out to avoid spurious intronic signal.  Reads were split into plus and minus strands, RPM-normalized bedgraphs were generated with genomeCoverageBed (UCSC utilities), and converted to bigWigs with bedgraphToBigWig (UCSC utilities).
Genome_build: mm9
Supplementary_files_format_and_content: BigWigs represent plus and minus strand RNA signal.  TXT files represent raw (HTseq output) and normalized (DESeq2 output) counts.

molecule: polyA RNA

extract_protocol:
Hepatocytes were resuspended in TRIzol (Thermo Fischer 15596026) and stored at -20°C until the day of library preparation, when RNA was isolated from TRIzol per the manufacturer’s protocol and brought through at least cDNA synthesis all on the same day. RNA isolated from TRIzol was resuspended in TE. Next, total RNA was polyA-selected using 50 μL Invitrogen Dynabeads (dT)25-61002 per the manufacturer’s protocol. Sequencing libraries were prepped from polyA+ RNA using the NEBNext Ultra Directional Library Prep Kit for Illumina (NEB 7420), with 12 cycles of PCR using NEBNext Oligos. After library prep, library size was assessed using a Bioanalyzer and Agilent DNA 1000 chip (Agilent 5067-1504), and the concentration of amplifiable DNA assessed with the NEBNext Library Quantification Kit (NEB E7630). Individual libraries were diluted to 2 nM, pooled, and the pooled library requantified with the NEBNext Next Library Quantification Kit. The pooled library was diluted to 3.2 pM using the NEBNext 500/550 High Output Reagent Cartridge V2 75 cycles (Ref 15057934) and loaded onto the NextSeq 500 for 75bp single-end sequencing.
NEBNext Ultra Directional Library Prep Kit for Illumina (NEB 7420)


title: M2.hep.Wt.sexF.bio1 (RNA-Seq)

description:
rawCounts.txt
normCounts.txt
M2.hep.Wt.sexF.Grindheim.SS.2462.3


title: M2.hep.Wt.sexM.bio2 (RNA-Seq)

description:
rawCounts.txt
normCounts.txt
M2.hep.Wt.sexM.Grindheim.SS.2462.4


title: M2.hep.Wt.sexM.bio1 (RNA-Seq)

description:
rawCounts.txt
normCounts.txt
M2.hep.Wt.sexM.Grindheim.SS.2462.3


title: P14.Wt.sexF.rep2 (srHC-seq)


title: P14.hep.Ezh12.sexF.bio4 (RNA-Seq)

description:
rawCounts.txt
normCounts.txt
P14.hep.Ezh12.sexF.Grindheim.SS.2462.4


title: P14.hep.Ezh12.sexF.bio1 (RNA-Seq)

description:
rawCounts.txt
normCounts.txt
P14.hep.Ezh12.sexF.Grindheim.SS.2462.1


title: P14.hep.Ezh12.sexF.bio2 (RNA-Seq)

description:
rawCounts.txt
normCounts.txt
P14.hep.Ezh12.sexF.Grindheim.SS.2462.2


title: P14.hep.Ezh12.sexF.bio3 (RNA-Seq)

description:
rawCounts.txt
normCounts.txt
P14.hep.Ezh12.sexF.Grindheim.SS.2462.3


title: P14.hep.Ezh12.sexM.bio2 (RNA-Seq)

description:
rawCounts.txt
normCounts.txt
P14.hep.Ezh12.sexM.Grindheim.SS.2462.2


title: P14.hep.Ezh12.sexM.bio1 (RNA-Seq)

description:
rawCounts.txt
normCounts.txt
P14.hep.Ezh12.sexM.Grindheim.SS.2462.1


title: P14.hep.Wt.sexF.bio2 (RNA-Seq)

description:
rawCounts.txt
normCounts.txt
P14.hep.Wt.sexF.Grindheim.SS.2462.2


title: P14.hep.Wt.sexF.bio1 (RNA-Seq)

description:
rawCounts.txt
normCounts.txt
P14.hep.Wt.sexF.Grindheim.SS.2462.1


title: P14.hep.Wt.sexM.bio1 (RNA-Seq)

description:
rawCounts.txt
normCounts.txt
P14.hep.Wt.sexM.Grindheim.SS.2462.1


title: Untreated cells (sole elctroporation) from donor A

city: Segrate

first: Ivan

last: Merelli

state: Milano

address: via F.lli Cervi 93

department: Istituto di Tecnologie Biomediche

country: Italy

institute: Consiglio Nazionale delle Ricerche

data_processing:
Library strategy: Clear-seq
Basecalling using blc2fastq and trimming using cutadapt
Alignment using bwa
Variant calling using GATK4
Genome_build: GRCh38

organism: Homo sapiens

source_name: HSPC cells

extract_protocol:
total DNA was isolated using QIAamp DNA Micro Kit (QIAGEN), according to the manufacturer’s instructions and purified with AMPure Beads
DNA library amplicons were then hybridized with ClearSeq Comprehensive Cancer library (Agilent), a panel of 151 disease-associated genes and the final enriched library was sequenced on an NextSeq 500 (Illumina) with 1000X coverage.
ClearSeq Comprehensive Cancer library preparation and sequencing

value: Cord blood derived CD34+ cells

tag: treatment

value: untreated

tag: time point

value: 14 days upon electroporation


title: Untreated cells (sole elctroporation) from donor B


title: HS RNP AAVS1 edited cells from donor C + GSE56

value: HS RNP AAVS1 edited


title: HS RNP AAVS1 edited cells from donor B + GSE56


title: Untreated cells (sole elctroporation) from donor C


title: BRG1_ChIPseq

city: shanghai

first: Yongfeng

last: Liu

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

country: China

institute: The Institute of Health Sciences, SIBS, CAS / SJTUSM

data_processing:
Sequence Analysis: The 75-nt sequence reads generated by Illumina sequencing (using NextSeq  500) are mapped to the genome using the BWA algorithm with default settings. Alignment  information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter,  align with no more than 2 mismatches, and map uniquely to the genome are used in the  subsequent analysis. In addition, unless stated otherwise, duplicate reads (“PCR duplicates”) are  removed.
Determination of Fragment Density: Since the 5´-ends of the aligned reads (= “tags”) represent the  end of ChIP/IP-fragments, the tags are extended in silico (using Active Motif software) at their 3´-  ends to a length of 150-250 bp, depending on the average fragment length in the size selected  library (normally 200 bp). To identify the density of fragments (extended tags) along the genome,  the genome is divided into 32-nt bins and the number of fragments in each bin is determined.
Peak Finding:The generic term “Interval” is used to describe genomic regions with local enrichments in tag numbers. Intervals are defined by the chromosome number and a start and end  coordinate. MACS is used  to identify the binding sites of transcription factors that bind to discrete sites.
Genome_build: mm10
Supplementary_files_format_and_content: bw

source_name: colon epthelial cells

growth_protocol: no treatment

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

treatment_protocol: mice were treated with 2% DSS for 3 day and isolated the colon epethelial cell

tag: genotype/variation

value: wildtype

value: EDTA isolated colon epithelial cells


title: P14.hep.Ezh12.sexF.bio5 (RNA-Seq)

description:
rawCounts.txt
normCounts.txt
P14.hep.Ezh12.sexF.Grindheim.SS.2462.5

value: hepatocytes


title: colon epthelial cells input DNA


title: HUVEC-IBH30656 infected  3hpi

city: Reno

first: Subhash

middle: C

last: Verma

state: NV

address: 1664 N Virginia Street, MS 320

department: Microbiology and Immunology

institute: University of Nevada, Reno

description: RNA-seq analysis

data_processing:
The libraries were run on Illumina Next-seq instrument and Illumina software was used for peak calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Sequence were imported into CLC Henomic Workbech 10.0.1 with NCBI/Sanger or Illumia pipeline 1.8 and later option.
Reads were mapped to the human genome database sequence to calculate the RPKM values of cellular gene using CLC Workbench
Relative expressions were calculated with reference of mock infected control cells
Genome_build: NCBI genome build of human genome, Homo sapiens (hg19) sequence
Supplementary_files_format_and_content: TPM, RPKM etc.

molecule: total RNA

source_name: HUVEC-IBH30656 infected  3hpi

growth_protocol: HUVEC cells were grown in Medium 200 with 10% FBS

extract_protocol:
Total mRNA was extracted from the mock infected control and ZIKV infected cells
The libraries were constructed using TrueSeq RNA sample preparation kit v2 from Illumina.

treatment_protocol: Cells were infected with ZIKV virus and allowed to grow for 12h

tag: cell line

value: HUVECs

tag: infection

value: IBH30656 ZIKV


title: HUVEC-PRVABC59 infected  3hpi

description: RNA-seq analysis

source_name: HUVEC-PRVABC59 infected  3hpi

value: PRVABC59 ZIKV


title: P14.hep.Wt.sexM.bio3 (RNA-Seq)

description:
rawCounts.txt
normCounts.txt
P14.hep.Wt.sexM.Grindheim.SS.2462.3

value: Wt


title: P14.hep.Wt.sexM.bio2 (RNA-Seq)

description:
rawCounts.txt
normCounts.txt
P14.hep.Wt.sexM.Grindheim.SS.2462.2


title: HeLa wt EMCV poly(A)-/Ribo- RNA replicate 2

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

description: HeLa cell EMCV poly(A)-/Ribo- RNA replicate 2

data_processing:
Library strategy: Ribo-seq
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Reads were aligned against the GRCh37/hg19 human reference genome with the UCSC Genes annotation (hg19 knownGene.txt updated at 2013/6/30) using HISAT2 (Kim et al., 2013) 2.0.5 (parameters: --known-splicesite-infile --no-softclip --rna-strandness RF --score-min L,-16,0 --mp 7,7 --rfg 0,7 --rdg 0,7 --max-seeds 20 -k 10 -t -p 12 -S).
Bam to Bedgraph using genomeCoverageBed(v2.26.0)
Bedgraph to bigwig using UCSC bedGraphToBigWig(v4)
Genome_build: hg19 for human samples
Supplementary_files_format_and_content: bigwig file (UCSC bigwig in an indexed binary format. http://genome.ucsc.edu/goldenPath/help/bigWig.html)

source_name: HeLa cells

growth_protocol: HeLa cells (Human cervical cancer cells) were cultured with DMEM medium supplemented with 10% FBS; PA-1 (human ovarian adenocarcinoma cell) were cultured with MEMα medium supplemented with 10% FBS.

