title: Spn1 ChIP-seq, ChIP DNA: Spn1-AID + IAA 2

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6
ChIP library from Spn1 ChIP-seq with Spn1 depleted.

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (ACTTGA) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig

extract_protocol:
Cultures were processed as previously described (doi:10.1093/nar/gkz119), and the final pellet after cell lysis was resuspended in 500 μL LB140 and sonicated in a QSonica Q800R machine for 15 minutes (30 seconds on, 30 seconds off, 70% amplitude) to achieve 100-500 bp DNA fragments. Protein concentrations were measured by Bradford assay, and 500 μg of chromatin was used as input. As a spike-in control, S. pombe chromatin from a strain encoding a V5-tagged protein (FWP485) was added to a final concentration of 10%, and the volume was brought up to 800 μL with WB140 buffer. For immunoprecipitation, 8 μL anti-V5 antibody (Invitrogen, R960-25) was used. Immunoprecipitation reactions were incubated at 4°C with end-over-end rotation overnight (~16-18 hr). Protein G Sepharose beads (GE Healthcare, 4 Fast Flow) were washed with WB140, and a 50% slurry was subsequently made in WB140. Fifty-μL aliquots of slurry were transferred into new Eppendorf tubes, and the WB140 was removed. The immunoprecipitation reactions were added directly to the beads and incubated at 4°C with end-over-end rotation for 4 hr. Bead-washing and elution were done are previously described (doi:10.1093/nar/gkz119). The 200 μL of eluate was incubated at 65°C overnight to reverse crosslinking. RNase A/T1 digestion, Proteinase K digestion, and DNA purification were done as previously described (doi:10.1093/nar/gkz119).
Library preparation was done as previously described (doi:10.1093/nar/gkz119). The number of PCR cycles for library amplification was determined empirically for each sample and ranged from 11-19 cycles. Samples were again purified twice using 0.7x volume SPRI beads and run on Agilent Bioanalyzer to assess size distribution, quality, and concentration.


title: CD34_Replicate1_H3

status: Public on Jul 01 2020

type: SRA

city: Montreal

first: Thomas

last: Milan

state: Quebec

address: 2950 Chemin de Polytechnique

country: Canada

institute: IRIC

library_source: genomic

data_processing:
Quality control steps (Trimmomatic (version 0.32) = Leading:3 ; trailing:3 slidingwindow:4:15 ; minlen:32) were performed on the raw data files.
ChIP-seq and ATAC-seq reads were aligned to the GRCH37/hg19 genome assembly using BWA version 0.7.10 with the default parameters.
Duplicates were removed by Samtools (version 1.9). For ATAC-seq data, mitochondrial DNA were removed (samtools idxstats input.bam | cut -f 1 | grep -v MT | xargs samtools view -b input.bam > output.bam)
Peaks were called using MACSPeaks version 2.2.4 with the following setting: callpeak -g hs -q 0.05 --format BAMPE
Analysis of correlated gene expression and histone modifications was perfomed using EaSeq (version 1.04)
Genome_build: GRCH37/hg19
Supplementary_files_format_and_content: BigWig files were generated using Homer (default parameters).
"Merge" files with all replicates:
CD34_H3K4me3 (Replicate 1 + 2):
CD34_Merge_Replicates_H3K4me3.bigWig, CD34_Merge_Replicates_H3K4me3.narrowPeak
CD34_H3K27me3 (Replicate 1 + 2 + 3):
CD34_Merge_Replicates_H3K27me3.bigWig, CD34_Merge_Replicates_H3K27me3.narrowPeak
CD34_H3K79me2 (Replicate 1 + 2 + 3):
CD34_Merge_Replicates_H3K79me2.bigWig, CD34_Merge_Replicates_H3K79me2.narrowPeak
CD34_KM3_H3K4me3 (Replicate 1 + 2):
CD34_KM3_Merge_Replicates_H3K4me3.bigWig, CD34_KM3_Merge_Replicates_H3K4me3.narrowPeak
CD34_KM3_H3K27me3 (Replicate 1 + 2):
CD34_KM3_Merge_Replicates_H3K27me3.bigWig, CD34_KM3_Merge_Replicates_H3K27me3.narrowPeak
CD34_KM3_H3K79me2 (Replicate 1 + 2):
CD34_KM3_Merge_Replicates_H3K79me2.bigWig, CD34_KM3_Merge_Replicates_H3K79me2.narrowPeak
CD34_KM3_ATAC-seq (Replicate 1 + 2 + 3):
CD34_KM3_Merge_ATAC-seq.bigWig, CD34_KM3_Merge_ATAC-seq.narrowPeak
Model_H3K4me3 (Replicate 1 + 2 + 3):
Model_Merge_H3K4me3.bigWig, Model_Merge_H3K4me3.narrowPeak
Model_H3K27me3 (Replicate 1 + 2 + 3 + 4):
Model_Merge_H3K27me3.bigWig, Model_Merge_H3K27me3.narrowPeak
Model_H3K79me2 (Replicate 1 + 2 + 3):
Model_Merge_H3K79me2.bigWig, Model_Merge_H3K79me2.narrowPeak
Model_ATAC-seq (Replicate 1 + 2 + 3 + 4):
Model_Merge_ATAC-seq.bigWig, Model_Merge_ATAC-seq.narrowPeak

molecule: genomic DNA

organism: Homo sapiens

source_name: human HSPCs

extract_protocol:
[ChIP-seq]  After crosslinking cells by using formaldehyde 1% (final concentration) for 7 minutes at room temperature, glycine 0.125nM (final concentration) was added for 5 minutes at room temperature to stop the reaction. Fixed cells were washed with PBS, resuspended in 1mL of a first lysis buffer (Triton 0.25%, Tris pH 8.0 10mM, EDTA 10mM, EGTA 0.5mM, protease inhibitor 1X) for 5 minutes, and in 1 mL of a second buffer for 30 minutes (NaCl 200mM, Tris pH 8.0 10mM, EDTA 1mM, EGTA 0.5mM, protease inhibitor 1X). Lysate was resuspended in another buffer (0.5% SDS, 0.5% Triton, Tris pH 8.0 10mM, NaCl 140mM, EDTA 1mM, EGTA 0.5mM, protease inhibitor 1X) and then sonicated by using a Covaris S2 sonicator. The parameters used were as follows: duty Factor 10%, 200 cycles per burst, 105W, 4 minutes. The supernatant collected after the spinning at 13000 rpm for 5 minutes was used for future experiments.  Beads (Protein G Dynabeads™ ; resuspension buffer : Triton 1%, Tris pH 8.0 10mM, NaCl 150mM, EDTA 2mM) were incubated overnight on a rotator at 4°C with 3μg of antibodies recognizing histone marks (H3 : #ab1791, H3K4me3 : #ab8580-100, H3K27me3 : Millipore 07-449, H3K79me2 : #ab3594, H3K27ac : Millipore 07-360). Sonicated chromatin was incubated with 250μL of beads during 4 hours on a rotator at 4°C. The beads were washed sequentially with different buffers: ‘Low Salt’ Buffer (0.5% NP40, 15mM KCl, 10mM Tris pH 8.0, 1mM EDTA), 3 different ‘High Salt’ buffers (0.5% Triton, 10mM Tris pH 8.0, 100mM (2) or 400mM (3) or 500mM (4) NaCl), twice in LiCl Buffer (0.5% NP40, 250mM LiCl, 10mM Tris pH 8.0, 1mM EDTA). ChIPed material was then eluted a classic elution buffer (10mM Tris pH8.0, 1mM EDTA) and incubated overnight at 65°C with shaking (1200rpm). An RNase and proteinase K digestion was performed in order to reverse crosslink. DNA was extracted and purified by a classic phenol-chloroform protocol.
[ATAC-seq]  ATAC-seq experiment was based on method published by Buenrostro et al. (PMID: 24097267)
TruSeq ChIP Library Preparation Kit by Illumina (#IP-202-9001) was used to construct DNA libraries as described in the manufacturer’s instructions with a PCR for a total of 12 cycles using the Illumina indexed library primers. NextSeq 500 was used to sequence samples (75pb paired-end) according to standard Illumina protocols.

treatment_protocol: Isolated cells from fresh umbilical cord blood (< 30 hours)

tag: cell type

value: HSPCs

tag: chip antibody

tag: development stage

value: Fresh purified CD34+ cells


title: m1_AY_Y3_J6

city: Stanford

first: Michelle

middle: Berkeley

last: Chen

address: 318 Campus Drive

country: USA

institute: Stanford

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: raw count table

molecule: total RNA

organism: Mus musculus

source_name: three-mo mouse BEC

growth_protocol: Mice 3 (young)

extract_protocol:
Brain tissues were dissected using Miltenyi neural dissociation kit. Brain endothelial cells were isolated via FACS.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: primary murine brain endothelial cells


title: Spn1 ChIP-seq, ChIP DNA: Spn1-AID + IAA 1

city: Boston

first: Fred

last: Winston

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (GCCAAT) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig

organism: Saccharomyces cerevisiae

treatment_protocol: Cells were grown in YPD at 30°C to OD600 ≈ 0.65, diluted back to OD600 ≈ 0.3-0.4 in pre-warmed YPD, treated with IAA at a final concentration of 25 μM, and allowed to grow for 90 minutes.

tag: strain

tag: genotype

value: MATa leu2delta1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6

tag: treatment

value: 25 microM IAA

tag: antibody


title: m1_Young2_J2


title: m1_Young2_O10


title: m1_Young2_A2


title: CD34_Replicate1_Input


title: 9_14month_array

type: RNA

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

institute: Dartmouth Medical School

description:
9_14month_252800422024_1_2.txt
disease

hyb_protocol: Fragmentation Buffer and Hybridization Buffer (Agilent Gene Expression Hybridization Kit) were added, and samples applied to Whole Human Genome microarrays

scan_protocol: Scanned on Agilent scanner

data_processing:
Images were quantified using Feature Extraction Software, log10 Green over Red.  Raw, individual array files need log2 adjusted and reversed for Red over Green.
Log(base2) of R/G Lowess Normalized Ratio (Mean), NONmedian centered data were multiplied by -3.321928 to convert to Log2(Cy3/Cy5) ratios, probes with > 20% data were removed

source_name: Sample: Human PBMC

label_protocol: 50ng of total RNA was reversed transcribed using Agilent Low Input Amp Labeling Kit and labeled with Perkin Elmer Cy3

extract_protocol: Total RNA extracted from PBMC following manufacturer's protocol. UHR is Stratagene, Universal Human Reference RNA Catalog #740000

treatment_protocol: Collection of PBMC in PAXgene

tag: diagnosis

value: SSc

value: Cyclophosphamide

tag: timepoint

value: post

tag: response

value: Responder

tag: tissue

value: PMBC

source_name: Universal Human Reference

tag: sample type

value: Universal Human Reference (UHR)


title: CD34_Replicate1_H3K79me2


title: Spn1 ChIP-seq, ChIP DNA: Spn1-AID + DMSO 2

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6
ChIP library from Spn1 ChIP-seq with Spn1 non-depleted.

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (CAGATC) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig

treatment_protocol: Cells were grown in YPD at 30°C to OD600 ≈ 0.65, diluted back to OD600 ≈ 0.3-0.4 in pre-warmed YPD, treated with DMSO, and allowed to grow for 90 minutes.

value: DMSO


title: 9_26month_array

description:
9_26month_252800422024_2_3.txt
disease


title: 9_8month_array

description:
9_8month_252800422024_1_3.txt
disease


title: 75_54month_array

description:
75_54month_252800422038_1_4.txt
disease


title: 75_Base_R_array

description:
75_Base_R_252800422020_2_4.txt
disease

value: base


title: Rpb1 ChIP-seq, ChIP DNA: Spn1-AID + DMSO 1

description:
MATa leu2∆1 ura3-52 CgLEU2::OsTIR1 SPN1-3xV5-AID2::KanMX6
ChIP library from Rpb1 ChIP-seq with Spn1 non-depleted.

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (GTCTACAT) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig

extract_protocol:
Cultures were processed as previously described (doi:10.1093/nar/gkz119), and the final pellet after cell lysis was resuspended in 500 μL LB140 and sonicated in a QSonica Q800R machine for 15 minutes (30 seconds on, 30 seconds off, 70% amplitude) to achieve 100-500 bp DNA fragments. Protein concentrations were measured by Bradford assay, and 500 μg of chromatin was used as input. As a spike-in control, S. pombe chromatin from a strain encoding an HA-tagged protein (FWP568) was added to a final concentration of 10%, and the volume was brought up to 800 μL with WB140 buffer. For immunoprecipitation, 10 μL anti-Rpb1 (Millipore, 8WG16) was used. Immunoprecipitation reactions were incubated at 4°C with end-over-end rotation overnight (~16-18 hr). Protein G Sepharose beads (GE Healthcare, 4 Fast Flow) were washed with WB140, and a 50% slurry was subsequently made in WB140. Fifty-μL aliquots of slurry were transferred into new Eppendorf tubes, and the WB140 was removed. The immunoprecipitation reactions were added directly to the beads and incubated at 4°C with end-over-end rotation for 4 hr. Bead-washing and elution were done are previously described (doi:10.1093/nar/gkz119). The 200 μL of eluate was incubated at 65°C overnight to reverse crosslinking. RNase A/T1 digestion, Proteinase K digestion, and DNA purification were done as previously described (doi:10.1093/nar/gkz119).
Library preparation was done as previously described (doi:10.1093/nar/gkz119). The number of PCR cycles for library amplification was determined empirically for each sample and ranged from 11-19 cycles. Samples were again purified twice using 0.7x volume SPRI beads and run on Agilent Bioanalyzer to assess size distribution, quality, and concentration.


title: 75_8month_array

description:
75_8month_252800420326_1_2.txt
disease


title: RNA-seq_Exp7_KGN_TGF_rep5

city: Copenhagen

first: Paul

middle: Andreas Compare

last: Cloos

address: Ole Maaløesvej5

department: Biotech Research Innovation Centre

country: Denmark

institute: Copenhagen University

description:
Exp7_KGN_TGF_rep5
Galaxy779-[DESeq2_result_file_on_KGN_TGF_vs_KGN].txt

data_processing:
Chip-seq data processing: Fastq datasets were concatenated using the "concatenate” tool (Galaxy tool ID: Cat1, version1.0.0) and trimmed with Trimmomatic version 0.36.0 (with  illuminaclip step, Truseq3 (single ended, Mi and Hiseq), max mismatch=2, sliding window, average quality 20). Mapped with Bowtie2 against hg38 using preset settings. Duplicates removed with rmdup.Peak calling with Easeq software: Adaptive Local Thresholding (default settings)  with respective knocout samples as negative controls.
RNA-seq data processing: Fastq datasets were concatenated using the "concatenate” tool (Galaxy tool ID: Cat1, version1.0.0) and trimmed with Trimmomatic version 0.36.0 (with  illuminaclip step, Truseq3 (single ended, Mi and Hiseq), max mismatch=2, sliding window, average quality 20). Sequencing data was aligned via RNAstar (version2.4.0d-2, single-end reads) using  hg38 (Canonical) as refgene and reads were counted using Htseq-count (version 0.6.1, galaxy1 using Union mode and Stranded with a minimum alignment quality of 10). Differential expression was analysed using Deseq2. Genes were called as differentially expressed for expression changes larger than 2-fold and an FDR ≤0.01. A minimum of three biological replicates of each sample were used.
Genome_build: hg38
Supplementary_files_format_and_content: GZIPped WIG file containing ChIP-Seq peaks and output txt files from Deseq2 analysis of RNA seq data. Collumns in Deseq2 data provide the following:  Collumn 1: Gene; Collumn 2: Total Counts; Collumn 3: log2 fold difference; Collumn 4: Standard deviation; Collumn 5: Wald Stats; Collumn 6: Wald P value; Collumn 7: Benjamini-Hochberg  P value

source_name: KGN cell-line

growth_protocol: Cells grown in Ham medium with 10% FCS

extract_protocol:
Preparation of total mRNA for RNA-seq analysis: Cells were harvested, washed in PBS and pelleted by centrifugation at 300g for 5 minutes. The pellets were kept on ice, resuspended in 350μl RLT Plus-Buffer (Qiagen) with 1% β-mercaptoethanol (Sigma) and passed through a 22G needle 5 times in order to lyse the cells properly. RNA was purified using the RNAeasy Kit (Qiagen) according to manufacturer´s instruction with final elution in 30μl of RNA- free water. The RNA concentration was measured on the NanoDrop 2000 Spectrophotometer (Thermo Scientific). RNA was stored at -80°C.
500ng of total RNA was used for library preparation. Sequencing adaptors were added using the Truseq RNA library prep kit v2 (Illumina) according to the manufacturer’s instructions. Library quality was assessed by analysis on a Bioanalyzer 2100.
RNA and ChIP sequencing libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: KGN

tag: genotype/variation

value: KGN Cell-line is Heterozygous for FOXL2 C134W mutation, here stimulated with TGF


title: 8_base_array

description:
08_base_252800422380_2_4.txt
disease

value: Non-responder


title: m1_AY_Y3_I10


title: Spn1 ChIP-seq, ChIP DNA: Spn1-AID + DMSO 1

data_processing:
The Snakemake pipelines used to process these data are archived at (doi.org/10.5281/zenodo.3901642). Reads were demultiplexed using fastq-multx, allowing one mismatch to the index sequence (ACAGTG) and A-tail. Cutadapt was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2, and alignments with a mapping quality of at least 5 were selected using SAMtools. The median fragment size estimated by MACS2 cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. For ChIP-seq coverage from IP samples, spike-in normalization was accomplished by scaling coverage proportionally to the normalization factor N_(input, spike-in) / (N_(IP, spike-in) * (N_(input, experimental)), where N_(IP, spikein) is the number of S. pombe alignments in the IP sample, N_(input, spike-in) is the number of S. pombe alignments in the corresponding input sample, and N_(input, experimental) is the number of S. cerevisiae alignments in the input sample. Coverage from input samples was normalized to N_(input, experimental). Coverage of the relative ratio of IP over input was obtained by first smoothing normalized IP and input fragment midpoint coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
"Midpoints" bigWig files are spike-in normalized coverage of estimated fragment midpoints obtained by shifting the 5′ end of alignments by half the median fragment size estimated by MACS2 over all samples for a factor. "Protection" bigWig files are spike-in normalized coverage of estimated fragments obtained by extending alignments to the median fragment size estimated by MACS2 over all samples for a factor. "Ratio" bigWig files contain the relative log2 ratio of an IP sample over its corresponding input sample, obtained by first smoothing each "midpoint" coverage using a Gaussian kernel with 20 bp bandwidth, and then taking the ratio.
Genome_build: Saccharomyces cerevisiae S288C R64-2-1, Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: bigWig


title: m1_Young2_B11


title: RNA-seq_Exp7_KGN_TGF_rep3

description:
Exp7_KGN_TGF_rep3
Galaxy779-[DESeq2_result_file_on_KGN_TGF_vs_KGN].txt


title: 75_14month_array

description:
75_14month_252800420365_2_2.txt
disease


title: RNA-seq_Exp7_KGN_TGF_rep2

description:
Exp7_KGN_TGF_rep2
Galaxy779-[DESeq2_result_file_on_KGN_TGF_vs_KGN].txt


title: replicate_2_ribosome_footprint_raw

city: Cambridge

first: Joseph

last: Replogle

state: Massachussetts

address: 455 Main St

institute: UCSF / Whitehead Institute / MIT

description: ribosome footprint

data_processing:
Ribosome profiling and RNA-seq libraries were sequenced on an Illumina HiSeq 4000 as single end 50-bp reads (UCSF Center for Advanced Technology) at a depth of 22-64 million reads per library. Ribosome profiling reads were processed by removing 3’ linker sequences using FASTX clipper and de-multiplexed using FASTX barcode splitter (http://hannonlab.cshl.edu/fastx_toolkit/).
Adapters were trimmed using fastx_clipper: "fastx_clipper -n -a AGATCGGAAGAGCACACGTCTGAACTC".
Sample barcodes were split with fastx_barcode_splitter.pl. Samples are marked with the following barcodes: Gal4: ATCG; NEMF: TAGC; GIGYF2: CGAT; EIF4E2: GCTA; ZNF598: AGTC; K562: GACT.
Sample barcodes and unique molecular identifiers were trimmed using a custom Python script. Next, abundant reads were filtered by aligning to a custom library of human rRNAs, tRNAs, and primer sequences using bowtie v1.2 (http://bowtie-bio.sourceforge.net/). All remaining reads were aligned to a modified human genome (GRCh38.92 with addition of our CRISPRi construct and the GFPNon-stop) using tophat v2.1.1 (https://ccb.jhu.edu/software/tophat/; relevant parameters: --read-mismatches=1 and --no-novel-juncs). After alignment, uniquely mapping reads were extracted, and plastid (https://plastid.readthedocs.io) was used to obtain gene-level read counts and normalized counts, reads per kilobase per million mapped reads (RPKM).
To assign reads to genomic positions, a p-site offset of 12 nucleotides was determined by calculating the average distance of the start codon peak from the start codon (plastid psite).
The RNA-seq libraries were processed using the same pipeline as the ribosome profiling libraries, with the exception that tophat was run with –read-mismatches=2 due to the longer RNAseq read length.
All downstream analyses were performed using the Python libraries pandas, plastid, matplotlib, seaborn, numpy, and scipy.
Genome_build: GRCh38.92 with addition of our CRISPRi construct and the GFPNon-stop
Supplementary_files_format_and_content: Processed data are presented as the output of plastid cs count.

source_name: K562-dCas9 cells with GFP non-stop reporter

growth_protocol: See Methods. K562-dCas9 cell line stably expressing GFPNon-stop were grown in RPMI-1640 with 25mM HEPES, 2.0 g/L NaHCO3, 0.3 g/L L-Glutamine supplemented with 10% FBS, 2 mM glutamine, 100 units/mL penicillin and 100 µg/mL streptomycin. Cells were maintained at a density between 250,000 cells per mL and 1,000,000 cells per mL throughout the course of the experiments.

extract_protocol:
Cyclohexamide was added (100mg/ul) to the cells and they were incubated for 5 minutes at 37 °C and then pelleted at 400g for 5 minutes. Media was removed and cell pellets were immediately snap frozen. Libraries were prepared according to McGlincy and Ingolia, Methods, 2017.
Libraries were prepared according to McGlincy and Ingolia, Methods, 2017.