extract_protocol:
For total RNA, 10μg of total RNAs isolated from HeLa cells were separated into polyadenylated and nonpolyadenylated fractionations by oligo(dT) magnetic beads (Invitrogen). The polyadenylated RNA population was purified by oligo(dT) magnetic beads and followed by DNase I treatment at 37 °C for 30 mins (Ambion, DNA-freeTM Kit). Ribosomal RNAs were further depleted by using RiboMinus kit (Invitrogen) (Yang et al., 2011) to get the poly (A)-/ribo- RNA population. Then poly (A)-/ribo- RNAs were subjected to Trizol extraction.
For SHAPE-MaP, isolated RNAs were treated with DNase I (Ambion, DNA-freeTM kit) to remove possible DNA contamination. About 50-100 μg of RNAs were obtained under each treatment, and were then used for SHAPE-MaP reverse transcription by adding 1 μL (200 U/μL) of SuperScript II (Invitrogen), 6 mM Mn2+ and gene-specific primers for linear or circular RNAs (5S rRNA was used as a spike-in control). Mn2+ was removed using G-25 micro-spin columns (GE Healthcare) after SHAPE-MaP reverse transcription. Second-strand synthesis was performed with Q5 hot start high-fidelity DNA polymerase and nested PCR was performed to further improve DNA yield.
For total RNA and ribo– RNA-seq libraries were prepared with Illumina TruSeq RNA LT Sample Prep Kit. Deep sequencing was performed on Illumina NextSeq 500 at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.
SHAPE-MaP libraries were prepared from 1 ng of DNAs for linear (linearSHAPE-MaP) or circular (circSHAPE-MaP) RNAs, and size-selected with AmpureXP beads (Agencourt) with a 1:1 (bead to sample) ratio to obtain library DNA products spanning 100-400 bp in length. Final libraries were quantified using Agilent Bioanalyzer 2100 and QuBit high-sensitivity dsDNA assay. Deep sequencing was performed by Illumina NextSeq 500 at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

treatment_protocol:
For total RNA, HeLa cells (Human cervical cancer cells) were cells were washed by DPBS (GIBCO), trypsinized, and collected by centrifugation.
For SHAPE-MaP, PA1 cells were incubated with 900 uL of fresh cell culture medium and 100 μL of 10x SHAPE Chemical in DMSO with the final concentration of NAI at 100 mM for 10 minutes at 37°C.
For poly (I:C) and EMCV stimulation, HeLa cells (Human cervical cancer cells) were transfected with poly (I:C) for 6 hour or infected with EMCV (0.1 moi) for 24h

value: HeLa

tag: type

value: poly(A)-/Ribo-

value: EMCV infection 24h


title: HeLa wt EMCV poly(A)-/Ribo- RNA replicate 1

description: HeLa cell EMCV poly(A)-/Ribo- RNA replicate 1


title: HS RNP AAVS1 edited cells from donor A


title: HS RNP AAVS1 edited cells from donor B


title: HS RNP AAVS1 edited cells from donor C


title: HS RNP AAVS1 edited cells from donor A + GSE56


title: HeLa wt ctrl poly(A)-/Ribo- RNA replicate 2

description: HeLa cell control poly(A)-/Ribo- RNA replicate 2


title: HeLa wt ctrl poly(A)+ RNA replicate 1

description: HeLa cell control poly(A)+ RNA replicate 1

data_processing:
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Reads were aligned against the GRCh37/hg19 human reference genome with the UCSC Genes annotation (hg19 knownGene.txt updated at 2013/6/30) using HISAT2 (Kim et al., 2013) 2.0.5 (parameters: --known-splicesite-infile --no-softclip --rna-strandness RF --score-min L,-16,0 --mp 7,7 --rfg 0,7 --rdg 0,7 --max-seeds 20 -k 10 -t -p 12 -S).
Bam to Bedgraph using genomeCoverageBed(v2.26.0)
Bedgraph to bigwig using UCSC bedGraphToBigWig(v4)
Genome_build: hg19 for human samples
Supplementary_files_format_and_content: bigwig file (UCSC bigwig in an indexed binary format. http://genome.ucsc.edu/goldenPath/help/bigWig.html)

value: poly(A)+ RNA


title: HeLa RNaseL KO ctrl poly(A)-/Ribo- RNA replicate 1

description: HeLa cell RNaseL KO control poly(A)-/Ribo- RNA replicate 1


title: HeLa RNaseL KO ctrl poly(A)+ RNA

description: HeLa cell RNaseL KO control poly(A)+ RNA


title: HeLa RNaseL KO poly(I:C) poly(A)+ RNA

description: HeLa cell RNaseL KO poly(I:C) poly(A)+ RNA

value: poly(I:C) stimulation 6h


title: HeLa RNaseL KO ctrl poly(A)-/Ribo- RNA replicate 2

description: HeLa cell RNaseL KO control poly(A)-/Ribo- RNA replicate 2


title: RNA.P14.hep.Ezh1.sexF.3

description:
rawCounts.txt
normCounts.txt

data_processing:
Merging: Sequencing replicates were concatenated before alignment.
Alignment: Reads were aligned to NCBI v37/mm9 build from the UCSC Genome Browser with STAR 2.4.2a with the following parameters: ----outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000
Quantitation: Alignments were assigned to mm9 RefSeq (refFlat, from UCSC genome table browser) transcripts with HTSeq v0.6.1p1 and the following arguments: -f sam -r pos -t exon -i gene_id -s no
Differential testing: The count table from HTSeq was normalized and differential gene expression called with DESeq2 v1.14.1
Track creation: Alignments greater than 75bp (corresponding to splicing events) were filtered out to avoid spurious intronic signal.  RPM-normalized bedgraphs were generated with genomeCoverageBed (UCSC utilities), and converted to bigWigs with bedgraphToBigWig (UCSC utilities).
Genome_build: mm9
Supplementary_files_format_and_content: BigWigs represent RPM-normalized RNA signal.  TXT files represent raw (HTseq output) and normalized (DESeq2 output) counts.

source_name: hepatocytes

extract_protocol:
Hepatocytes were resuspended in TRIzol (Thermo Fischer 15596026) and stored at -20°C until the day of library preparation, when RNA was isolated from TRIzol per the manufacturer’s protocol and brought through at least cDNA synthesis all on the same day. RNA isolated from TRIzol was resuspended in TE. Next, total RNA was polyA-selected using 50 μL Invitrogen Dynabeads (dT)25-61002 per the manufacturer’s protocol.  Libraries were prepped from polyA+ RNA using the NEBNext mRNA librarpy prep master mix set for Illumina (NEB E6110) and sequenced with a  NEBNext 500/550 High Output Reagent Cartridge V2 75 cycles (Ref 15057934) and loaded onto the NextSeq 500 for 75bp single-end sequencing.
NEBNext mRNA Library Prep Master Mix Set for Illumina E6110

value: female

value: postnatal day 14


title: HeLa RNaseL KO poly(I:C) poly(A)-/Ribo- RNA replicate 1

description: HeLa cell RNaseL KO poly(I:C) poly(A)-/Ribo- RNA replicate 1


title: HeLa RNaseL KO poly(I:C) poly(A)-/Ribo- RNA replicate 2

description: HeLa cell RNaseL KO poly(I:C) poly(A)-/Ribo- RNA replicate 2


title: HeLa ctrl poly(A)-/Ribo- RNA replicate 2

value: untreated


title: HeLa poly(I:C) poly(A)-/Ribo- RNA replicate 2

description: HeLa cell poly(I:C) poly(A)-/Ribo- RNA replicate 2


title: HeLa poly(I:C) poly(A)-/Ribo- RNA replicate 1

description: HeLa cell poly(I:C) poly(A)-/Ribo- RNA replicate 1


title: HUVEC-mock infected 3hpi

description: RNA-seq analysis

source_name: HUVEC-mock infected 3hpi

value: Mock


title: HeLa wt EMCV poly(A)+ RNA replicate 1

description: HeLa cell EMCV poly(A)+ RNA replicate 1


title: HeLa poly(I:C) poly(A)+ RNA

description: HeLa cell poly(I:C) poly(A)+ RNA


title: HeLa wt ctrl poly(A)-/Ribo- RNA replicate 1

description: HeLa cell control poly(A)-/Ribo- RNA replicate 1


title: HeLa ctrl poly(A)-/Ribo- RNA replicate 1


title: HeLa wt EMCV poly(A)+ RNA replicate 2

description: HeLa cell EMCV poly(A)+ RNA replicate 2


title: HeLa wt ctrl poly(A)+ RNA replicate 2

description: HeLa cell control poly(A)+ RNA replicate 2


title: gRNA-SOCS3 Rep 1

city: Toronto

first: Graham

last: MacLeod

state: ON

address: 144 College Street

department: Pharmaceutical Sciences

country: Canada

institute: University of Toronto

data_processing:
Reads were mapped using Kallito pseudoalignment to Homo_sapiens.GRCh38.rel79.cdna.all transcriptome using Kallisto pseudoalignment program (Bray et al., 2016)
Kallisto count data was prepared for DeSeq2 using TXImport function and differential expression analysis was performed using DeSeq
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include tpm values for each Sample (G510_Count_table.txt) and differential expression analysis per gene (G510_SOCS3KO_DeSeq2.txt)

growth_protocol: Adherent cultures grown on Laminin coated plates

extract_protocol: GSCs were dissociated, flash frozen, and RNA was harvested using Trizol reagent.

value: Glioblastoma Stem Cells

value: SOCS3 targeting gRNA


title: HeLa ctrl poly(A)+ RNA

description: HeLa cell control poly(A)+ RNA


title: gRNA-SOCS3 Rep 2


title: gRNA-LacZ Rep 3

value: non-targeting (gRNA-LacZ)


title: gRNA-SOCS3 Rep 3


title: gRNA-LacZ Rep 1


title: beta_16191

city: Worcester

first: Alan

middle: G

last: Derr

state: Massachusetts

address: 55 Lake Ave North

department: Program in Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

data_processing:
Quality control check :FastQC v0.10.1
Low-quality end trimming :FASTX-Toolkit v0.0.13
rRNA and snRNA removal :Bowtie v0.12.9
Genome alignment :Tophat2 v2.0.14
Transcriptome alignment and quantification :RSEM v1.2.18; calls Bowtie v0.12.9
Correction of batch effects caused by different sample prep methods (Nugen Ovation Human FFPE RNA-Seq kit vs Clontech SMARTer Stranded Total RNA-Seq kit). Custom R script that uses Harman batch correction, converting batch-corrected output from expected counts to TPM. :R v3.3.2, Harman v1.2.0
Calculation of differentially expressed genes :DESeq2 v1.10.2
parameters: parametric fitting, row sum=10
called via DEBrowser web interface (available from https://bioconductor.org/packages/release/bioc/html/debrowser.html)
Genome_build: hg19
Supplementary_files_format_and_content: text file, batch-corrected raw counts, DEBrowser output of DE genes

source_name: non-diabetic_pancreatic beta cells

extract_protocol:
RNA was released from fixed and stained islet cells by treatment with resuspension buffer and Proteinase K from the Ambion Recoverall kit at 50˚C for 3 hours.  Depending on cell number, RNA was purified and DNA removed on a Recoverall column or RNA-Clean XP beads.
Random primed, Clontech SMARTer Stranded Total RNA-Seq kit or Nugen Ovation Human FFPE RNA-Seq Library System (sample-specific)

tag: donor condition

value: non-diabetic

value: sorted pancreatic beta cells

tag: library kit


title: beta_nPOD6367

source_name: type I diabetic_pancreatic beta cells

value: type I diabetic

value: Clontech SMARTer Stranded Total RNA-Seq kit


title: beta_nPOD6268

value: Nugen Ovation Human FFPE RNA-Seq Library System


title: beta_T1D.6


title: beta_16278


title: beta_15049


title: beta_17103


title: ZFN

data_processing:
Preliminary analysis using the 10X Genomics pipeline relying on cellranger (base calling, alignment, feature count) using default parameters
Filtering, Normalization, Scaling using the R package Seurat
Identification of clusters using the Louvin algorithm privded by the R package Seurat
Identification of differentially expressed genes using the MAST algorithm provided by the R package Saurat
Computation of pseudotime trajectories using the R package Monocle
Genome_build: GRCh38

source_name: FACS-sorted primitive and progenitors HSPC in ratio 1 to 1

extract_protocol:
Droplet-based digital 3′ end scRNA-Seq was performed on a Chromium Single-Cell Controller (10X Genomics) using the Chromium Single Cell 3′ Reagent Kit v2 according to the manufacturer’s instructions. Single cells were partitioned in Gel Beads in Emulsion (GEMs) and lysed, followed by RNA barcoding, reverse transcription and PCR amplification (12-14 cycles, according to the available cDNA quantity).
scRNA-Seq libraries were prepared according to the manufacturer’s instructions

value: 24h upon nuclease delivery

value: Cord blood derived CD34+ cells


title: beta_nPOD6414


title: HS RNP


title: beta_16181


title: minus DSB (RNP)


title: beta_13255


title: beta_13226


title: beta_17188


title: LS RNP


title: HS/AAV6 GFP-


title: HS/AAV6 GFP+


title: gRNA-LacZ Rep 2


title: beta_16338


title: 9 plus DSB AAVS1 (repl. 3)

description: counts.txt

data_processing:
Basecalling using blc2fastq and trimming using cutadapt
Alignment using HISAT2 and gene abundance estimation using featurecounts
Differential gene expression computed using edgeR
Genome_build: GRCh38

source_name: FACS sorted progenitors HSPC cells

extract_protocol:
Total RNA was isolated using miRNeasy Micro Kit (QIAGEN), and DNase treatment was performed using RNase-free DNase Set (QIAGEN), according to the manufacturer’s instructions.
300 ng of total RNA were used for library preparation with TruSeq Stranded Total RNA with Ribo-Zero Gold kit (Illumina) and sequenced on an NextSeq 500 (Illumina)

value: 24h upon ZFN nuclease delivery


title: 7 plus DSB IL2RG (repl. 3)

description: counts.txt


title: 8 minus DSB (repl. 3)

description: counts.txt


title: 4 plus DSB IL2RG (repl. 2)

description: counts.txt


title: 5 minus DSB (repl. 2)

description: counts.txt


title: 3 plus DSB AAVS1 (repl. 1)

description: counts.txt


title: 1 plus DSB IL2RG (repl. 1)

description: counts.txt


title: 2 minus DSB (repl. 1)

description: counts.txt


title: beta_16029


title: I plus DSB AAVS1 (repl. 3)

description: counts.txt

source_name: FACS sorted primitive HSPC cells


title: beta_14223


title: H minus DSB (repl. 3)

description: counts.txt


title: beta_16149


title: F plus DSB AAVS1 (repl. 2)

description: counts.txt


title: E minus DSB (repl. 2)

description: counts.txt


title: D plus DSB IL2RG (repl. 2)

description: counts.txt


title: A plus DSB IL2RG (repl. 1)

description: counts.txt


title: G plus DSB IL2RG (repl. 3)

description: counts.txt


title: 6 plus DSB AAVS1 (repl. 2)

description: counts.txt


title: C plus DSB AAVS1 (repl. 1)

description: counts.txt


title: B minus DSB (repl. 1)

description: counts.txt


title: Control TAC 2

type: RNA

city: Madrid

first: Jesus

middle: Maria

last: Gómez-Salnero

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

hyb_protocol: One-Color MicroArray-Based Gene Expression Analysis Protocol (Agilent Technologies). Samples were hibridice for 17hours with 1.65μg of Cy3 at 65ºC in a hybridization oven.

scan_protocol: Arrays were scanned at 5μm resolution on an Agilent DNA Microarray Scanner (G2565BA) using default setting for 4x44k format one-color arrays. Images were analyzed using Feature Extraction software version 9.5.3.1 (Agilent Technologies)

data_processing: Data was normaliced with RMA in GeneSpring software.

source_name: Control Heart tissue 21 Days after surgery TAC

growth_protocol: Mice were sacrificed 21 days after surgery (Sham and TAC).

extract_protocol: Qiagen RNeasy Mini Kit using DNAse treatment

treatment_protocol: The heart of the mice were extracted and a section of the left ventricule was selected for RNA purification.

value: wild type

value: trans aortic banding

tag: time


title: Control Sham 3

source_name: Control Heart tissue 21 Days after surgery NO TAC

label_protocol: One-Color MicroArray-Based Gene Expression Analysis Protocol (Agilent Technologies)

value: sham


title: Control Sham 1


title: Transgenic TAC 1

source_name: Transgenic Heart tissue 21 Days after surgery TAC

value: CnAb1 transgenic overexpressing


title: Control TAC 1


title: Control TAC 3


title: Transgenic TAC 3


title: Transgenic TAC 2


title: Transgenic Sham 3

source_name: Transgenic Heart tissue 21 Days after surgery NO TAC


title: CD8+ T cells, Sm. intestine (aHSCT + Day 4) 5

city: Budapest

first: Nikolett

last: Lupsa

state: Pest

address: Nagyvárad tér 4

department: Genetics, Cell-and Immunbiology

country: Hungary

institute: Semmelweis University

description: Gene expression

hyb_protocol: Amplified samples were hybridized to 4x44k mouse whole genome microarrays using the Gene Expression Hybridization Kit (Agilent).

scan_protocol: Samples were scanned on an Agilent Microarray Scanner using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent). Raw data were quantile normalized and further analyzed by GeneSpring (Agilent).

source_name: CD8+ Teff, Sm. intestine (aHSCT + Day 4)

label_protocol: 300pg of total RNA per sample was reverse transcribed and two rounds of linear RNA amplificaton were performed by the Arcturus RiboAmp PLUS, Cy3 Kit (Life Technologies) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: On aHSCT + Day 0 and aHSCT + Day 4 transplanted recipients were sacrificed to obtain the small intestine, lungs, liver and peripheral blood. Grafted CD8+ T cells were labeled with anti-CD45.1 antibodies (Miltenyi Biotec), anti-Biotin Microbeads were added, and grafted CD45.1 CD8+ OT-I T cells were retrieved by positive selection using the AutoMACS Pro system (Miltenyi Biotec). Total RNA was extracted from MACS-separated T cells using the RNeasy Plus Micro Kit (Qiagen) following the manufacturer's recommendations. RNA yield was measured and integrity checked on an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Lethal acute graft versus host disease (aGVHD) was induced in healthy m-act OVA C57Bl/6 female mice by aHSCT.On the day of aHSCT (aHSCT + Day 0) recipient m-act OVA mice (C57Bl/6-Tg(CAG-OVA)-916Jen/J) received 11Gy total body irradiation (TBI) in two split doses (5,5 Gy each), 3 hours apart, using a linear accelerator (1,07Gy/min). Irradiated animals were transplanted with 3x106 bone allogeneic marrow cells and 1,5x107 splenocytes via retroorbital injection, under ketamine-xylazine anesthesia from donor OT-I mice (C57BL/6-Tg(TcraTcrb) 1100Mjb/J). Graft OT-I CD8+ T cells were obtained from CD45.1 animals, while all other graft cells and recipients carried the CD45.2 allele. On the day of transplantation (aHSCT + Day 0) and four days after aHSCT (aHSCT + Day 4) recipients were euthanized for sample retrieval.

tag: tissue

value: Sm. intestine

tag: gender

value: female

value: 8-16 weeks


title: Transgenic Sham 2

tag: strain


title: CD8+ T cells, Sm. intestine (aHSCT + Day 4) 1

description: Gene expression


title: CD8+ T cells, Sm. intestine (aHSCT + Day 4) 3

description: Gene expression


title: CD8+ T cells, P. blood (aHSCT + Day 4) 5

description: Gene expression

source_name: CD8+ T cells, P. blood (aHSCT + Day 4)

value: P. blood


title: CD8+ T cells, Sm. intestine (aHSCT + Day 4) 2

description: Gene expression


title: Transgenic Sham 1


title: CD8+ T cells, Sm. intestine (aHSCT + Day 4) 4

description: Gene expression


title: CD8+ T cells, P. blood (aHSCT + Day 4) 4

description: Gene expression


title: CD8+ T cells, P. blood (aHSCT + Day 4) 2

description: Gene expression


title: CD8+ T cells, P. blood (aHSCT + Day 4) 1

description: Gene expression


title: CD8+ T cells, Lung (aHSCT + Day 4) 2

description: Gene expression

source_name: CD8+ T cells, Lung (aHSCT + Day 4)

value: Lung


title: CD8+ T cells, P. blood (aHSCT + Day 4) 3

description: Gene expression


title: CD8+ T cells, Lung (aHSCT + Day 4) 1

description: Gene expression


title: CD8+ T cells, Lung (aHSCT + Day 4) 5

description: Gene expression


title: CD8+ T cells, Lung (aHSCT + Day 4) 3

description: Gene expression


title: CD8+ T cells, Lung (aHSCT + Day 4) 4

description: Gene expression


title: CD8+ T cells, Liver (aHSCT + Day 4) 5

description: Gene expression

source_name: CD8+ T cells, Liver (aHSCT + Day 4)

value: Liver


title: CD8+ T cells, Liver (aHSCT + Day 4) 4

description: Gene expression


title: CD8+ T cells, Liver (aHSCT + Day 4) 3

description: Gene expression


title: CD8+ T cells, Graft (aHSCT + Day 0) 4

description: Gene expression

source_name: CD8+ T cells, Graft (aHSCT + Day 0)

value: Graft


title: Fab9b_TP3

city: Guildford

first: Jonathan

last: Johnston

address: Stag Hill campus

country: United Kingdom

institute: University of Surrey

hyb_protocol: Labelled cRNA with a yield of 1.65 μg  and specific activity of 6pmol Cy3/ µg was hybridized on a Whole Human Genome 4 x 44K custom oligonucleotide microarray (G2514F, AMADID 026817; Agilent Technologies); standard manufacturer’s protocol was followed. The microarrays were hybridized for 17 hours at 65°C in an Agilent hybridization oven, at a rotation of 10 rpm. Microarrays were then washed with Agilent Wash Buffer 1 and pre-warmed Wash Buffer 2 (37°C).

scan_protocol: Microarrays were scanned using an Agilent Scanner C (Agilent Technologies Scanner G2505C US45102984) with a resolution of 5 μm. Scan resolution was set to Agilent HD (61 x 21.6mm) and a tiff file dynamic range to 20 bit.

data_processing: The scanned images were analysed with Agilent Feature Extraction Software v11.5.1.1  (Agilent Technologies) using protocol GE1_1105_Oct12 and grid 026817_D_F_20100112ANNOTATED. Log2 values of “gProcessedSignal” were quantile-normalized using the R Bioconductor package limma. Non-control replicated probes, along with their corresponding flags, were averaged. Due to loss of data (Fab2b had excessive background signal for TP5; Fab9b missed the TP5 biopsy), these two subjects were excluded from further analysis.

label_protocol: cRNA was synthesized and fluorescently labelled with Cyanine 3-CTP from 100 – 200 ng of total RNA using Agilent's Low Input Quick Amp Labeling Kit (Agilent Technologies). Prior to hybridization, cRNA was purified using the RNeasy mini kit (Qiagen) and yield and specific activity determined using the NanoDrop 2000 (Thermo Scientific).