treatment_protocol: K562-dCas9 cell line stably expressing GFPNon-stop was infected with lentiviral vectors containing a guide RNA against one gene or non-targeting guide RNA (Table 2).  Cells were selected using FACS to recover cells containing sgRNA (labeled with RFP).

tag: sgrna

value: mixed

tag: sgrna target

tag: replicate


title: 75_26month_array

description:
75_26month_252800420325_2_1.txt
disease


title: m1_Young1_N13

tag: cell type


title: m1_Young2_D6


title: replicate_1_ribosome_footprint_raw

description: ribosome footprint


title: RNA-seq_Exp7_KGN_TGF_rep1

description:
Exp7_KGN_TGF_rep1
Galaxy779-[DESeq2_result_file_on_KGN_TGF_vs_KGN].txt


title: m1_Young2_H14


title: RNA-seq_Exp7_KGN_rep4

description:
Exp7_KGN_rep4
Galaxy779-[DESeq2_result_file_on_KGN_TGF_vs_KGN].txt

value: KGN Cell-line is Heterozygous for FOXL2 C134W mutation


title: RNA-seq_Exp7_KGN_TGF_rep4

description:
Exp7_KGN_TGF_rep4
Galaxy779-[DESeq2_result_file_on_KGN_TGF_vs_KGN].txt


title: m1_Young1_H7


title: m1_Young2_N18


title: sgZNF598_r1_rnaseq

description: total RNA


title: sgNEMF_r2_rnaseq

description: total RNA

value: sgNEMF

value: NEMF


title: 74_8month_array

description:
74_8month_252800420320_1_3.txt
disease

value: Transplant


title: RNA-seq_Exp7_KGN_rep3

description:
Exp7_KGN_rep3
Galaxy779-[DESeq2_result_file_on_KGN_TGF_vs_KGN].txt


title: m1_AY_Y3_F5

value: primary murine brain endothelial cells


title: RNA-seq_Exp7_KGN_rep2

description:
Exp7_KGN_rep2
Galaxy779-[DESeq2_result_file_on_KGN_TGF_vs_KGN].txt


title: sgNEMF_r1_rnaseq

description: total RNA


title: 74_base_array

description:
74_base_252800420365_2_3.txt
disease

value: SSc


title: 74_54month_array

description:
74_54month_252800422222_2_3.txt
disease


title: m1_Young2_I1


title: 74_26month_array

description:
74_26month_252800420326_1_4.txt
disease


title: sgZNF598_r2_rnaseq

description: total RNA


title: RNA-seq_Exp7_KGN_rep1

description:
Exp7_KGN_rep1
Galaxy779-[DESeq2_result_file_on_KGN_TGF_vs_KGN].txt


title: RNA-seq_Exp6_HGrC1_C134W_TGF_rep3

description:
Exp6_HGrC1_C134W_TGF_rep3
Galaxy764-[DESeq2_result_file_on_MUT_TGF_vs_EV_TGF].txt

source_name: HGrC1 cell-line

value: HGrC1 cell-line transduced with C134W mutant (C134W) FOXL2 and stimulated with TGF


title: m1_Young1_G13


title: 74_38month_array

description:
74_38month_252800422222_1_3.txt
disease

value: post


title: 73_base_array

description:
73_base_252800421273_2_3.txt
disease

value: Cyclophosphamide

value: Responder


title: none_r2_rnaseq

description: total RNA

source_name: K562-dCas9 cells


title: m1_AY_Y3_H18


title: sgGIGYF2_r2_rnaseq

description: total RNA


title: sgGIGYF2_r1_rnaseq

description: total RNA


title: 74_14month_array

description:
74_14month_252800421274_2_4.txt
disease

value: PMBC

value: Universal Human Reference (UHR)


title: m1_Young1_K14


title: RNA-seq_Exp6_HGrC1_WT_TGF_rep3

description:
Exp6_HGrC1_WT_TGF_rep3
Galaxy758-[DESeq2_result_file_on_MUT_TGF_vs_WT_TGF].txt

value: HGrC1 cell-line transduced with wildtype (WT) FOXL2 and stimulated with TGF


title: 73_8month_array

description:
73_8month_252800420325_2_2.txt
disease


title: RNA-seq_Exp6_HGrC1_EV_TGF_rep3

description:
Exp6_HGrC1_EV_TGF_rep3
Galaxy764-[DESeq2_result_file_on_MUT_TGF_vs_EV_TGF].txt

value: HGrC1 cell-line transduced with empty vector (EV) control and stimulated with TGF


title: sgGal4_r2_rnaseq

description: total RNA

value: non-targeting


title: RNA-seq_Exp6_HGrC1_C134W_rep3

description:
Exp6_HGrC1_C134W_rep3
Galaxy762-[DESeq2_result_file_on_MUT_vs_WT].txt

value: HGrC1 cell-line transduced with C134W mutant (C134W) FOXL2


title: m1_AY_Y3_E14


title: sgGal4_r1_rnaseq

description: total RNA


title: m1_Young2_H5


title: RNA-seq_Exp6_HGrC1_WT_rep3

description:
Exp6_HGrC1_WT_rep3
Galaxy762-[DESeq2_result_file_on_MUT_vs_WT].txt

value: HGrC1 cell-line transduced with wildtype (WT) FOXL2


title: sgEIF4E2_r2_rnaseq

description: total RNA


title: m1_Young1_F9


title: none_r1_rnaseq

description: total RNA


title: 73_38month_array

description:
73_38month_252800422222_2_2.txt
disease


title: RNA-seq_Exp6_HGrC1_C134W_TGF_rep2

description:
Exp6_HGrC1_C134W_TGF_rep2
Galaxy764-[DESeq2_result_file_on_MUT_TGF_vs_EV_TGF].txt


title: RNA-seq_Exp6_HGrC1_EV_rep3

description:
Exp6_HGrC1_EV_rep3
Galaxy766-[DESeq2_result_file_MUT_vs_EV].txt

value: HGrC1 cell-line transduced with empty vector (EV) control


title: sgEIF4E2_r1_rnaseq

description: total RNA


title: m1_Young2_G9


title: RNA-seq_Exp6_HGrC1_WT_TGF_rep2

description:
Exp6_HGrC1_WT_TGF_rep2
Galaxy758-[DESeq2_result_file_on_MUT_TGF_vs_WT_TGF].txt


title: ATAC-Seq AHR KD

first: Juyong

middle: Brian

last: Kim

state: CA

address: 300 Pasteur Dr.

institute: Stanford University

data_processing:
Quality control of ChIPseq data was performed using Fastqc, and then low-quality bases and adaptor contamination were trimmed by cutadapt. Filtered reads were mapped to hg19 using BWA mem algorithm. Duplicate reads were marked by Picard Markduplicate module and removed with unmapped reads by samtools view -f 2 -F 1804
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: HCASMC_ATAC-Seq AHR KD

growth_protocol: HCASMC media, passages 5-8

extract_protocol: HCASMC was transfected with AHR siRNA, then followed the Omni-ATAC-Seq protocol. Nextera barcodes were used to generate the libraries.

value: Human Coronary Artery Smooth Muscle Cells (HCASMC)

value: coronary artery

tag: genotype/treatment

value: AHR knockdown


title: m1_Young1_E2

value: primary murine brain endothelial cells


title: RNA-seq_Exp6_HGrC1_EV_TGF_rep2

description:
Exp6_HGrC1_EV_TGF_rep2
Galaxy764-[DESeq2_result_file_on_MUT_TGF_vs_EV_TGF].txt


title: m1_Young2_M1


title: 73_54month_array

description:
73_54month_252800422222_1_1.txt
disease

value: SSc


title: ATAC-Seq Control (knockdown)

source_name: HCASMC_ATAC-Seq Control (knockdown)

extract_protocol: HCASMC was transfected with scrambled siRNA control, then followed the Omni-ATAC-Seq protocol. Nextera barcodes were used to generate the libraries.

value: control


title: ATAC-Seq AHR OE

source_name: HCASMC_ATAC-Seq AHR OE

extract_protocol: HCASMC was transduced with AHR overexpressing lentivirus for 24 hours, then followed the Omni-ATAC-Seq protocol. Nextera barcodes were used to generate the libraries.

value: AHR OE


title: RNA-seq_Exp6_HGrC1_C134W_rep2

description:
Exp6_HGrC1_C134W_rep2
Galaxy762-[DESeq2_result_file_on_MUT_vs_WT].txt


title: ATAC-Seq Control (AHR OE)

source_name: HCASMC_ATAC-Seq Control (AHR OE)

extract_protocol: HCASMC was transduced with control lentivirus for 24 hours, then followed the Omni-ATAC-Seq protocol. Nextera barcodes were used to generate the libraries.


title: 73_26month_array

description:
73_26month_252800420325_2_3.txt
disease

value: Cyclophosphamide

value: post


title: m1_AY_Y3_K10


title: 71_base_array

description:
71_base_252800422380_1_1.txt
disease

value: Transplant

value: base

value: Responder

value: PMBC


title: 72_base_array

description:
72_base_252800422381_2_3.txt
disease

value: Universal Human Reference (UHR)


title: 70_base_array

description:
70_base_252800422038_1_3.txt
disease

value: Non-responder


title: m1_AY_Y3_C13


title: 73_14month_array

description:
73_14month_252800420326_2_4.txt
disease


title: RNA-seq_Exp6_HGrC1_EV_rep2

description:
Exp6_HGrC1_EV_rep2
Galaxy766-[DESeq2_result_file_MUT_vs_EV].txt


title: TCF21 ChIP-Seq

source_name: HCASMC_TCF21 ChIP-Seq

extract_protocol: ChIP-seq was performed using TCF21 antibody (Sigma HPA013189) in HCASMC between passages 5-8, and library was constructed using the KAPA Hyper Prep Kit.

value: no dioxin

tag: chip antibody

value: TCF21 antibody (Sigma HPA013189)


title: m1_Young2_D11


title: m1_Young2_N4


title: Input ChIP-Seq (for TCF21 ChIP)

source_name: HCASMC_Input ChIP-Seq (for TCF21 ChIP)

extract_protocol: Cross-linked DNA from HCASMC between passages 5-8 was sonicated and extracted with Zymo DNA extraction kit, and library was constructed using the KAPA Hyper Prep Kit.

value: Human Coronary Artery Smooth Muscle Cells (HCASMC)


title: RNA-seq_Exp6_HGrC1_C134W_TGF_rep1

description:
Exp6_HGrC1_C134W_TGF_rep1
Galaxy764-[DESeq2_result_file_on_MUT_TGF_vs_EV_TGF].txt

value: HGrC1 cell-line transduced with C134W mutant (C134W) FOXL2 and stimulated with TGF


title: m1_Young1_G6


title: RNA-seq_Exp6_HGrC1_WT_rep2

description:
Exp6_HGrC1_WT_rep2
Galaxy762-[DESeq2_result_file_on_MUT_vs_WT].txt

value: HGrC1 cell-line transduced with wildtype (WT) FOXL2


title: RNA-seq_Exp6_HGrC1_EV_TGF_rep1

description:
Exp6_HGrC1_EV_TGF_rep1
Galaxy764-[DESeq2_result_file_on_MUT_TGF_vs_EV_TGF].txt

value: HGrC1 cell-line transduced with empty vector (EV) control and stimulated with TGF


title: CTRL005

city: New Haven

first: Jonas

last: Schupp

state: CT

address: 300 Cedar Street

department: PCCSM

institute: YALE UNIVERSITY

description: Raw data to be made available through dbGaP

data_processing:
fastq read 2 sequences were trimmed of the reverse complement sequence of the template switch oligo, as well as for poly(A) contaminants. Paired reads with a trimmed read 2 less than 25 bp long were discarded.
Downstream processing was conducted with STAR v2.7.3a and its single cell seq implementation "STARsolo".
Cells being accepted had to pass the following filters: at least 750 transcripts profiled, having at least 10% of transcripts arising from intron spanning or unspliced reads, less than 15% of their transcriptome of mitochondrial origin
Genome_build: GENECODE release 31 (GRCh38.p12)
Supplementary_files_format_and_content: gene vs barcode sparse matrix (raw counts and normalized data) of all samples
Supplementary_files_format_and_content: Sputum.raw.counts.processed.mtx: sparse matrix file of processed raw counts
Supplementary_files_format_and_content: Sputum.data.processed.mtx: sparse matrix file of processed normalized data
Supplementary_files_format_and_content: Sputum.processed.genes.tsv: gene IDs to sparse matrix files of processed raw counts and normalized data
Supplementary_files_format_and_content: Sputum.processed.barcodes.tsv: barcode IDs to sparse matrix files of processed raw counts and normalized data
Supplementary_files_format_and_content: Sputum.processed.meta.data.txt: meta data to sparse matrix files of processed raw counts and normalized data

source_name: Sputum cells

extract_protocol:
Sputum cell were obtained from spontaneous (CF) and induced sputum (CTRL)
Single-cell libraries were prepared using the standard 10x Genomics single cell 3' reagent kits v3 processing workflow.
Standard10x genomics single cell 3' reagent kits v3 library preparation. Sequencing on Illumina HiSeq 4000 sequencer, aiming for 150 million reads per sample.

tag: disease state

value: Sputum cells

tag: subject

tag: group

value: CTRL

tag: age

tag: Sex

value: F

tag: smoking

value: no

tag: fev1 % predicted

tag: platform

value: 10x Genomics

tag: technology

value: Chromium Single Cell 3' Kits (v3 Chemistry)


title: m1_AY_Y3_K17

value: primary murine brain endothelial cells


title: RNA-seq_Exp6_HGrC1_WT_rep1

description:
Exp6_HGrC1_WT_rep1
Galaxy762-[DESeq2_result_file_on_MUT_vs_WT].txt

tag: cell line


title: 70_14month_array

description:
70_14month_252800422038_2_3.txt
disease

tag: diagnosis

value: SSc

tag: treatment

value: Cyclophosphamide

tag: timepoint

value: post

tag: response

tag: tissue

tag: sample type


title: RNA-seq_Exp6_HGrC1_C134W_rep1

description:
Exp6_HGrC1_C134W_rep1
Galaxy762-[DESeq2_result_file_on_MUT_vs_WT].txt

tag: genotype/variation

value: HGrC1 cell-line transduced with C134W mutant (C134W) FOXL2


title: CTRL003

tag: disease state

value: control

value: M


title: RNA-seq_Exp6_HGrC1_EV_rep1

description:
Exp6_HGrC1_EV_rep1
Galaxy766-[DESeq2_result_file_MUT_vs_EV].txt

value: HGrC1 cell-line transduced with empty vector (EV) control


title: 7_base_array

description:
07_base_252800422380_1_3.txt
disease

value: base

value: Responder

value: PMBC

value: Universal Human Reference (UHR)


title: AHR ChIP-Seq

source_name: HCASMC_AHR ChIP-Seq

extract_protocol: ChIP-seq was performed using AHR antibody (Santa Cruz, sc-5579) in HCASMC between passages 5-8 in the presence of 10nM of TCDD, and library was constructed using the KAPA Hyper Prep Kit.

value: Human Coronary Artery Smooth Muscle Cells (HCASMC)

value: coronary artery

tag: genotype/treatment

value: dioxin (TCDD) 10nM

tag: chip antibody

value: AHR antibody (Santa Cruz, sc-5579)


title: 68_base_array

description:
68_base_252800422379_1_4.txt
disease


title: RNA-seq_Exp6_HGrC1_WT_TGF_rep1

description:
Exp6_HGrC1_WT_TGF_rep1
Galaxy758-[DESeq2_result_file_on_MUT_TGF_vs_WT_TGF].txt

value: HGrC1 cell-line transduced with wildtype (WT) FOXL2 and stimulated with TGF


title: 70_26month_array

description:
70_26month_252800422040_2_1.txt
disease

value: Non-responder


title: CTRL004

value: Sputum cells

tag: subject

tag: group

value: CTRL

tag: age

value: F

value: no

value: 10x Genomics

value: Chromium Single Cell 3' Kits (v3 Chemistry)


title: Input ChIP-Seq (for AHR ChIP)

source_name: HCASMC_Input ChIP-Seq (for AHR ChIP)

extract_protocol: Cross-linked DNA from HCASMC between passages 5-8 in the presence of 10nM of TCDD was sonicated and extracted with Zymo DNA extraction kit, and library was constructed using the KAPA Hyper Prep Kit.


title: CTRL001

value: control

tag: Sex

value: M

tag: smoking

tag: fev1 % predicted


title: M2814

city: Philadelphia

first: Lachlan

middle: James

last: Smith

state: Pennsylvania

address: 371 Stemmler Hall, 3450 Hamilton Walk

department: Department of Orthopaedic Surgery

institute: University of Pennsylvania

data_processing:
Illumina Casava-1.8.2 software was used for basecalling. Fastq files were generated from base calls using Illumina software bcl2fastq.
RNA-Seq - Low quality reads as well as ribosomal and other repeat sequences were filtered out before alignment. RUM software (version 2.0.4) was used for aligning reads to canine genome CanFam3.1 and Refseq transcriptome and for transcript quantitation. Differential expression analysis was carried out using a custom script implementing EdgeR software.
Sequences were mapped to CanFam3.1 using STAR v2.4.0j with default parameters.
Reads mapping uniquely to genomic features as annotated in Ensembl build 77 were counted using htseq-count.
Genome_build: CanFam3.1
Supplementary_files_format_and_content: text files for raw counts per sample

organism: Canis lupus familiaris

source_name: vertebral epiphyseal cartilaginous tissue

extract_protocol:
Flash frozen epiphyseal tissue was pulverized using a mortar and pestle, and RNA was extracted using serial TRIzol (Ambion; Austin, TX)-chloroform extractions, with a modification to the standard protocol that we previously reported in the RNA precipitation step to account for the high GAG content in cartilage that can co-precipitate with RNA. Briefly, 100% isopropanol and a solution of 1.2 M NaCl and 0.8 M sodium citrate (Sigma-Aldrich; St. Louis, MO) in ddH2O was used in a 1:1 mixture to separate contaminating GAGs from the RNA pellet. Following precipitation, extracted RNA was in-column treated with RNase-free DNase (Qiagen; Valencia, CA) on miRNeasy columns (Qiagen; Valencia, CA) and eluted following the manufacturer’s protocols. The quality of each RNA sample was verified via BioAnalyzer using the Agilent RNA 6000 Pico Kit (Agilent; Santa Clara, CA), to ensure all samples used for library preparation had an RNA Integrity Number (RIN) value > 7.
High quality total RNA from each sample was used to prepare RNA-Seq libraries using the TruSeq mRNA stranded kit (Illumina; San Diego, CA). Paired-end, 100-base pair sequencing was performed using the Illumina HiSeq 2500 with the results mapped to the canine genome version CanFam3.1 (NCBI) using Ensembl build 77. Pathway analysis was performed using Ingenuity Pathway Analysis (IPA; Qiagen, Valencia, CA, USA).

value: vertebral epiphyseal tissue from T12 vertebrae

tag: genotype

value: MPS VII

tag: tissue type

value: primary tissue

value: postnatal day 14


title: M2817

value: Heterozygote


title: M2815


title: M2818


title: M2812


title: 67_8month_array

description:
67_8month_252800422034_1_2.txt
disease

tag: diagnosis

value: SSc

tag: treatment

value: Cyclophosphamide

value: post

value: Responder

value: PMBC

value: Universal Human Reference (UHR)


title: 67_base_array

description:
67_base_252800422034_2_4.txt
disease

tag: timepoint

value: base

tag: response


title: Exp5_KGN_T_K27Ac_ChIP

extract_protocol:
Confluent cell plates of KGN or HGrC1 cells were washed in PBS and cells were released by treatment with trypsin. Cells were collected by centrifugation (300g, 5 minutes), washed with PBS and centrifuged again. Cells were cross-linked with 0.2-mM DSG for 30 min. at room-temperature followed by cross-linking with 1% formaldehyde for 5 min at room temperature. Glycine was added at a final concentration of 125mM to quench the formaldehyde. Cells was washed twice with ice cold PBS and harvested in SDS buffer (50mM TrisHCl pH 8.1, 100mM NaCl, 5mM EDTA pH 8.0, 0,2% NaN3, 0.5% SDS). Cells were spun down, resuspended in Triton X-IP buffer (100mM Tris pH 8.6, 0.3% SDS, 1.7% Triton X-100 and 5mM EDTA) and the chromatin was sonicated to get DNA fragments of <600bp (with average DNA fragment size of 300bp) and then cleared by centrifugation. 1mg (transcription factors) or 100  g of chromatin (histone modifications) was precleared with Protein G coupled Sepharose beads (GE Healthcare) for 3hrs and incubated with 0,5-10  g antibody overnight at 4  C. The next day, Protein G coupled sepharose beads were added and samples were incubated end-over-end for 4hrs at 4  C. Beads were washed for a total of five times in low salt buffer (20mM Tris-HCl pH 8.0, 1% Triton X-100, 0.1% SDS, 150mM NaCl, 2mM EDTA pH 8.0), two times in RIPA buffer (50mM Tris-HCl pH 7.5, 150mM NaCl, 1% NP40, 0.1% SDS, 0.5% DOC, 1mM EDTA), and one time with high salt buffer (20mM Tris-HCl pH 8.0, 1% Triton X-100, 0.1% SDS, 500mM NaCl, 2mM EDTA pH 8.0). Beads were incubated with elution buffer (1% SDS, 0.1M sodium bicarbonate) at 65  C overnight to de-crosslink. The DNA was isolated using QIAquick PCR Purification kit (Qiagen) and eluted in 50  l EB buffer.)
ChIP sequencing libraries were prepared for sequencing using standard Illumina protocols
RNA and ChIP sequencing libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: KGN

value: Rabbit polyclonal anti-H3K27Ac (Abcam, Ab4729)

value: KGN Cell-line is Heterozygous for FOXL2 C134W mutation, here stimulated with TGF


title: CTRL002

value: control

tag: tissue

value: Sputum cells

value: CTRL

value: no

tag: platform

value: 10x Genomics

tag: technology

value: Chromium Single Cell 3' Kits (v3 Chemistry)


title: CF010

tag: disease state

value: cystic fibrosis

value: CF

value: F


title: Exp5_KGN_K4me1_ChIP

tag: chip antibody

value: Rabbit monoclonal anti-H3K4Me1 (Cell Signaling, #5356S)