extract_protocol: Total RNA was extracted from thawed adipose tissue using the RNeasy mini kit (Qiagen, Hilden, Germany) and following the manufacturer’s protocol. Total RNA from each sample was quantified using the NanoDrop 2000 spectrophotometer (Thermo Scientific, Massachusetts, USA) and quality of total RNA was checked by using the Agilent Bioanalyzer 2100 (Agilent Technologies, California, USA) with the RNA 6000 Nano Kit (Agilent Technologies). One biopsy had RNA of an inadequate quality and yield and was excluded from further processing.

treatment_protocol: Subcutaneous adipose tissue biopsies were taken at each sampling point under constant routine conditions. 200mg of tissue were flash frozen in liquid nitrogen within 5 minutes of collection; note that the 200mg of tissue may have been split across multiple collection tubes to ensure freezing within the stated time. Prior to the RNA extraction adipose tissue was cut into smaller pieces and were weighed. To the adipose tissue, 10 volumes compared to weight of pre-chilled (-80°C) of RNAlater-ICE frozen tissue transition solution (Ambion/Life Technologies, Massachusetts, USA) was added to the frozen adipose tissue. Tissue was then thawed for a minimum of 16 hours at -20°C.

value: Subcutaneous adipose

tag: subject

value: Male

tag: time sample taken

tag: circadian phase


title: CD8+ T cells, Liver (aHSCT + Day 4) 1

description: Gene expression

tag: age


title: Fab9b_TP1


title: Control Sham 2


title: Fab8b_TP5


title: CD8+ T cells, Graft (aHSCT + Day 0) 2

description: Gene expression


title: Fab9b_TP2


title: CD8+ T cells, Graft (aHSCT + Day 0) 3

description: Gene expression


title: Fab8b_TP2


title: Fab7b_TP3


title: Fab9b_TP4


title: Fab8b_TP1


title: Fab8b_TP4


title: Fab7b_TP2


title: Fab7b_TP4


title: Fab7b_TP1


title: Fab7b_TP5


title: Fab8b_TP3


title: Fab4b_TP4


title: Fab4b_TP1


title: Fab4b_TP5


title: Fab4b_TP2


title: CD8+ T cells, Liver (aHSCT + Day 4) 2

description: Gene expression


title: Fab3b_TP4


title: Fab3b_TP5


title: Fab4b_TP3


title: Fab3b_TP3


title: Fab3b_TP1


title: Fab2b_TP4


title: Fab2b_TP3


title: Fab2b_TP1


title: Fab2b_TP2


title: CD8+ T cells, Graft (aHSCT + Day 0) 1

description: Gene expression


title: Fab1b_TP4


title: Fab1b_TP3


title: Fab1b_TP2


title: Fab1b_TP1


title: POR_CD_18

city: Leuven

first: Sare

last: Verstockt

address: O&N4 Herestraat 49 box 610

country: Belgium

institute: KU Leuven

description: Biopsy from ileal mucosa of a post-operative recurrent CD patient

hyb_protocol: Incubation at 99°C for 5 minutes, followed by 45°C for another 5 minutes. Hybridization to GeneChip miRNA 2.0 arrays (Affymetrix) was performed under rotation (60 rpm) at 48°C for 16 hours. The arrays were washed and stained on an automated Fluidics Station (Affymetrix).

scan_protocol: Microarrays were scanned on the Affymetrix 3000 GeneScanner. Intensity values for each probe cell (.cel file) were calculated using Affymetrix GeneChip Command Console (AGCC).

data_processing: Quality control of the array data was performed with the Affymetrix Expression Console Software, version 1.4. Probe level analysis was performed on the Affymetrix raw data (.cel files) with the robust multichip average (RMA) method using the Affymetrix Expression Console Software.

label: biotin

label_protocol: Total RNA (250 ng) was used in a tailing reaction followed by ligation of the biotinylated signal molecule, using the FlashTag™ Biotin HSR RNA Labeling Kit (Genesphere) protocol for Affymetrix GeneChip miRNA arrays. As recommended, the labeling efficiency is verified with the ELOSA QC assay (Genesphere).

extract_protocol: Total RNA was extracted using the miRVAna miRNA isolation Kit (Ambion), according to the manufacturer's instructions. The integrity and quantity of total RNA and small RNA were assessed with a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies) and a 2100 Bioanalyzer (Agilent) using the Agilent RNA 6000 Nano kit and the Agilent Small RNA kit, respectively.

tag: disease

value: Crohn's disease

value: ileum


title: Fab1b_TP5


title: POR_CD_14

source_name: Biopsy from ileal mucosa of a post-operative recurrent CD patient


title: POR_CD_19


title: POR_CD_20


title: POR_CD_13


title: POR_CD_15


title: POR_CD_09


title: POR_CD_17


title: POR_CD_11


title: POR_CD_10


title: POR_CD_16


title: POR_CD_08


title: POR_CD_12


title: Fab3b_TP2


title: POR_CD_05


title: POR_CD_06


title: POR_CD_04


title: POR_CD_02


title: new_CD_07

description: Biopsy from ileal mucosa of a newly diagnosed CD patient


title: POR_CD_03


title: new_CD_05

source_name: Biopsy from ileal mucosa of a newly diagnosed CD patient


title: POR_CD_07


title: POR_CD_01


title: new_CD_04


title: new_CD_08


title: new_CD_01


title: late_CD_05

description: Biopsy from ileal mucosa of a late stage CD patient


title: late_CD_02

source_name: Biopsy from ileal mucosa of a late stage CD patient


title: new_CD_02


title: late_CD_06


title: late_CD_03


title: late_CD_04


title: control_05

description: Biopsy from normal ileal mucosa of control individual

value: normal


title: new_CD_03


title: late_CD_01


title: BFUE_24 (Set2)

city: Cambridge

first: Hojun

last: Li

state: MA

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

description:
allIDs_BFUE.Set2.Counts.txt
BFUE-H3

data_processing:
Reads were mapped against the GRCm38 mouse genome using STAR version 2.4, gene annotations from ENSEMBL version 87 (using only canonical chromosomes) and the overhang parameter from STAR set to 49.
Read counts per gene were obtained with featureCounts using the option –p and the same GTF file used to map the reads.
Genome_build: GRCm38
Supplementary_files_format_and_content: Text file with gene counts per gene.

source_name: burst forming unit-erythroid

growth_protocol: Erythroid progenitor cell isolation. Fetal liver was dissected from embryonic day 14.5 mice and disrupted and homogenized with manual pipetting, followed by lysis of mature red blood cells with ammonium chloride solution (Stem Cell Technologies).  Remaining fetal liver cells were stained with biotinylated antibodies against the following surface proteins: CD3e, CD45R, Ly-6G, CD11b, Ter119 (all 5 from the BD-Pharmingen biotin mouse linage depletion panel), Ly-6A/E (i.e. Sca-1, cloned D7, E-Biosciences), CD16/32 (clone 93, E-Biosciences), CD41 (clone EbioMWReg30, E-Biosciences), and Ter119 (E-biosciences). Cells were then incubated with streptavidin-labeled magnetic beads (BD) to deplete cells labeled with biotinylated antibodies.  Remaining unlabeled cells were then purified by FACS (staining procedure described below) on a FACS Aria sorter (BD).

extract_protocol:
[FACS selection protocol] Antibody staining and FACS.For FACS purification of erythroid progenitors, lineage-depleted fetal liver cells were stained with the following: Propidium Iodide (Sigma), APC or PE-Cy7 anti-CD117 (clone ACK2, E-Biosciences), PE anti-CD71 (clone R127217, E-Biosciences), PE anti-CD24 (clone M1/69, E-biosciences), FITC streptavidin (E-Biosciences).   Flow cytometry for erythroid differentiation markers was performed on a FACS Fortessa cytometer (BD)
Single cell transcriptome library preparation.  SmartSeq2 library prep was performed by depositing single cells in PCR plate wells by FACS.  Single cells were lysed in 0.2% Triton X-100 (Sigma), containing RNase inhibitor (Clontech), Oligo-dT (5’-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’, IDT), and dNTPs (Invitrogen).  Lysates were then reverse transcribed at 42 deg C with SuperScript II reverse transcriptase (Invitrogen) in the presence of First-Strand Buffer (Invitrogen) containing DTT (Invitrogen), betaine (Sigma), magnesium chloride (Sigma), and template switching oligonucleotide (5’ -AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3’ where rG = riboguanosine, and +G = LNA-modified guanosine, Exiqon/Qiagen).  Reverse-transcribed products were then amplified using Kapa HiFi Hotstart PCR master mix (Kapa) and an IS PCR oligo primer (5’ -AAGCAGTGGTATCAACGCAGAGT-3’, IDT). Amplified double-stranded cDNA libraries were then purified using Agencourt Ampure XP beads (Beckman Coulter), followed by DNA concentration quantification using the Qubit dsDNA HS kit (Life Technologies).  0.2 ng of double-stranded cDNA was used in a tagmentation reaction using the Nextera XT DNA sample preparation kit (Illumina) per manufacturers protocol. Tagmented transcriptomes were then indexed using the Nextera XT 96-index kit for 384 samples (Illumina) per manufacturers instructions, and samples were then sequenced on a HiSeq 2500 sequencer (Illumina).
Non stranded RNAseq

tag: cell type

value: BFUE


title: BFUE_23 (Set2)

description:
allIDs_BFUE.Set2.Counts.txt
BFUE-H2


title: control_08

source_name: Biopsy from normal ileal mucosa of control individual


title: BFUE_21 (Set2)

description:
allIDs_BFUE.Set2.Counts.txt
BFUE-G3


title: control_06


title: control_07


title: new_CD_06


title: BFUE_22 (Set2)

description:
allIDs_BFUE.Set2.Counts.txt
BFUE-H1


title: control_03


title: control_02


title: control_01


title: BFUE_20 (Set2)

description:
allIDs_BFUE.Set2.Counts.txt
BFUE-G2


title: BFUE_19 (Set2)

description:
allIDs_BFUE.Set2.Counts.txt
BFUE-G1


title: BFUE_17 (Set2)

description:
allIDs_BFUE.Set2.Counts.txt
BFUE-F2


title: BFUE_18 (Set2)

description:
allIDs_BFUE.Set2.Counts.txt
BFUE-F3


title: BFUE_15 (Set2)

description:
allIDs_BFUE.Set2.Counts.txt
BFUE-E3


title: BFUE_16 (Set2)

description:
allIDs_BFUE.Set2.Counts.txt
BFUE-F1


title: late_CD_07


title: BFUE_14 (Set2)

description:
allIDs_BFUE.Set2.Counts.txt
BFUE-E2


title: BFUE_13 (Set2)

description:
allIDs_BFUE.Set2.Counts.txt
BFUE-E1


title: BFUE_12 (Set2)

description:
allIDs_BFUE.Set2.Counts.txt
BFUE-D3


title: BFUE_11 (Set2)

description:
allIDs_BFUE.Set2.Counts.txt
BFUE-D2


title: BFUE_10 (Set2)

description:
allIDs_BFUE.Set2.Counts.txt
BFUE-D1


title: control_04


title: BFUE_7 (Set2)

description:
allIDs_BFUE.Set2.Counts.txt
BFUE-C1


title: BFUE_6 (Set2)

description:
allIDs_BFUE.Set2.Counts.txt
BFUE-B3


title: BFUE_4 (Set2)

description:
allIDs_BFUE.Set2.Counts.txt
BFUE-B1


title: BFUE_5 (Set2)

description:
allIDs_BFUE.Set2.Counts.txt
BFUE-B2


title: BFUE_3 (Set2)

description:
allIDs_BFUE.Set2.Counts.txt
BFUE-A3


title: UBR4_siRNA7_n003 [SJMMNORM047379_G1]

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm9 whole genome using an internal pipeline that employs bwa and STAR
Htseq was used to extract raw counts, which were library size normalized and genes size corrected to produce FPKM.
Genome_build: mm9
Supplementary_files_format_and_content: Gene symbol Ensembl Id  and FPKM values for all samples are included in one tab deliminated matrix txt file.

source_name: UBR4_siRNA7_tibialis anterior muscles

extract_protocol:
trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: electroporation of siRNA or control

value: 6 month old

value: siRNA construct 7 targeting UBR4

value: tibialis anterior muscles


title: UBR4_siRNA7_n001 [SJMMNORM047377_G1]


title: BFUE_2 (Set2)

description:
allIDs_BFUE.Set2.Counts.txt
BFUE-A2


title: UBR4_siRNA5_n003 [SJMMNORM047376_G1]

source_name: UBR4_siRNA5_tibialis anterior muscles

value: siRNA construct 5 targeting UBR4


title: UBR4_siRNA5_n002 [SJMMNORM047375_G1]


title: UBR4_siRNA7_n002 [SJMMNORM047378_G1]


title: NT_siRNA_n001 [SJMMNORM047371_G1]

source_name: NT_siRNA_tibialis anterior muscles

value: non targeting control


title: NT_siRNA_n002 [SJMMNORM047372_G1]


title: NT_siRNA_n003 [SJMMNORM047373_G1]


title: M360S_ATAC

first: Sofie

last: Demeyer

address: Herestraat 49 / bus 912

department: Center for Cancer Biology

institute: KULeuven / VIB

description: JAK3 mutant + Suz12 inactivated - CD8+ SP

data_processing:
cleaning .fastq files with fastq-mcf, quality control with fastQC
mapping to genome with Bowtie2 / TopHat2
count reads with htseq-count
call peaks with MACS2
normlization with deepTools
Genome_build: Mus Musculus (mm10)
Supplementary_files_format_and_content: tab-delimited text files contain raw mRNA counts
Supplementary_files_format_and_content: narrowpeak / bed files with the called peaks (macs2)
Supplementary_files_format_and_content: bedgraph files with normalized signals

source_name: spleen

extract_protocol: all libraries were prepared for sequencing using standard Illumina protocols

tag: protocol

value: ATAC-sequencing


title: 169S_CD8SP

description: JAK3 mutant - CD8+ SP


title: M361S_ATAC


title: BFUE_9 (Set2)

description:
allIDs_BFUE.Set2.Counts.txt
BFUE-C3


title: BFUE_8 (Set2)

description:
allIDs_BFUE.Set2.Counts.txt
BFUE-C2


title: M165S_ATAC

description: JAK3 mutant - CD8+ SP


title: M170S_ATAC

description: JAK3 mutant - CD8+ SP


title: M333T_ATAC

description: Suz12 inactivated - CD4+/CD8+ DP

source_name: thymus


title: 331T_CD8CD4DP

description: Suz12 inactivated - CD4+/CD8+ DP


title: 371T_CD8SP_secTxfrom332

description: Suz12 inactivated - CD4+/CD8+ DP


title: BFUE_1 (Set2)

description:
allIDs_BFUE.Set2.Counts.txt
BFUE-A1


title: WT_Thy_CD8CD4DP_3

description: wildtype - CD4+/CD8+ DP


title: UBR4_siRNA5_n001 [SJMMNORM047374_G1]

tag: genotype/variation


title: WT_Thy_CD8CD4DP_2

description: wildtype - CD4+/CD8+ DP


title: ATAC_SCC1_shPitx1_2

city: New York

first: Markus

last: Schober

state: NY

address: 550 First Ave, Smilow 407

department: Dermatology

institute: New York University School of Medicine

data_processing:
Mouse assembly version mm10/NCBI m38 build were used for sequence alignments with bowtie 45 version 2.1.0.
ATAC-seq peaks were called with PeaKDEck55 and the parameter (-sig 0.0001).
Genome_build: mm10
Supplementary_files_format_and_content: File with PeakDEck peak calling

growth_protocol: 15,000 cells were injected intradermally to form tumor allografts. In the end point of the experiment, 50,000 cells were sorted gatting in integrin α6 and integrin b1

extract_protocol: 50,000  tumor-propagating cells (TPCs)  were isolated by FACS and washed once with cold 1x PBS. Cells were pelleted and lysed in 50 μl and spun at 500g for 25min at 4C to collect nuclei. Pelleted nuclei were incubated for 30min at 37 C with 2.5ul of Tn5 transposase (Illumina Cat #FC-121-1030) before transposed DNA fragments were purified with a Qiagen MinElute Kit for ATAC-seq library generation.

tag: strain background

value: skin

tag: tissue subtype

value: squamous cell carcinoma (SCC)


title: 170T_ATAC

description: JAK3 mutant - CD8+ SP


title: ATAC_SCC1_shPitx1_1


title: ATAC_SCC1_shScr_1


title: M358S_ATAC


title: HIPPO_427_Primiparous

city: Tallahassee

first: Michelle

last: Arbeitman

state: FL

address: 1115 W Call Street, College of Medicine

department: Biomedical Sciences

institute: FSU

description:
Hippo_B_427
100 base single end reads

data_processing:
Basecalls performed using CASAVA
Read mapping was performed using Hisat2 and the UCSC reference genome mm10 from the HiSat2 webpage.
The featureCounts function with Rsubread package was used to obtain count tables, using the inbuilt mm10 annotation files, to obtain meta-feature level 'reads that map a singe time'.
Count tables were import into iDEP81 to inspect the data and pre-process.
Three sampes were not used in the analysis as they were outliers based on PCA analysis: HIPPO_4490_Virgin, CER_4490_Virgin, AMY_4487_Virgin
The data was then pre-processed, with a minimum of 5 counts per million (CPM) in at least 8 libraries, for a gene to be further analyzed. This cut-off was chosen based on visualization of the expression values, where a bimodal distribution was observed. The count data was transformed, using EdgeR: log2(CPM+c), with pseudocount c =4. For differential expression analysis, limma-voom was used within the iDEP.81 workspace.
Genome_build: mm10
Supplementary_files_format_and_content: One processed data file contains the count table for all genes in mm10. The file format is a .csv. The file is called: Count.csv.
Supplementary_files_format_and_content: One processed data file contains normalized reads, generated using EdgeR. The file contains Log2(CountsPerMillion+4). The file is called edgeR.csv

growth_protocol: All mice were housed in the same animal barrier room, on the same light dark cycle, at Jackson Laboratory. All mice are age-matched all born on the same day +/- 3 days.

extract_protocol:
Brain samples were harvested on the same day and snap frozen in RNA later solution (Ambion), within a two-hour window. Frozen brain tissue was shipped to FSU.RNA and protein were extracted from the frozen brain tissue using the NucleoSpin RNA/Protein purification kit (Macherey-Nagel). The brain tissue was homogenized using a motorized homogenizer
1 ug of total RNA was used for subsequent mRNA isolation (New England Biolabs Inc. PolyA magnetic mRNA isolation kit). The External RNA Controls Consortium (ERCC) RNA Spike-in Controls (Ambion 4456740) were diluted 1:100 and added to total RNA before mRNA isolation. RNA-seq libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs Inc. E7530L). The qualities of the libraries were examined using Agilent High Sensitivity DNA Bioanalyzer Chips (Agilent Technologies 5067-4626) and quantified by KAPA Library Quantification Kits
Libraries were sequenced on an Illumina 2500 platform, single end, 100 base reads.

treatment_protocol: To generate primiparous females, one male and one eight week old female were housed per pen for two weeks and then the males were removed. Tissue was harvested by Jackson Laboratory three weeks after weaning pups, or in age-matched virgins