tag: genotype/variation

value: KGN Cell-line is Heterozygous for FOXL2 C134W mutation


title: 67_54month_array

description:
67_54month_252800422222_2_4.txt
disease

value: SSc

value: Cyclophosphamide

value: post

value: Responder

value: PMBC

tag: sample type


title: M2811

value: vertebral epiphyseal tissue from T12 vertebrae

value: MPS VII

value: primary tissue

tag: age

value: postnatal day 14


title: CF009

value: Sputum cells

tag: subject

tag: group

tag: Sex

value: M

tag: smoking

value: no


title: 65_8month_array

description:
65_8month_252800422021_2_2.txt
disease

tag: diagnosis

value: Transplant

value: Universal Human Reference (UHR)


title: 65_base_array

description:
65_base_252800422032_1_1.txt
disease

tag: treatment

value: base


title: M2810

tag: genotype

tag: tissue type


title: Exp5_KGN_T_K4me1_ChIP

tag: cell line

value: KGN

value: Rabbit monoclonal anti-H3K4Me1 (Cell Signaling, #5356S)

value: KGN Cell-line is Heterozygous for FOXL2 C134W mutation, here stimulated with TGF


title: 67_26month_array

description:
67_26month_252800422034_1_4.txt
disease

value: SSc

value: Cyclophosphamide

tag: timepoint

tag: response

tag: tissue


title: 67_38month_array

description:
67_38month_252800422222_1_4.txt
disease

value: post

value: Responder


title: 65_38month_array

description:
65_38month_252800422222_2_1.txt
disease

value: PMBC


title: 65_54month_array

description:
65_54month_252800422222_1_2.txt
disease


title: M2809

value: vertebral epiphyseal tissue from T12 vertebrae

value: Heterozygote


title: CF008

tag: disease state

value: cystic fibrosis

value: CF

value: F

tag: fev1 % predicted

tag: platform

value: 10x Genomics

tag: technology

value: Chromium Single Cell 3' Kits (v3 Chemistry)


title: Exp4_HGrC1_SMAD2/3KO_C134W_TGF_H3K4me1_ChIP

source_name: HGrC1 (SMAD2/3 KO)

tag: chip antibody

tag: genotype/variation

value: HGrC1 (knockout for SMAD2 and SMAD3)


title: Exp5_KGN_K27Ac_ChIP

value: Rabbit polyclonal anti-H3K27Ac (Abcam, Ab4729)

value: KGN Cell-line is Heterozygous for FOXL2 C134W mutation


title: CF007

value: Sputum cells

tag: subject

tag: group

tag: age

value: no


title: CF006

tag: Sex

tag: smoking


title: Exp4_HGrC1_SMAD2/3KO_C134W_TGF_SMAD2/3_ChIP

value: Rabbit monoclonal anti-SMAD2/3 (Cell Signaling, #86855)


title: CF005

value: M


title: 65_14month_array

description:
65_14month_252800422034_2_2.txt
disease

source_name: Sample: Human PBMC

tag: diagnosis

value: SSc

tag: treatment

value: Transplant

value: post

tag: sample type

value: Universal Human Reference (UHR)


title: M2807

value: vertebral epiphyseal tissue from T12 vertebrae

tag: genotype

value: MPS VII

tag: tissue type

value: primary tissue

value: postnatal day 14


title: 65_20month_array

description:
65_20month_252800422021_1_3.txt
disease

tag: timepoint

tag: response

value: Responder

tag: tissue

value: PMBC

source_name: Universal Human Reference


title: M2850

value: postnatal day 9


title: Exp4_HGrC1_SMAD2/3KO_C134W_TGF_SMAD4_ChIP

tag: cell line

value: Rabbit polyclonal anti-SMAD4 (Proteintech, 10231-1-AP)

value: HGrC1 (knockout for SMAD2 and SMAD3)


title: M2848

value: Heterozygote


title: CF004

tag: disease state

value: cystic fibrosis

value: Sputum cells

value: CF

value: F

value: no

tag: fev1 % predicted

tag: platform

value: 10x Genomics

tag: technology

value: Chromium Single Cell 3' Kits (v3 Chemistry)


title: CF002

tag: subject

tag: group


title: Exp4_HGrC1_SMAD2/3KO_C134W_TGF_FOXL2_ChIP

tag: chip antibody

value: Goat polyclonal antibody to  FOXL2 (Abcam Ab5096)

tag: genotype/variation


title: Exp4_HGrC1_SMAD2/3KO_C134W_TGF_Input

value: No antibody


title: M2839

value: vertebral epiphyseal tissue from T12 vertebrae

value: primary tissue

tag: age


title: CF001

tag: Sex

value: M

tag: smoking


title: Exp4_HGrC1_SMAD2/3KO_C134W_TGF_H3K27ac_ChIP

value: Rabbit polyclonal anti-H3K27Ac (Abcam, Ab4729)


title: M2840

tag: genotype

value: MPS VII

value: postnatal day 9


title: Exp4_HGrC1_SMAD2/3KO_C134W_TGF_IgG_ChIP

value: Normal Goat IgG Control (R&D Systems AB-108-C)

value: HGrC1 (knockout for SMAD2 and SMAD3)


title: M2836

tag: tissue type


title: M2808

value: Heterozygote

value: postnatal day 14


title: Exp4_HGrC1_SMAD4KO_C134W_TGF_H3K4me1_ChIP

source_name: HGrC1 (SMAD4 KO)

value: Rabbit monoclonal anti-H3K4Me1 (Cell Signaling, #5356S)

value: HGrC1 (knockout for SMAD4)


title: OCI-AML3_MI503_3_S6

city: Mainz

first: Margarita

last: Dzama

address: Langenbeckstr. 1

department: Department of Hematology, Medical Oncology, and Pulmonary Medicine,

country: Germany

institute: University Medical Center, Johannes Gutenberg-University

description:
ERCC synthetic spike-in controls were added, RNA-seq
OCI-AML3_DESeq_MI503_DMSO_ERCC_norm.txt

data_processing:
Sequencing of mRNA (50 base pair paired-end sequencing) was performed on an Illumina HiSeq 4000 Next Generation machine.
Each library yielded 30-40 million reads.
Read counts were normalized to ERCC spike-in controls.
Differentially expressed genes between the treatment groups were calculated using DESeq version 2.
Genome_build: For gene expression analysis, reads were mapped to the human genome (Hg38).
Supplementary_files_format_and_content: All processed data files are in the .txt format and contain read counts

molecule: polyA RNA

source_name: Leukemia cell line

growth_protocol: MV411, MOLM13 and OCI-AML3 were grown in liquid cell culture

extract_protocol:
1x106 cells were harvested and 2 µL of 1:100 ERCC RNA Spike-in mix (Thermo Fisher) were added to each of the samples for normalization. RNA was isolated using the RNeasy Mini Kit (Qiagen) including on-column DNAse digestion.
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-seq, paired-end sequencing 50 base pair, 30-40 million reads.

treatment_protocol: MV411 cells were treated with MI-503 for 3 days [2.5 µM], with AC220 for 24 hours [3 nM], with their combination [MI-503, 3 days, 2.5 µM; AC220, 24 hours, 3nM] or with DMSO. MOLM13 and OCI-AML3 cells were treated with MI-503 [2.5 µM] and DMSO for 4 days.

value: OCI-AML3, Acute Myeloid Leukemia cell line


title: M2835


title: 63_base_array

description:
63_base_252800422022_2_3.txt
disease

tag: diagnosis

value: SSc

tag: treatment

value: Cyclophosphamide

tag: timepoint

value: base

value: Responder

value: PMBC

tag: sample type

value: Universal Human Reference (UHR)


title: 64_base_array

description:
64_base_252800422381_2_4.txt
disease

tag: response

value: Non-responder

tag: tissue


title: Exp4_HGrC1_SMAD4KO_C134W_TGF_H3K27ac_ChIP

tag: cell line

value: Rabbit polyclonal anti-H3K27Ac (Abcam, Ab4729)


title: 63_8month_array

description:
63_8month_252800422033_1_2.txt
disease

value: post


title: M2825

value: vertebral epiphyseal tissue from T12 vertebrae

value: primary tissue

value: postnatal day 9


title: OCI-AML3_MI503_2_S5


title: 63_54month_array

description:
63_54month_252800422211_2_3.txt
disease


title: CF003

tag: disease state

value: cystic fibrosis

value: Sputum cells

value: CF

value: M

value: no

tag: fev1 % predicted

tag: platform

value: 10x Genomics

tag: technology

value: Chromium Single Cell 3' Kits (v3 Chemistry)


title: Exp4_HGrC1_SMAD4KO_C134W_TGF_SMAD2/3_ChIP

tag: chip antibody

value: Rabbit monoclonal anti-SMAD2/3 (Cell Signaling, #86855)

tag: genotype/variation

value: HGrC1 (knockout for SMAD4)


title: 62_base_array

description:
62_base_252800422033_1_3.txt
disease

value: SSc

value: Cyclophosphamide

value: base

value: Responder

value: PMBC


title: 63_26month_array

description:
63_26month_252800422023_2_3.txt
disease

value: post

value: Universal Human Reference (UHR)


title: M2823

value: vertebral epiphyseal tissue from T12 vertebrae

value: Heterozygote

value: primary tissue

tag: age

value: postnatal day 9


title: OCI-AML3_MI503_1_S4

value: OCI-AML3, Acute Myeloid Leukemia cell line


title: Exp4_HGrC1_SMAD4KO_C134W_TGF_SMAD4_ChIP

value: Rabbit polyclonal anti-SMAD4 (Proteintech, 10231-1-AP)


title: OCI-AML3_DMSO_3_S3


title: M2822

value: MPS VII


title: 62_38month_array

description:
62_38month_252800422211_1_3.txt
disease


title: 63_14month_array

description:
63_14month_252800422021_1_2.txt
disease


title: OCI-AML3_DMSO_2_S2


title: 62_20month_array

description:
62_20month_252800422023_2_1.txt
disease


title: OCI-AML3_DMSO_1_S1


title: Exp4_HGrC1_SMAD4KO_C134W_TGF_FOXL2_ChIP

value: Goat polyclonal antibody to  FOXL2 (Abcam Ab5096)


title: 62_14month_array

description:
62_14month_252800422034_1_3.txt
disease


title: Exp4_HGrC1_Parental_C134W_TGF_H3K4me1_ChIP

source_name: HGrC1 (Parental)

value: Rabbit monoclonal anti-H3K4Me1 (Cell Signaling, #5356S)

value: HGrC1 (Parental, wildtype for SMAD4 and SMAD2/3)


title: D395A_2

city: wuhan

first: linjian

last: xia

address: wuhan

country: China

institute: wuhan University

description: RNA-seq.count

data_processing:
Quality control of MeRIP-Seq data was performed using FastQC. Low quality bases and adaptor contamination were deleted by Trimmomatic (v. 0.33.0) 8 . Raw Sequencing reads were aligned using Hisat2 (v. 2.1.0) 9 with default parameters to the hg38 or mm10 reference genome. The mapped reads were filtered with Picard (http://broadinstitute.github.io/picard, v. 2.16.0) to remove PCR duplicates and SAMtools (v. 1.7) 10 to remove the reads with mapping quality below 30. MACS2 (v. 2.1.1) 11 was used to identify peaks (p-value of 1e-4).
For ChIP-seq, raw sequencing reads were aligned using Bowtie (v. 2.3.4.1) 15 with default parameters to the mm10 reference genome. The mapped reads were filtered with Picard (http://broadinstitute.github.io/picard, v. 2.16.0) to remove PCR duplicates and SAMtools10 to remove the reads with mapping quality below 30. MACS2 11 was used to identify peaks (p-value of 1e-4).
For RNA-seq, reads mapping and processing were performed as described for MeRIP-seq data above. FeatureCounts (v. 1.6.3) 5 was used to calculate the number of reads mapped to each gene. EdgeR (v.3.22.5) 19 was used for differential expression analysis.
Genome_build: hg38/mm10

growth_protocol: HEK293T cells were grown in DMEM medium (Invitrogen) containing 10% FBS, and 1% penicillin-streptomycin. Mouse embryonic stem cell (mESC) E14TG2a was cultured with N2B27 base medium supplemented with 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.15 mM 1-thioglycerol (Sigma), 100 U/mL penicillin-streptomycin (Invitrogen), 25 μg/ml BSA (Sigma), 1μM MEK inhibitor PD0325901 (Selleck Chemicals), 3μM GSK3β inhibitor CHIR99021 (Selleck Chemicals), 2% KOSR (Thermofisher) and 1000 U/ml ESGRO leukemia inhibitory factor LIF (Millipore) on plates coated with 0.2% gelatin.