tag: animal identification

value: Hippocampus

tag: reproductive state

value: Primiparous


title: ATAC_SCC1_shScr_2


title: HIPPO_421_Primiparous

description:
Hippo_B_421
100 base single end reads


title: HIPPO_425_Primiparous

description:
Hippo_B_425
100 base single end reads


title: HIPPO_414_Primiparous

description:
Hippo_B_414
100 base single end reads


title: HIPPO_415_Primiparous

description:
Hippo_B_415
100 base single end reads


title: HIPPO_418_Primiparous

description:
Hippo_B_418
100 base single end reads


title: HIPPO_4488_Virgin

description:
Hippo_V_4488
100 base single end reads

value: Virgin


title: HIPPO_4490_Virgin

description:
Not included
100 base single end reads


title: HIPPO_413_Primiparous

description:
Hippo_B_413
100 base single end reads


title: HIPPO_4491_Virgin

description:
Hippo_V_4491
100 base single end reads


title: HIPPO_4486_Virgin

description:
Hippo_V_4486
100 base single end reads


title: HIPPO_4487_Virgin

description:
Hippo_V_4487
100 base single end reads


title: HIPPO_409_Virgin

description:
Hippo_V_409
100 base single end reads


title: M333S_ATAC

description: Suz12 inactivated - CD4+/CD8+ DP


title: HIPPO_4489_Virgin

description:
Hippo_V_4489
100 base single end reads


title: HIPPO_405_Virgin

description:
Hippo_V_405
100 base single end reads


title: WT_Thy_CD8CD4DP_1

description: wildtype - CD4+/CD8+ DP


title: HYPO_4493_Primiparous

description:
Hypo_B_4493
100 base single end reads

value: Hypothalamus


title: HIPPO_4493_Primiparous

description:
Hippo_B_4493
100 base single end reads


title: HYPO_427_Primiparous

description:
Hypo_B_427
100 base single end reads


title: HYPO_425_Primiparous

description:
Hypo_B_425
100 base single end reads


title: HYPO_418_Primiparous

description:
Hypo_B_418
100 base single end reads


title: HYPO_415_Primiparous

description:
Hypo_B_415
100 base single end reads


title: HYPO_4489_Virgin

description:
Hypo_V_4489
100 base single end reads


title: HYPO_4490_Virgin

description:
Hypo_V_4490
100 base single end reads


title: HYPO_4491_Virgin

description:
Hypo_V_4491
100 base single end reads


title: HYPO_414_Primiparous

description:
Hypo_B_414
100 base single end reads


title: HYPO_409_Virgin

description:
Hypo_V_409
100 base single end reads


title: HYPO_4486_Virgin

description:
Hypo_V_4486
100 base single end reads


title: HYPO_4487_Virgin

description:
Hypo_V_4487
100 base single end reads


title: HYPO_4488_Virgin

description:
Hypo_V_4488
100 base single end reads


title: HYPO_421_Primiparous

description:
Hypo_B_421
100 base single end reads


title: HYPO_405_Virgin

description:
Hypo_V_405
100 base single end reads


title: AMY_427_Primiparous

description:
Amy_B_427
100 base single end reads

value: Amygdala


title: HYPO_413_Primiparous

description:
Hypo_B_413
100 base single end reads


title: AMY_421_Primiparous

description:
Amy_B_421
100 base single end reads


title: AMY_4493_Primiparous

description:
Amy_B_4493
100 base single end reads


title: AMY_418_Primiparous

description:
Amy_B_418
100 base single end reads


title: AMY_414_Primiparous

description:
Amy_B_414
100 base single end reads


title: AMY_425_Primiparous

description:
Amy_B_425
100 base single end reads


title: AMY_4491_Virgin

description:
Amy_V_4491
100 base single end reads


title: AMY_4490_Virgin

description:
Amy_V_4490
100 base single end reads


title: AMY_4489_Virgin

description:
Amy_V_4489
100 base single end reads


title: AMY_413_Primiparous

description:
Amy_B_413
100 base single end reads


title: AMY_4487_Virgin

description:
Not included
100 base single end reads


title: AMY_4488_Virgin

description:
Amy_V_4488
100 base single end reads


title: AMY_4486_Virgin

description:
Amy_V_4486
100 base single end reads


title: AMY_409_Virgin

description:
Amy_V_409
100 base single end reads


title: AMY_405_Virgin

description:
Amy_V_405
100 base single end reads


title: AMY_415_Primiparous

description:
Amy_B_415
100 base single end reads


title: CTX_427_Primiparous

description:
Ctx_B_427
100 base single end reads

value: Neocortex


title: CTX_4493_Primiparous

description:
Ctx_B_4493
100 base single end reads


title: CTX_425_Primiparous

description:
Ctx_B_425
100 base single end reads


title: CTX_421_Primiparous

description:
Ctx_B_421
100 base single end reads


title: CTX_418_Primiparous

description:
Ctx_B_418
100 base single end reads


title: CTX_4491_Virgin

description:
Ctx_V_4491
100 base single end reads


title: CTX_413_Primiparous

description:
Ctx_B_413
100 base single end reads


title: CTX_414_Primiparous

description:
Ctx_B_414
100 base single end reads


title: CTX_415_Primiparous

description:
Ctx_B_415
100 base single end reads


title: CTX_4489_Virgin

description:
Ctx_V_4489
100 base single end reads


title: CTX_4490_Virgin

description:
Ctx_V_4490
100 base single end reads


title: CER_427_Primiparous

description:
Cer_B_427
100 base single end reads

value: Cerebellum


title: CTX_405_Virgin

description:
Ctx_V_405
100 base single end reads


title: CTX_4488_Virgin

description:
Ctx_V_4488
100 base single end reads


title: CER_421_Primiparous

description:
Cer_B_421
100 base single end reads


title: CER_413_Primiparous

description:
Cer_B_413
100 base single end reads


title: CTX_4486_Virgin

description:
Ctx_V_4486
100 base single end reads


title: CTX_4487_Virgin

description:
Ctx_V_4487
100 base single end reads


title: CTX_409_Virgin

description:
Ctx_V_409
100 base single end reads


title: CER_4493_Primiparous

description:
Cer_B_4493
100 base single end reads


title: CER_414_Primiparous

description:
Cer_B_414
100 base single end reads


title: CER_418_Primiparous

description:
Cer_B_418
100 base single end reads


title: CER_415_Primiparous

description:
Cer_B_415
100 base single end reads


title: CER_4489_Virgin

description:
Cer_V_4489
100 base single end reads


title: CER_4491_Virgin

description:
Cer_V_4491
100 base single end reads


title: CER_4487_Virgin

description:
Cer_V_4487
100 base single end reads


title: PhageCocktailTreatment_5

city: Salt Lake City

first: Chris

last: Stubben

state: Utah

address: 2000 Cir of Hope Dr

department: University of Utah

institute: Huntsman Cancer Institute

description:
11844R_Treat_vs_Control_gender.xlsx
P5

data_processing:
Reads were aligned to the mouse transcriptome index using Novoalign (v2.08.03), allowing up to 50 alignments for each read
USeq’s (v8.8.8) SamTranscriptomeParser application was used to select the best alignment for each read and convert the coordinates of reads aligning to splices back to genomic space
Read counts for each gene were generated using USeq’s DefinedRegionDifferentialSeq application
Genome_build: mm10
Supplementary_files_format_and_content: normalized counts from DESeq2 in Excel file

source_name: Ileum

extract_protocol:
5 mm of ileum was collected and stored in Trizol. RNA was extracted with the Qiagen RNeasy kit.
Illumina sequencing libraries were prepared with the Illumina TruSeq Stranded RNA Kit with Ribo-Zero Gold according to manufacturer's recommendations.

value: Ileum

tag: genotype

tag: treatment

value: PhageCocktailTreatment

tag: ID


title: CER_405_Virgin

description:
Cer_V_405
100 base single end reads

tag: tissue


title: CER_409_Virgin

description:
Cer_V_409
100 base single end reads

tag: strain


title: CER_4488_Virgin

description:
Cer_V_4488
100 base single end reads


title: PhageCocktailTreatment_3

description:
11844R_Treat_vs_Control_gender.xlsx
P3


title: PhageCocktailTreatment_2

description:
11844R_Treat_vs_Control_gender.xlsx
P2


title: PhageCocktailTreatment_6

description:
11844R_Treat_vs_Control_gender.xlsx
P6


title: CER_4486_Virgin

description:
Cer_V_4486
100 base single end reads


title: Control_2

description:
11844R_Treat_vs_Control_gender.xlsx
NC2

value: Control


title: CER_425_Primiparous

description:
Cer_B_425
100 base single end reads


title: Control_3

description:
11844R_Treat_vs_Control_gender.xlsx
NC3


title: CER_4490_Virgin

description:
Not included
100 base single end reads


title: Control_1

description:
11844R_Treat_vs_Control_gender.xlsx
NC1


title: JS_H3K4me1

data_processing:
cleaning .fastq files with fastq-mcf, quality control with fastQC
mapping to genome with Bowtie2 / TopHat2
count reads with htseq-count
call peaks with MACS2
normlization with deepTools
Genome_build: Mus Musculus (mm10), Homo Sapiens (GRCh37/hg19)
Supplementary_files_format_and_content: tab-delimited text files contain raw mRNA counts
Supplementary_files_format_and_content: narrowpeak / bed files with the called peaks (macs2)
Supplementary_files_format_and_content: bedgraph files with normalized signals

tag: antibody

tag: extra protocol

value: ChIPmentation (see De Bock et al 2018; Vanden Bemtp et al 2018)

value: JAK3 mutant + Suz12 inactivated - CD8+ SP


title: JS_H3K4me3


title: JS_H3K27me3


title: JS_H3K27Ac


title: EED KO MEF_H2AK119ub, ChIP DNA, rep2

city: Boston

first: Hongjae

last: Sunwoo

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital, Harvard Medical School, HHMI

data_processing:
CHART-seq and ChIP-seq: Reads were aligned separately to the mus/129 and cas genomes using novoalign with default parameters for paired-end alignment, the coordinates of these alignments were then converted to mm9 coordinates with custom scripts. Following alignment, coverage files were generated for the composite set of reads (comp), as well as allelic reads that aligned better to mus (mus) or cas (cas) using custom perl scripts, SAMtools and bedtools to extract and sort allelic reads, remove duplicates and generate coverage files. After input normalization using SPP, the coverage tracks presented in the paper were further normalizated between experiments to have equal coverage within a 1-MB region flanking the Xist locus (chrX:100150712-100650712 and 100683572-101183572).
ChIP-seq: Reads were aligned separately to the mus/129 and cas genomes using novoalign with default parameters for paired-end alignment, the coordinates of these alignments were then converted to mm9 coordinates with custom scripts. Following alignment, coverage files were generated for the composite set of reads (comp), as well as allelic reads that aligned better to mus (mus) or cas (cas) using custom perl scripts, SAMtools and bedtools to extract and sort allelic reads, remove duplicates and generate coverage files. The coverage files presented in the paper are input normalized using SPP.
RNA-seq: PCR duplicates were removed and reads separately aligned to custom mus/129 and cas genomes using Tophat. Final allele-specific mapping to reference mm9 genome was generated based on SNPs. Only uniquely aligned concordantly mapped sequences were used in downstream analysis. Counts per gene were calculated using featureCounts. Using MatLab, library sizes were normalized and genes with insufficient allelic information (<13 allele-specific reads) were removed. We also removed potentially miscalled genes from our alignment pipeline, defined as genes incorrectly assigned to mus from a pure cas RNA-seq library. Allele-specific RPKM was calculated using allelic ratio (allele-specific counts) applied to comp RPKM (total counts).
In situ Hi-C:  Reads were trimmed using cutadapt with the options --adapter=GATCGATC (MboI ligation junction) and --minimum-length=20. Reads of each pair were individually mapped to the mus (Xi) and cas (Xa) reference genomes using novoalign and default parameters, then merged into Hi-C summary files and filtered using HOMER with custom scripts (parameters for HOMER filtering (makeTagDirectory): -removePEbg -restrictionSite GATC -both -removeSelfLigation). Hi-C contact maps were generated from reads in the filtered HOMER mus and cas tag directories using the ‘pre’ command of Juicer tools with the genomeID mm9 .
Genome_build: mm9
Supplementary_files_format_and_content: CHARTP-seq: bigWig (bw) files for all reads (.comp), regardless of whether they are allele-specific or not, cas-specific (.cas) and mus-specific (.mus). All bigWig files are input normalized. Log2 ration bw files are ratio after further normalization to have equal coverage within a 1-MB region flanking the Xist locus (chrX:100150712-100650712 and 100683572-101183572).
Supplementary_files_format_and_content: ChIP-seq: bigWig (bw) files for all reads (.comp), regardless of whether they are allele-specific or not, cas-specific (.cas) and mus-specific (.mus). All bigWig files are input normalized.
Supplementary_files_format_and_content: RNA-seq: bigWig (bw) files for all reads (.comp), regardless of whether they are allele-specific or not, cas-specific (.cas) and mus-specific (.mus). All bw files are rpkm values.  Raw exonic reads in each RNA-seq library were quantified and summarized in RNAseq_experiment_count_rep1 or 2.txt.
Supplementary_files_format_and_content: In situ Hi-C:  Compressed Hi-C matrix (.hic) files for cas-specific and mus-specific filtered Hi-C reads. File can be loaded onto Juicebox to view either raw or normalized Hi-C interaction matrices at 5kb to 2.5Mb resolutions.

source_name: EED KO MEF

growth_protocol: MEF cells were cultured in regular fibroblast medium (1% Pen/Strep, high-glucose DMEM+GlutaMAX) with 10% FBS

extract_protocol:
CHART-seq: Sheared chromatin from 2.5x10^7 cells was prepared as described earlier as in Simon et al., Nature 504, 465-469 (2013).  160 μL chromatin was mixed with 320 μL 2X hybridization buffer (50 mM Tris-HCl pH 7.0, 750 mM NaCl, 1% SDS, 1 mM EDTA, 15% formamide, 1 mM DTT, 200 mM PMSF, 1 cOmplete EDTA-free protease inhibitor cocktail tablet [Roche], and 100 U/mL RNase Inhibitor [Roche]) and pre-cleared with 60 μl MyOne Streptavidin C1 beads blocked with yeast total RNA and bovine serum albumin at room temperature for 1 hr. The pre-cleared chromatin was mixed with 36 pmol of either antisense (Xist-targeting) or sense (control) capture probes. We used a pool of 9 capture probes (biotinylated oligos). Hybridization was carried out at 37°C for 4 hr followed by incubation with 240 μL blocked MyOne Streptavidin C1 beads at 37°C for 1 hr. The beads were washed once with 1X hybridization buffer (1:2 mixture of sonication buffer and 2X hybridization buffer) at 37°C for 10 min, five times with wash buffer (10 mM HEPES pH 7.6, 150 mM NaCl, 2% SDS, 2 mM EDTA, 2 mM EGTA, and 1 mM DTT) at 37°C for 5 min, and twice with elution buffer (10 mM HEPES pH 7.6, 150 mM NaCl, 0.5% NP-40, 3 mM MgCl2, and 10 mM DTT) at 37°C for 5 min. CHART-enriched DNA was eluted by 20 μL RNase H (5 U/μL, New England BioLabs) in 200 μL elution buffer two times at 37°C for 30 min. Eluent was treated with 10 μL RNase A (20 mg/mL) at 37°C for 1 hr and then treated with SDS (final 1%), EDTA (final 10 mM), and 10 μL proteinase K (20 mg/mL) at 55°C for 1 hr. Reversal of crosslinks was performed by supplementing the eluent with NaCl (final 0.3 M) and incubation at 65°C overnight. DNA was extracted by phenol-chloroform and further sheared to below 500-bp fragments.
ChIP-seq: Cells were crosslinked with 1% formaldeyde for 10 min, then nuclei were isolated and lysed. Chromatin was sheared by sonication to a size of ~200-400 bp. Cleared lysates were precleared for 1 hour, then 10% saved as input, and lysates were incubated with Dynabeads Protein G pre-bound with the antibody of choice. After stringent washes, ChIP DNA was eluted from beads, and together with input chromtain was reverse-crosslinked with proteinase K. DNA was purified by phenol/chloroform extraction and ethanol precipitation.
RNA-seq: Total cell RNA was extracted using TRIzol (Thermo Fisher), from which mRNA was isolated using oligo(dT) beads and RNA-seq libraries prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) as per manufacturer’s instructions.
in situ Hi-C: As described in Rao et al. (2014), 3-5 million cells were crosslinked with 1% formaldehyde for 10min. Crosslinked cell pellets were lysed with 300uL ice-cold HiC lysis buffer (10mM Tris HCl pH 8, 10mM NaCl, 0.2% Igepal CA630) with protease inhibitors (Roche). Cell suspension was incubated for 30min at 4C with rotation, then pelleted at 2500xg for 5min. Pelleted nuclei were then washed with 500ul ice-cold HiC lysis buffer and resuspended in 50uL 0.5% SDS solution and incubated at 62C for 10min. 145ul H2O and 25ul 10% Triton X-100 were added to quench SDS and nuclei incubated at 37C for 15min. 26.1ul of 10X NEB Buffer 2 and 100U of MboI restriction enzyme were added and nuclei digested overnight at 37C with rotation. MboI was then heat activated at 62C for 20min, then nuclei cooled to room temperature. To fill in MboI fragment overhangs and mark DNA ends with biotin, 50ul of fill-in master mix was added (37.5ul 0.4mM biotin-14-dATP, 1.5ul 10mM dCTP, 1.5ul 10mM dGTP, 1.5ul 10mM dTTP, 8ul 5U/ul DNA Polymerase I, Large (Klenow) Fragment) and mixed by pipetting. Nuclei were then incubated at 37C for 1h with rotation. To ligate biotinylated DNA ends together, 900ul ligation master mix was added (649ul H2O, 120ul 10X NEB T4 ligase buffer, 100ul 10% Triton X-100, 6ul of 20mg/ml BSA, 25ul of 400U/ul T4 DNA ligase). Reaction was mixed by inverting and incubated at room temperature for 4h with rotation. Reaction was then centrifuged at 1700xg for 5min at room temperature. Pelleted nuclei were resuspended in 750ul TES buffer (1mM EDTA, 10mM Tris-HCl pH 8, 0.5% SDS), 50ul Proteinase K (20mg/ml) added and incubated at 55C for 1h with rotation. To reverse crosslinks, 88.9ul 3M NaCl was added and crosslinks reversed by incubated overnight at 65C with shaking (Eppendorf thermomixer, 950rpm). Samples were cooled to room temperature and DNA extracted with phase-lock gel tubes (5Prime). RNA was digested from purifying DNA by adding 2ul RNAse A (20mg/ml) and incubating at 37C for 1h. DNA was then extracted with phase-lock gel tubes (5Prime) and resuspended in 130ul 1X Tris buffer (10mM Tris-HCl, pH 8). To ensure complete resuspension, DNA was then incubated at 37C for 15min. DNA was then sonicated to a size of 300-500bp using a Covaris with the following parameters: 140W, 10% duty cycle, 200 bursts/cycle, 100s. Samples were then size selected to 300-500bp using AMPure XP beads and eluted in 300ul 1X Tris buffer. To pulldown biotinylated ligation products, 30ul (per sample) of MyOne Streptavidin C1 beads were washed with 400ul of 1X Tween washing buffer (5mM Tris-HCl pH 7.5, 0.5mM EDTA, 1M NaCl, 0.05% Tween 20) and resuspended in 300ul 2X binding buffer (10mM Tris-HCl pH 7.5, 1mM EDTA, 2M NaCl). Beads were then added to purified DNA and sample incubated at room temperature for 15min with rotation. Beads were washed twice with 600ul 1X Tween Washing buffer. Subsequent library preparation steps were then done directly on beads.
Libraries were constructed using the NEBNext ChIP-seq Library Preparation Kit with no modifications to the protocol. We used 9-14 cycles of PCR amplification, depending on library concentration measured by qPCR.

value: CAST/Ei x 129/Sv/Jae

value: Mouse embryonic fibroblasts (MEF)

value: EED KO

value: H2AK119ub (Cell Signaling Technology, 8240, lot 2)


title: JAK3_H3K4me3

value: JAK3 mutant - CD8+ SP


title: PhageCocktailTreatment_4

description:
11844R_Treat_vs_Control_gender.xlsx
P4


title: JAK3_H3K27Ac


title: RING1A/B KO MEF_Xist CHART, rep2

data_processing:
Library strategy: CHART-seq
CHART-seq and ChIP-seq: Reads were aligned separately to the mus/129 and cas genomes using novoalign with default parameters for paired-end alignment, the coordinates of these alignments were then converted to mm9 coordinates with custom scripts. Following alignment, coverage files were generated for the composite set of reads (comp), as well as allelic reads that aligned better to mus (mus) or cas (cas) using custom perl scripts, SAMtools and bedtools to extract and sort allelic reads, remove duplicates and generate coverage files. After input normalization using SPP, the coverage tracks presented in the paper were further normalizated between experiments to have equal coverage within a 1-MB region flanking the Xist locus (chrX:100150712-100650712 and 100683572-101183572).
ChIP-seq: Reads were aligned separately to the mus/129 and cas genomes using novoalign with default parameters for paired-end alignment, the coordinates of these alignments were then converted to mm9 coordinates with custom scripts. Following alignment, coverage files were generated for the composite set of reads (comp), as well as allelic reads that aligned better to mus (mus) or cas (cas) using custom perl scripts, SAMtools and bedtools to extract and sort allelic reads, remove duplicates and generate coverage files. The coverage files presented in the paper are input normalized using SPP.
RNA-seq: PCR duplicates were removed and reads separately aligned to custom mus/129 and cas genomes using Tophat. Final allele-specific mapping to reference mm9 genome was generated based on SNPs. Only uniquely aligned concordantly mapped sequences were used in downstream analysis. Counts per gene were calculated using featureCounts. Using MatLab, library sizes were normalized and genes with insufficient allelic information (<13 allele-specific reads) were removed. We also removed potentially miscalled genes from our alignment pipeline, defined as genes incorrectly assigned to mus from a pure cas RNA-seq library. Allele-specific RPKM was calculated using allelic ratio (allele-specific counts) applied to comp RPKM (total counts).
In situ Hi-C:  Reads were trimmed using cutadapt with the options --adapter=GATCGATC (MboI ligation junction) and --minimum-length=20. Reads of each pair were individually mapped to the mus (Xi) and cas (Xa) reference genomes using novoalign and default parameters, then merged into Hi-C summary files and filtered using HOMER with custom scripts (parameters for HOMER filtering (makeTagDirectory): -removePEbg -restrictionSite GATC -both -removeSelfLigation). Hi-C contact maps were generated from reads in the filtered HOMER mus and cas tag directories using the ‘pre’ command of Juicer tools with the genomeID mm9 .
Genome_build: mm9
Supplementary_files_format_and_content: CHARTP-seq: bigWig (bw) files for all reads (.comp), regardless of whether they are allele-specific or not, cas-specific (.cas) and mus-specific (.mus). All bigWig files are input normalized. Log2 ration bw files are ratio after further normalization to have equal coverage within a 1-MB region flanking the Xist locus (chrX:100150712-100650712 and 100683572-101183572).
Supplementary_files_format_and_content: ChIP-seq: bigWig (bw) files for all reads (.comp), regardless of whether they are allele-specific or not, cas-specific (.cas) and mus-specific (.mus). All bigWig files are input normalized.
Supplementary_files_format_and_content: RNA-seq: bigWig (bw) files for all reads (.comp), regardless of whether they are allele-specific or not, cas-specific (.cas) and mus-specific (.mus). All bw files are rpkm values.  Raw exonic reads in each RNA-seq library were quantified and summarized in RNAseq_experiment_count_rep1 or 2.txt.
Supplementary_files_format_and_content: In situ Hi-C:  Compressed Hi-C matrix (.hic) files for cas-specific and mus-specific filtered Hi-C reads. File can be loaded onto Juicebox to view either raw or normalized Hi-C interaction matrices at 5kb to 2.5Mb resolutions.