extract_protocol:
For RNA-seq, RNA was isolated using TRNzol reagent. After DNase I treatment, rRNA was removed using QIAseq FastSelect RNA Removal Kit (QIAGEN). For RIP-seq, chromatin RNA was extracted, then fragmented to about 100-300 nt-long, and incubated with anti-m6A antibody (Millipore). Then the mixture was subjected to Dynabeads protein G binding. After washing, the bound RNA was eluted by RLT and retrieved by RNeasy Plus Micro Kit (Qiagen). H3K9me2 ChIP-seq was performed using the iDeal ChIP-seq Kit for Histones (Diagenode). For KDM3B, METTL3 and Pol II ChIP-seq, cells were crosslinked, sonicated, and subjected to ChIP.
RNA-seq libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB). RIP-seq libraries were generated using  SMARTer Stranded Total RNA-Seq Kit v2 -Pico Input Mammalian (Takara) following the manual. ChIP-seq libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina.
RNA-seq, RIP-seq and ChIP-seq

treatment_protocol: GFP/FTO/ALKBH5/YTHDC1 shRNA knockdown cells were generated by lentiviral infection and puromycin selection.

value: untreated

tag: protocol

value: RNA-seq


title: Exp4_HGrC1_Parental_C134W_TGF_H3K27ac_ChIP

value: Rabbit polyclonal anti-H3K27Ac (Abcam, Ab4729)


title: D395A_1

description: RNA-seq.count


title: M2820

tag: genotype


title: 60_base_array

description:
60_base_252800420363_1_4.txt
disease

extract_protocol: Total RNA extracted from PBMC following manufacturer's protocol. UHR is Stratagene, Universal Human Reference RNA Catalog #740000

value: SSc

value: Transplant

value: base

value: Responder


title: MOLM13_MI503_3_S6

description:
ERCC synthetic spike-in controls were added, RNA-seq
MOLM13_DESeq_MI503_DMSO_ERCC_norm.txt

value: MOLM13, Acute Myeloid Leukemia cell line


title: MOLM13_MI503_2_S5


title: Exp4_HGrC1_Parental_C134W_TGF_SMAD2/3_ChIP

value: Rabbit monoclonal anti-SMAD2/3 (Cell Signaling, #86855)


title: 60_8month_array

description:
60_8month_252800420365_1_4.txt
disease

value: post

value: PMBC

value: Universal Human Reference (UHR)


title: WT_2

description: RNA-seq.count


title: Exp4_HGrC1_Parental_C134W_TGF_SMAD4_ChIP

value: Rabbit polyclonal anti-SMAD4 (Proteintech, 10231-1-AP)


title: Exp4_HGrC1_Parental_C134W_TGF_FOXL2_ChIP


title: MOLM13_DMSO_3_S3


title: MOLM13_MI503_1_S4


title: Exp4_HGrC1_Parental_C134W_TGF_Input

value: No antibody


title: WT_1

description: RNA-seq.count


title: Exp4_HGrC1_Parental_C134W_TGF_IgG_ChIP

value: Normal Goat IgG Control (R&D Systems AB-108-C)


title: MOLM13_DMSO_1_S1


title: 60_54month_array

description:
60_54month_252800422211_1_1.txt
disease


title: 60_38month_array

description:
60_38month_252800422211_2_2.txt
disease


title: SKO_D60_C3_HBS_seq

city: Beijing

first: Wei

last: Xie

address: Haidian District

institute: Tsinghua University

description: hairpin BS-seq

data_processing:
ChIP-seq reads were mapped to the mm9 reference genome using Bowtie2 with parameters -t -q -N 1 -L 25. All ummapped reads, non-uniqurely mapped reads and PCR duplicates were removed. For downstream analysis, we computed the numbers of reads per kilobase of bin per million reads sequenced (RPKM) which were further normalized by input. A resolution of 100bp bin in genome was used in the rpkm file.
RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11). The gene expression levels were calculated by Cufflinks (version 2.2.1). RefFlat database from UCSC genome browser was used with microRNA and repeats excluded.
MethylC-seq reads were mapped to the mm9 reference genome using Bsmap with parameters -r 0 -w 100 -v 0.1. Adaptor sequences were removed with parameter -A. PCR duplicates were also removed. Pair-end reads with a flag equal 177 or 129 were also removed from this data. Only samples with bisulfite conversion rates greater than 99% were accepted. 200bp bins were used for most analyses and those with total CG coverage less than 5 were removed. Methylation ratio was calculated using methylated CG verses total CG for each bin.
The paired-end reads of hairpin bisulfite sequencing were processed using HBS-Tools as described (Sun et al., 2015; Zhao et al., 2014). Briefly, adaptor and hairpin sequences were searched by cross match. Original genomic sequences were then recovered from the bisulfite converted reads derived from two DNA strands. Original sequences were mapped to the mm9 reference genome using Bowtie2 (Langmead and Salzberg, 2012) with parameters -n 2 -l 40 -k 1. Only those CpGs with minimal coverages of 15 in all the analyzed samples (79.7% of total CpGs) were used for downstream analysis. For each CpG site, four methylation states were computed, including MM (methylated + methylated for the two strands, or fully methylated), MU (methylated + unmethylated, or hemi methylated), UM (unmethylated + methylated, or hemi methylated) and UU (unmethylated on both strands). The methylation level was calculated as (2*MM+MU+UM)/(2*(MM+MU+UM+UU)). Fidelity was calculated as (MM+UU)/(MM+UM+MU+UU).
Genome_build: mm9
Supplementary_files_format_and_content: CpG_context.txt

source_name: mESC

growth_protocol: Mouse ES cells were cultured on 0.1% gelatin of porcine skin in DMEM (Gibco Cat. 11995-065) containing 15% FBS (Hyclone Cat. SH30396.03), leukemia inhibiting factor (LIF) (Millipore Cat. GSE1107), penicillin/streptomycin (Millipore Cat. TMS-AB2-C), GlutaMAX (Gibco Cat. 35050-061), nucleotides (Millipore Cat. ES-008-D), β-mercaptoethanol (Gibco Cat. 21985-023), and non-essential amino acids (Gibco Cat. 25-025-CIR).

extract_protocol:
Cells were digested using Cell Lysis Solution (Qiagen, Cat. 1045723) and proteins were removed using Protein Precipitation Solution (Qiagen, Cat. 1045701). Genome DNA was precipitated by isopropyl alcohol and cleaned by wash with 75% ethanol.
A total amount of 10 μg genomic DNA was mixed with 25 ng lambda and sonicated to 200-bp fragments with Covaris S2 (AB). After purification (PureLink PCR Purification Kit, Invitrogen), DNA fragments were then subjected to end repair with the end repair enzyme mix (NEB), dA tailing using Klenow 3′-5′ exo- (NEB) with purification at each step. Ligation to hairpin adapter (P-GATCGGATGAGCAAGTGAAGCTCATCCGATCT) and Illumina TruSeq adapters were performed using T4 DNA ligase (NEB) overnight. Bisulfite conversion was performed using the EpiTect Bisulphite Kit (Qiagen). After bisulfite conversion, the single-stranded uracil-containing DNA was subjected to 12 cycles of PCR reaction with Illumina TruSeq PCR primers (with specific index) and 2.5 U Pfu TurboCx Hotstart DNA polymerase (Agilent) to recover enough DNA for sequencing. Libraries were sequenced using Illumina HiSeq X10.

value: Tet1-/- Tet2-/- Tet3-/- Dnmt3a-/- Dnmt3b-/- Dnmt3c-/-

tag: strain


title: MV411_Combo_3_S12

description:
ERCC synthetic spike-in controls were added, RNA-seq
MV4-11_DESeq_DMSO_MI503_AC220_Combo_ERCC_norm.txt

value: MV411, Acute Myeloid Leukemia cell line


title: 60_14month_array

description:
60_14month_252800420364_2_1.txt
disease

tag: diagnosis


title: SKO_D30_C3_HBS_seq

description: hairpin BS-seq


title: MOLM13_DMSO_2_S2


title: SKO_D60_C2_HBS_seq

description: hairpin BS-seq


title: Exp3_HGrC1_C134W_H3K4me1_ChIP

source_name: HGrC1 cell-line

value: Rabbit monoclonal anti-H3K4Me1 (Cell Signaling, #5356S)

value: HGrC1 cell-line transduced with C134W mutant (C134W) FOXL2


title: 60_26month_array

description:
60_26month_252800420320_2_1.txt
disease

tag: treatment


title: 61_base_array

description:
61_base_252800422379_2_1.txt
disease

value: Cyclophosphamide

tag: timepoint

value: Non-responder


title: Exp3_HGrC1_C134W_TGF_H3K4me1_ChIP

value: HGrC1 cell-line transduced with C134W mutant (C134W) FOXL2 and stimulated with TGF


title: MV411_Combo_2_S11


title: SKO_D15_C3_HBS_seq

description: hairpin BS-seq


title: Exp3_HGrC1_C134W_TGF_H3K27ac_ChIP

value: Rabbit polyclonal anti-H3K27Ac (Abcam, Ab4729)


title: Exp3_HGrC1_C134W_H3K27ac_ChIP


title: MV411_Combo_1_S10


title: SKO_D15_C2_HBS_seq

description: hairpin BS-seq


title: SKO_D60_C1_HBS_seq

description: hairpin BS-seq


title: 6_base_array

description:
06_base_252800422381_1_3.txt
disease

value: SSc

value: Transplant

value: base

value: Responder

tag: sample type


title: MV411_AC220_3_S9


title: Exp3_HGrC1_WT_TGF_H3K4me1_ChIP

value: HGrC1 cell-line transduced with wildtype (WT) FOXL2 and stimulated with TGF


title: MV411_AC220_2_S8


title: Exp3_HGrC1_WT_H3K4me1_ChIP

value: HGrC1 cell-line transduced with wildtype (WT) FOXL2


title: 59_base_array

description:
59_base_252800421274_1_2.txt
disease

tag: response

value: PMBC

value: Universal Human Reference (UHR)


title: MV411_AC220_1_S7


title: SKO_D30_C1_HBS_seq

description: hairpin BS-seq


title: SKO_D30_C2_HBS_seq

description: hairpin BS-seq


title: 59_8month_array

description:
59_8month_252800420365_1_1.txt
disease

value: post

tag: tissue


title: 59_48month_array

description:
59_48month_252800422211_2_4.txt
disease


title: 59_38month_array

description:
59_38month_252800422211_1_4.txt
disease


title: MV411_MI503_2_S5

tag: cell line


title: WT_Nocodazole_Hairpin_BS_seq_rep1

description: Hairpin BS-seq

data_processing:
ChIP-seq reads were mapped to the mm9 reference genome using Bowtie2 with parameters -t -q -N 1 -L 25. All ummapped reads, non-uniqurely mapped reads and PCR duplicates were removed. For downstream analysis, we computed the numbers of reads per kilobase of bin per million reads sequenced (RPKM) which were further normalized by input. A resolution of 100bp bin in genome was used in the rpkm file.
RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11). The gene expression levels were calculated by Cufflinks (version 2.2.1). RefFlat database from UCSC genome browser was used with microRNA and repeats excluded.
MethylC-seq reads were mapped to the mm9 reference genome using Bsmap with parameters -r 0 -w 100 -v 0.1. Adaptor sequences were removed with parameter -A. PCR duplicates were also removed. Pair-end reads with a flag equal 177 or 129 were also removed from this data. Only samples with bisulfite conversion rates greater than 99% were accepted. 200bp bins were used for most analyses and those with total CG coverage less than 5 were removed. Methylation ratio was calculated using methylated CG verses total CG for each bin.
Hairpin BS-seq reads were mapped to the mm9 reference genome using Bowtie2 with parameters -n 2 –l 40 –k 1. Methylation levels and fidelities for all CpGs were calculated based on the mapping results and used for downstream analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig for ChIP-seq tracks, gene expression table for RNA-seq data

growth_protocol: Mouse ES cells were cultured on 0.1% gelatin of porcine skin in DMEM (Gibco Cat. 11995-065) containing 15% FBS (Hyclone Cat. SH30396.03), leukemia inhibiting factor (LIF) (Millipore Cat. GSE1107), penicillin/streptomycin (Millipore Cat. TMS-AB2-C), GlutaMAX (Gibco Cat. 35050-061), nucleotides (Millipore Cat. ES-008-D), β-mercaptoethanol (Gibco Cat. 21985-023), and non-essential amino acids (Gibco Cat. 25-025-CIR). The cells were further treated with nocodazole for 16h.

extract_protocol:
Cells were digested using Cell Lysis Solution (Qiagen, Cat. 1045723) and proteins were removed using Protein Precipitation Solution (Qiagen, Cat. 1045701). Genome DNA was precipitated by isopropyl alcohol and cleaned by wash with 75% ethanol.
Cells were digested using Cell Lysis Solution (Qiagen, Cat. 1045723) and proteins were removed using Protein Precipitation Solution (Qiagen, Cat. 1045701). Genome DNA was precipitated by isopropyl alcohol and cleaned by washing with 75% ethanol. A total amount of 10 μg genomic DNA was mixed with 25 ng lambda and sonicated to 200-bp fragments with Covaris S2 (AB). After purification (PureLink PCR Purification Kit, Invitrogen), DNA fragments were then subjected to end repair with the end repair enzyme mix (NEB), dA tailing using Klenow 3′-5′ exo- (NEB) with purification at each step. Ligation to biotin-modified hairpin adapter (P-GATCGGATGAGCAAG/iBiodT/GAAGCTCATCCGATCT) and Illumina TruSeq adapters were performed using T4 DNA ligase (NEB) overnight. After purification, DNA fragments were then pulled down using Dynabeads MyOne Streptavidin C1 beads (Invitrogen). Bisulfite conversion was performed using the EpiTect Bisulphite Kit (Qiagen). After bisulfite conversion, the single-stranded uracil-containing DNA was subjected to 12 cycles of PCR reaction with Illumina TruSeq PCR primers (with specific index) and 2.5 U Pfu TurboCx Hotstart DNA polymerase (Agilent) to recover enough DNA for sequencing. Libraries were sequenced using Illumina HiSeq X10.

value: WT

tag: cell type

value: mESC


title: 59_26month_array

description:
59_26month_252800420326_2_2.txt
disease


title: SKO_D15_C1_HBS_seq

description: hairpin BS-seq

value: Tet1-/- Tet2-/- Tet3-/- Dnmt3a-/- Dnmt3b-/- Dnmt3c-/-


title: Exp3_HGrC1_WT_H3K27ac_ChIP


title: 59_14month_array

description:
59_14month_252800420365_1_2.txt
disease


title: Exp3_HGrC1_WT_TGF_H3K27ac_ChIP


title: MV411_MI503_1_S4

value: MV411, Acute Myeloid Leukemia cell line


title: WT_Con_Hairpin_BS_seq_rep2

description: Hairpin BS-seq


title: Exp3_HGrC1_EV_H3K4me1_ChIP

value: Rabbit monoclonal anti-H3K4Me1 (Cell Signaling, #5356S)

value: HGrC1 cell-line transduced with empty vector (EV) control


title: Exp3_HGrC1_EV_TGF_H3K4me1_ChIP

value: HGrC1 cell-line transduced with empty vector (EV) control and stimulated with TGF


title: MV411_DMSO_3_S3


title: WT_Con_Hairpin_BS_seq_rep1

description: Hairpin BS-seq


title: MV411_DMSO_2_S2


title: 58_14month_array

description:
58_14month_252800422040_1_2.txt
disease

value: Non-responder


title: Exp3_HGrC1_EV_TGF_H3K27ac_ChIP

value: Rabbit polyclonal anti-H3K27Ac (Abcam, Ab4729)


title: Exp3_HGrC1_EV_H3K27ac_ChIP


title: MV411_MI503_3_S6


title: WT_Nocodazole_Hairpin_BS_seq_rep2

description: Hairpin BS-seq


title: R-PKO_Nocodazole_HBS_seq_rep1

description: Hairpin BS-seq

value: J1 129S4/SvJae


title: MV411_DMSO_1_S1


title: R-PKO_Con_HBS_seq_rep1

description: Hairpin BS-seq


title: 58_8month_array

description:
58_8month_252800422040_2_4.txt
disease

value: SSc

value: Transplant


title: 57_base_array

description:
57_base_252800422380_2_3.txt
disease

value: base

value: Responder


title: 58_base_array

description:
58_base_252800422038_1_1.txt
disease

value: PMBC


title: Exp3_HGrC1_C134W_TGF_SMAD2/3_ChIP

value: Rabbit monoclonal anti-SMAD2/3 (Cell Signaling, #86855)

value: HGrC1 cell-line transduced with C134W mutant (C134W) FOXL2 and stimulated with TGF


title: conditioned_4

city: West Haven

first: Arun

middle: Rajendra

last: Chavan

address: 850 West Campus Drive

department: Ecology and Evolutionary Biology

institute: Yale University

description: Conditioned decidual cell medium was added to differentiating Th17 cells

data_processing:
BaseCalls performed using CASAVA
Reads were aligned to the Homo sapiens genome GRCh37.75 using Tophat2 v2.1.1
Aligned reads mapping to each gene were counted using HTSeq-count. GTF file for Ensembl genebuild GRCh37.87 was used.
Supplementary_files_format_and_content: HTseq counts

source_name: T cells

extract_protocol:
Cells from 24-well plates were harvested by centriguation and RNA was extracted using Qiagen RNeasy Micro Kit.
Standard Illumina protocol

value: conditioned

tag: naive t cell isolation

value: CD4+ CD45RO-


title: 56_44month_array

description:
56_44month_252800422221_1_1.txt
disease

value: Cyclophosphamide

value: post

value: Universal Human Reference (UHR)


title: conditioned_3


title: Exp3_HGrC1_WT_TGF_SMAD2/3_ChIP

value: HGrC1 cell-line transduced with wildtype (WT) FOXL2 and stimulated with TGF


title: conditioned_2


title: 56_base_array

description:
56_base_252800422221_1_3.txt
disease


title: PKO_Nocodazole_HBS_seq_rep1

description: Hairpin BS-seq

value: mESC


title: PKO_Nocodazole_HBS_seq_rep2

description: Hairpin BS-seq


title: Exp3_HGrC1_C134W_SMAD2/3_ChIP

value: HGrC1 cell-line transduced with C134W mutant (C134W) FOXL2


title: SKO_Nocodazole_HBS_seq_rep2

description: Hairpin BS-seq

value: Tet1-/- Tet2-/- Tet3-/- Dnmt3a-/- Dnmt3b-/- Dnmt3c-/-


title: conditioned_1


title: 56_38month_array

description:
56_38month_252800422221_2_2.txt
disease

value: Non-responder


title: SKO_Nocodazole_HBS_seq_rep1

description: Hairpin BS-seq


title: SKO_Con_HBS_seq_rep2

description: Hairpin BS-seq


title: 56_14month_array

description:
56_14month_252800422221_1_4.txt
disease

value: SSc


title: control_3

description: Unconditioned decidual cell medium was added to differentiating Th17 cells

value: control


title: 56_26month_array

description:
56_26month_252800422221_2_4.txt
disease


title: SKO_Con_HBS_seq_rep1

description: Hairpin BS-seq


title: 55_8month_array

description:
55_8month_252800422034_2_1.txt
disease

value: Transplant


title: Exp3_HGrC1_EV_TGF_SMAD2/3_ChIP

value: HGrC1 cell-line transduced with empty vector (EV) control and stimulated with TGF


title: control_2


title: PKO_Con_HBS_seq_rep2

description: Hairpin BS-seq


title: control_1


title: 55_base_array

description:
55_base_252800422023_1_1.txt
disease

value: base

value: Responder

value: PMBC


title: Exp3_HGrC1_EV_SMAD2/3_ChIP

value: Rabbit monoclonal anti-SMAD2/3 (Cell Signaling, #86855)

value: HGrC1 cell-line transduced with empty vector (EV) control


title: Exp3_HGrC1_WT_SMAD2/3_ChIP

value: HGrC1 cell-line transduced with wildtype (WT) FOXL2


title: Exp3_HGrC1_EV_TGF_SMAD4_ChIP

value: Rabbit polyclonal anti-SMAD4 (Proteintech, 10231-1-AP)


title: Exp3_HGrC1_WT_TGF_SMAD4_ChIP


title: 55_54month_array

description:
55_54month_252800422211_1_2.txt
disease

value: post

value: Universal Human Reference (UHR)


title: 55_38month_array

description:
55_38month_252800422211_2_1.txt
disease


title: control_4

value: CD4+ CD45RO-


title: LoVo_Hi-C

city: Houston

first: Kadir

middle: Caner

last: Akdemir

state: TX

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

data_processing:
Library strategy: HiC-Seq
Hi-C libraries were sequenced on a HiSeq 4000. Reads were aligned to the hg19 reference genome using BWA-MEM, and PCR duplicates were removed with Picard.
Genomic Locations of Bin Numbers: hg19_40kb.txt
Genome_build: hg19
Supplementary_files_format_and_content: Hi-C interaction matrices were generated using 40kb as window size, and matrices were normalized using the iterative correction method (Imakaev et al., 2012). Sparse matrices represent the normalized contact frequency between two interacting genomic loci. Genomic coordinates of the bin numbers can be found in hg19_40kb.txt file.

source_name: Colon cancer cell line

extract_protocol:
Hi-C was performed using the in situ Hi-C protocol as previously described in Rao et al., 2014, using 2-5 million cells per experiment digested with the MboI restriction enzyme.
The libraries were prepared according to Illumina's instructions accompanying the Illumina TruSeq LT adaptors.