source_name: RING1A/B KO MEF

value: RING1A/B KO


title: JAK3_H3K4me1


title: RING1A/B KO MEF_H3K27me3, ChIP DNA, rep2


title: Suz12gRNA_H3K4me3

value: Suz12 inactivated - CD4+/CD8+ DP


title: EED KO MEF_Xist CHART, rep2


title: Suz12gRNA_H3K27Ac


title: JAK3_H3K27me3


title: Suz12gRNA_H3K4me1


title: Control_4

description:
11844R_Treat_vs_Control_gender.xlsx
NC4


title: Suz12gRNA_Suz12


title: JAK3_Suz12


title: WT_H3K4me1

value: wildtype - CD4+/CD8+ DP


title: WT_H3K4me3


title: WT_Suz12


title: R_SL_4X13_DP

value: Maxwell 16 LEV simplyRNA Cells Kit according to manufacturers instructions (Promega)

value: JAK3 mutant + Suz12 inactivated - CD4+/CD8+ DP


title: Suz12gRNA_H3K27me3


title: WT_H3K27Ac


title: L_S344_S161_DP


title: T030S.JS.SP


title: WT_H3K27me3


title: M161T.JS.SP


title: M159S.JS.SP


title: M159T.JS.SP


title: JS_Suz12


title: M160T.JS.SP


title: M160S.JS.SP


title: M333S.S.DP


title: M332S.S.DP


title: M332T.S.DP


title: M167S.J.SP


title: M333T.S.DP


title: WT.SP.3

value: wildtype - CD8+ SP


title: WT.SP.2


title: WT.T.DP.4


title: WT.T.DP.2


title: WT.T.DP.1


title: WT.T.DP.3


title: WT_wTbrg4_L10_RNAseq_rep2

city: Haining

first: Chaochen

last: Wang

address: 718 East Haizhou Rd

department: ZJU-UoE Institute

institute: Zhejiang University

data_processing:
RNA-seq reds were mapped to the reference genome mm10 using STAR aligner
The UCSC known gene database was used as gene coordinates reference. To count the RNA-seq reads on exons and introns, exons from all the transcripts of each gene were collapsed. The introns coordinates were then calculated based on the collapsed exon coordinates for each gene. HTSeq was used to count the RNA-seq reads over exons and introns and FPKM values were generated using DESeq2 package in R
Genome_build: mm10
Supplementary_files_format_and_content: txt file, exonic and intronic FPKM values of genes

source_name: WT_wTbrg4, L10 mammary gland

extract_protocol:
Total RNA from L10 mammary gland of WT/wTbrg4 mice was isolated using PureLink RNA Mini Kit (Ambion). RNA quality was measured by bio-analyzer (Bio-Rad).  One microgram of total RNA from each sample was used to generate the sequencing library using the TruSeq Stranded Total RNA Library Prep kit (Illumina) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mammary gland

tag: developmental stage


title: RR_S029_230_DP


title: WT_wTbrg4_L10_RNAseq_rep1


title: delE_wTbrg4_L10_Pol II_ChIPseq

data_processing:
ChIP-seq reds were mapped to the reference genome mm10 using Bowtie aligner.
BedGraph files were generated using HOMER
Genome_build: mm10
Supplementary_files_format_and_content: BedGraph

source_name: delE_wTbrg4_Pol II, L10 mammary gland

extract_protocol:
Frozen-stored mammary tissues were ground into powder with a mortar and pestle. Chromatin was fixed with 1% formaldehyde at room temperature for 10 min and the fixation was quenched with Glycine at a final concentration of 0.125M. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit following the manufacturer's protocols.

tag: chip antibody

value: Pol II (Abcam, ab5408)


title: WT_wTbrg4_L10_STAT5_ChIPseq

source_name: WT_wTbrg4_STAT5, L10 mammary gland

value: STAT5 (Santa Cruz, sc-835)


title: seTbrg4_L10_STAT5_ChIPseq

source_name: seTbrg4_STAT5, L10 mammary gland


title: WT_wTbrg4_L10_H3K27ac_ChIPseq

source_name: WT_wTbrg4_H3K27ac, L10 mammary gland

value: H3K27ac (Abcam, ab4729)


title: WT_L10_Pol II_ChIPseq

source_name: WT_Pol II, L10 mammary gland

value: WT


title: WT_L10_H3K27ac_ChIPseq

source_name: WT_H3K27ac, L10 mammary gland


title: seTbrg4_L10_Pol II_ChIPseq

source_name: seTbrg4_Pol II, L10 mammary gland


title: WT_L10_STAT5_ChIPseq

source_name: WT_STAT5, L10 mammary gland


title: delE_wTbrg4_L10_STAT5_ChIPseq

source_name: delE_wTbrg4_STAT5, L10 mammary gland


title: M170T.J.SP


title: delE_wTbrg4_L10_H3K27ac_ChIPseq

source_name: delE_wTbrg4_H3K27ac, L10 mammary gland


title: SRF delta/delta iPSC ATAC-seq rep1

city: New Haven

first: Xiao

last: Hu

state: CT

address: 10 Amistad ST

department: Cell Biology

institute: Yale University

data_processing:
For RNA-seq data analysis, the RNA-seq reads were mapped to mouse genome (mm10) with Bowtie2 in local mode, which allows the reads spanning the exon-exon junctions to get mapped to one of the two exons (whichever gives the higher mapping score) independent of the transcriptome annotation. Differentially expressed genes were identified by DESeq2 (v1.16.0) followed by cutting off with FDR-adjusted P value < 0.05 and fold changes > 2. MA plot of differentially expressed genes was also done with the R software. Gene Set Enrichment Analysis (GSEA) was performed with the GSEA software.  Reference gene sets were obtained from Polo et al. Gene Ontology (GO) analysis of differentially expressed genes was performed with DAVID (https://david.ncifcrf.gov).
ChIP-seq reads were aligned to the mouse genome mm10 using Bowtie2 (v2.2.6) with default settings. The resulting BAM files were filtered to remove the reads that have the same sequence, and converted to reads coverage files using the BamCoverage in DeepTools (v2.5.0). Reads coverage files were normalized as RPKM (Reads Per Kilobase of transcript per Million mapped reads) and visualized in IGV (v2.3). For transcription factors, filtered BAM files were used for peak calling and differential peak analysis using MACS2 (v2.1.1). Differential peaks were annotated with PAVIS (https://manticore.niehs.nih.gov/pavis2/).
For ATAC-seq analysis, sequence reads were trimmed using the trimmomatic software to remove nextera adapters and low quality bases at the beginning and end of the reads in paired end mode. Reads were then aligned to the mouse mm10 genome sequence using the bwa mem mapper (arXiv:1303.3997 [q-bio.GN]). Reads were sorted and duplicates were marked using the Picard software (http://broadinstitute.github.io/picard/).  Sequence reads that aligned with poor mapping quality to problematic black list regions or mitochondrial regions were removed. Peaks were called on reads with reads with insert size smaller than 250 bases using the MACS2 peak caller using the paired end mode -f BAMPE option.  Differentially bound peaks were identified using the DiffBind R package utilizing the Deseq2 method with parameters fragmentSize=300 and bFullLibrarySize = TRUE (http://bioconductor.org/packages/release/bioc/html/DiffBind.html). Peaks were normalized by the total number of reads from all the samples.
Genome_build: mm10
Supplementary_files_format_and_content: csv, BAM, BAM index, bigwig

source_name: SRF delta/delta iPSC

growth_protocol: Reprogramming cells were cultured in standard mouse ES cell medium with 1 ug/mL Dox. ES cells or iPS cells were cultured in standard ES cell medium on feeder layer. caMKL1 blocked iPS-like cells were cultured in standard ES cell medium on feeder layer, with 1 ug/mL Dox.

extract_protocol:
RNA was extracted with Trizol; ChIP DNA was extracted with Qiagen Gel Extraction kit; ATAC-seq DNA was extracted with Qiagen MinElute PCR purification kit
RNA-seq libraries were prepared with TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101); ChIP DNA libraries were constructed with ThruPLEX® DNA-seq Kit (Rubicon Genomics), ATAC-seq libraries were prepared with Illumina Nextera DNA Library Prep Kit (15028212).

treatment_protocol: Overexpression was achived by pMSCV mediated viral delivery

value: iPSCs

tag: passages


title: SRF delta/delta iPSC ATAC-seq rep2

tag: cell type


title: WT.SP.1


title: caMKL1 mESC ATAC-seq rep2

source_name: caMKL1 mESC

value: mESCs


title: caMKL1 mESC ATAC-seq rep1


title: WT_wTbrg4_L10_Pol II_ChIPseq

source_name: WT_wTbrg4_Pol II, L10 mammary gland


title: SRF f/f iPSC ATAC-seq rep1

source_name: SRF f/f iPSC


title: SRF f/f iPSC ATAC-seq rep2


title: WT mESC ATAC-seq rep2

source_name: WT mESC


title: M169T.J.SP

source_name: thymus


title: ATAC_L_MEP_2

city: Houston

first: Daisuke

last: Nakada

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Basecalling and fastq generation were performed using Illumina’s software (Casava, bcl2fastq)
Reads were trimmed for quality using Trimmomatic (version 0.36)
Trimmed reads were aligned to mm10 using bowtie2 (version 2.2.6)
Peaks were called using PePr (version 1.1.18)
Peaks were annotated using HOMER (version 4.10)
Peaks were analyzed for motifs using HOMER
bedGraph files were generated using deepTools (version 3.1.0; bamCoverage)
Genome_build: mm10
Supplementary_files_format_and_content: UCSC formatted bedGraph files, generated using deepTools (bamCoverage); scores are CPM normalized.

source_name: Prdm16s Leukemic-MEP cells

extract_protocol:
10,000 L-MEPs and normal MEPs were lysed and tagmented using Tn5 according to ATAC-seq protocol.
Tagmentated DNA was amplified with NEBNext Q5 Hot Start HiFi PCR Master Mix (New England Biolab, Ipswich, MA) for library preparation. Barcoded libraries were purified and sequenced on a HiSeq2500 platform.

treatment_protocol: L-MEP were isolated from leukemic recipient mice and control MEPs were isolated from wild-type mice.

value: leukemic megakaryocyte-erythroid progenitor (MEP) cells


title: ATAC_L_MEP_3


title: seTbrg4_L10_H3K27ac_ChIPseq

source_name: seTbrg4_H3K27ac, L10 mammary gland


title: H3K27ac_L-MEP_3

data_processing:
Basecalling and fastq generation were performed using Illumina’s software (Casava, bcl2fastq)
Reads were trimmed for quality using Trimmomatic (version 0.36)
Trimmed reads were aligned to mm10 using bowtie2 (version 2.2.6)
bedGraph files were generated using deepTools (version 3.1.0; bamCoverage)
Enhancer and super-enhancer prediction was performed using HOMER (version 4.10)
Genome_build: mm10
Supplementary_files_format_and_content: UCSC formatted bedGraph files, generated using deepTools (bamCoverage); scores are CPM normalized.

growth_protocol: We transduced wild-type murine MEP cells with retroviral vectors encoding Prdm16s and transplanted them into syngeneic recipient mice. L-MEPs were sorted in mice the developed leukemia for library preparation.

extract_protocol:
10,000 L-MEP and normal MEP were sorted and treated with Mnase, histone-DNA complexes were isolated with antibody
ChIP DNA was purified for end repair, adapter ligation, and amplification using a NEB Ultra II library preparation kit following the manufacturer’s protocols (New England BioLabs, Ipswich, MA)

value: H3K27ac (#ab4729, Abcam, Cambridge, MA)


title: ATAC_Ctrl_MEP_3

source_name: Ctrl MEP cells

value: wild type

value: megakaryocyte-erythroid progenitor (MEP) cells


title: ATAC_Ctrl_MEP_1


title: ATAC_Ctrl_MEP_2


title: H3K27ac_L-MEP_2


title: H3K27ac_L-MEP_1


title: WT mESC ATAC-seq rep1


title: H3K4me3_L-MEP_3

value: H3K4me3 (#04-745, Millipore, Billerica, MA)


title: H3K27ac_Ctrl-MEP_3


title: H3K27ac_Ctrl-MEP_2


title: H3K4me3_L-MEP_2


title: H3K27ac_Ctrl-MEP_1


title: H3K4me3_Ctrl-MEP_1


title: H3K4me3_L-MEP_1


title: Input_L-MEP_2


title: Input_L-MEP_1