value: LoVo


title: 55_14month_array

description:
55_14month_252800422033_2_2.txt
disease


title: PKO_13D_RNA_seq_rep2

data_processing:
ChIP-seq reads were mapped to the mm9 reference genome using Bowtie2 with parameters -t -q -N 1 -L 25. All ummapped reads, non-uniqurely mapped reads and PCR duplicates were removed. For downstream analysis, we computed the numbers of reads per kilobase of bin per million reads sequenced (RPKM) which were further normalized by input. A resolution of 100bp bin in genome was used in the rpkm file.
RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11). The gene expression levels were calculated by Cufflinks (version 2.2.1). RefFlat database from UCSC genome browser was used with microRNA and repeats excluded.
MethylC-seq reads were mapped to the mm9 reference genome using Bsmap with parameters -r 0 -w 100 -v 0.1. Adaptor sequences were removed with parameter -A. PCR duplicates were also removed. Pair-end reads with a flag equal 177 or 129 were also removed from this data. Only samples with bisulfite conversion rates greater than 99% were accepted. 200bp bins were used for most analyses and those with total CG coverage less than 5 were removed. Methylation ratio was calculated using methylated CG verses total CG for each bin.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig for ChIP-seq tracks, gene expression table for RNA-seq data

growth_protocol: ES cells were cultured in non-adhesive bacterial dishes using ES culture medium minus LIF for 4 days. Then retinoic acid (RA) (Sigma Cat. R2625) was added in to medium to the final concentration of 2ug/ml. Medium was changed every day. On the 5th day of adding RA, embryonic bodies were dissociated by 0.25% Trypsin-EDTA (Gibco Cat. 25200-056) and plated to poly-L-ornithine (Sigma Cat. P3655) and Laminin (Invitrogen Cat. 23017-015) pre-coated dish. Cells were cultured in DMEM/F-12 (Gibco Cat. 11330-032) with B27 (Life tech. Cat. 17504-044) and were incubated for two days. The medium was switched to BME (Gibco, Cat. 21010-046) with B27 for another two days. Differentiated neurons were then harvested for subsequent analyses.

extract_protocol:
Cells were lysed using TRIzol reagent (Ambion, Cat. 15596026). RNA was extracted by isopropanol precipitation and diluted in DEPC-treated water.
10ug RNA was DNase I (Fermentas, Cat. EN0521) treated at 37°C for 1 hour. RNA was purified using AMPure beads. Then ribosomal RNA was removed using Ribo-Zero Magnetic Gold Kit (Epicentre). Purified RNA was fragmented with RNA Frag. Buffer (NEB, Cat. E6186A) at 95°C for 5 min. Reaction was stopped and RNA was purified. First stand cDNA was synthesized with commercial kit using both oligo dT and random primers (Invitrogen, Cat. 18080-051). Second strand cDNA was synthesized with second strand synthesis buffer (Invitrogen, Cat. 10812014), MgCl2, DTT, dUNTP, RNase H (Fermentas, Cat. EN0202), E. coli DNA ligase (NEB, Cat. M0205S) and DNA polymerase I (NEB, Cat. M0209S). DNA was purified after 2 hour incubation on thermomixer at 16°C. Then, synthesized cDNA was end-repaired, adenylated and ligated to TruSeq sequencing adaptors. Libraries were then treated with UDG (AMPErase, Cat. N808-0096) at 37°C for 1 hour and purified before PCR amplification. 200-500bp fragments were selected for subsequent sequencing.

value: mESC-derived cell


title: Exp3_HGrC1_WT_SMAD4_ChIP


title: Exp3_HGrC1_C134W_TGF_SMAD4_ChIP

value: HGrC1 cell-line transduced with C134W mutant (C134W) FOXL2 and stimulated with TGF


title: WT_RA_7D_H3K27me3_rep2

growth_protocol: ES cells were cultured on 0.1% gelatin of porcine skin in DMEM (Gibco Cat. 11995-065) containing 15% FBS (Hyclone Cat. SH30396.03),  penicillin/streptomycin (Millipore Cat. TMS-AB2-C), GlutaMAX (Gibco Cat. 35050-061), nucleotides (Millipore Cat. ES-008-D), β-mercaptoethanol (Gibco Cat. 21985-023), non-essential amino acids (Gibco Cat. 25-025-CIR) and retinoic acid (RA) (Sigma Cat. R2625) (the final concentration of 2ug/ml).

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at 37◦C; then, crude nuclei were purified. Chromatin was fragmented by sonication to obtain fragments 200–2000 bp in length. For each ChIP assay, 2–5 ug of antibodies were added and incubated at 4◦C overnight. Chromatin was reverse-crosslinked, purified and quantified with a Qubit fluorometer using the Quant-iT dsDNA HS assay kit
DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. DNA was purified by AMPure beads or DNA purification kit according to the DNA amount. Library DNA was amplified by Phusion HF (NEB, Cat. M0530L). The amplified DNA was size selected using 2% agarose gel for 200-500bp DNA fragments.

value: WT

tag: chip-antibody

value: Homemade


title: Exp3_HGrC1_EV_SMAD4_ChIP


title: SW480_Hi-C


title: PKO_Con_HBS_seq_rep1

description: Hairpin BS-seq

value: mESC


title: WT_RA_7D_H3K27me3_rep1


title: 55_26month_array

description:
55_26month_252800422021_1_4.txt
disease

value: SSc

value: Transplant


title: Exp3_HGrC1_C134W_TGF_FOXL2_ChIP

value: Goat polyclonal antibody to  FOXL2 (Abcam Ab5096)


title: PKO_mES_RNA_seq_rep2


title: CaCo2_Hi-C


title: WT_RA_7D_GSK126_H3K27me3_rep2

growth_protocol: ES cells were cultured on 0.1% gelatin of porcine skin in DMEM (Gibco Cat. 11995-065) containing 15% FBS (Hyclone Cat. SH30396.03),  penicillin/streptomycin (Millipore Cat. TMS-AB2-C), GlutaMAX (Gibco Cat. 35050-061), nucleotides (Millipore Cat. ES-008-D), β-mercaptoethanol (Gibco Cat. 21985-023), non-essential amino acids (Gibco Cat. 25-025-CIR), retinoic acid (RA) (Sigma Cat. R2625) (the final concentration of 2ug/ml) and GSK126 (Catalog No.S7061) (the final concentration of 10uM) for 7 days.


title: Exp3_HGrC1_C134W_SMAD4_ChIP

value: HGrC1 cell-line transduced with C134W mutant (C134W) FOXL2


title: WT_RA_7D_GSK126_H3K27me3_rep1


title: Exp3_HGrC1_WT_TGF_FOXL2_ChIP

value: HGrC1 cell-line transduced with wildtype (WT) FOXL2 and stimulated with TGF


title: 9B replicate 2

city: Rochester

first: Steven

middle: R.

last: Gill

state: NY

address: 601 Elmwood Avenue

department: Microbiology & Immunology

institute: University of Rochester

data_processing:
Sequences were cleaned using Trimmomatic-0.32 "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
Alignment using STAR-2.4.2a "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
Differential expression using cuffdiff(cufflinks-2.0.2) - "--library-type fr-firststrand --FDR 0.05 -u -b GENOME"
Genome_build: All sequences were aligned to NCTC 8325 (GenBank ID = NC_007795.1).
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample in "PDT_Gill101315_fpkm.txt"

organism: Staphylococcus aureus

growth_protocol: Individual S. aureus colonies for each strain were cultured  in TSB overnight at 37C with shaking, washed twice in phosphate buffered saline (PBS) and adjusted to OD600=1.0

extract_protocol:
Aliquots from each culture were transferred to RNAProtect and then RNA extracted by acid phenol/mechanical lysis.
Illumina TruSeq library preparation from RiboZero depleted total RNA

treatment_protocol: Washed cells were incubated with methylene blue for 30 minutes at room temperature, centrifuged to remove methylene blue, and expose to light at a fluence of 2.4  J/cm2

tag: passaged

value: 7x 39 uM methylene blue and 2.4 J/cm2 light

tag: growth phase

value: exponential in TSB (OD600=~0.6)


title: Exp3_HGrC1_EV_TGF_FOXL2_ChIP

tag: chip antibody

tag: genotype/variation

value: HGrC1 cell-line transduced with empty vector (EV) control and stimulated with TGF


title: 5B replicate 2

value: 7x 39uM methylene blue

value: 39 uM methylene blue and 2.4 J/cm2 light


title: 53_38month_array

description:
53_38month_252800422221_1_2.txt
disease

data_processing:
Images were quantified using Feature Extraction Software, log10 Green over Red.  Raw, individual array files need log2 adjusted and reversed for Red over Green.
Log(base2) of R/G Lowess Normalized Ratio (Mean), NONmedian centered data were multiplied by -3.321928 to convert to Log2(Cy3/Cy5) ratios, probes with > 20% data were removed

value: post

value: Responder

value: PMBC

value: Universal Human Reference (UHR)


title: DLD1_Hi-C


title: 52_base_array

description:
52_base_252800422220_2_2.txt
disease

value: base


title: 5A replicate 1


title: 52_8month_array

description:
52_8month_252800422220_1_3.txt
disease


title: 53_base_array

description:
53_base_252800422021_1_1.txt
disease


title: WT_mES_H3K27me3_rep2

value: WT

value: Homemade


title: 53_26month_array

description:
53_26month_252800422021_2_3.txt
disease

value: SSc


title: Exp3_HGrC1_WT_FOXL2_ChIP

value: HGrC1 cell-line transduced with wildtype (WT) FOXL2


title: 51_base_array

description:
51_base_252800422220_1_4.txt
disease

value: Transplant

value: Non-responder


title: 52_54month_array

description:
52_54month_252800422220_1_1.txt
disease


title: WT_13D_H3K4me3_rep2

value: mESC-derived cell


title: 53_14month_array

description:
53_14month_252800422021_2_1.txt
disease


title: 3B replicate 2


title: Exp3_HGrC1_EV_FOXL2_ChIP

value: Goat polyclonal antibody to  FOXL2 (Abcam Ab5096)

value: HGrC1 cell-line transduced with empty vector (EV) control


title: 9A replicate 1

value: 7x 39 uM methylene blue and 2.4 J/cm2 light

value: exponential in TSB (OD600=~0.6)


title: 3A replicate 1

value: 39 uM methylene blue and 2.4 J/cm2 light


title: Exp2_KGN_TGF_SMAD2/3_ChIP

source_name: KGN cell-line

value: KGN

value: Rabbit monoclonal anti-SMAD2/3 (Cell Signaling, #86855)

value: KGN Cell-line is Heterozygous for FOXL2 C134W mutation


title: 1B replicate 2


title: WT_mES_H3K4me3_rep2

value: mESC


title: Exp2_KGN_TGF_SMAD4_ChIP

value: Rabbit polyclonal anti-SMAD4 (Proteintech, 10231-1-AP)


title: 1A replicate 1


title: WT_13D_H3K27me3_rep2

value: WT


title: Exp3_HGrC1_C134W_FOXL2_ChIP

value: HGrC1 cell-line transduced with C134W mutant (C134W) FOXL2


title: 50_base_array

description:
50_base_252800422381_1_2.txt
disease

value: SSc

value: Cyclophosphamide

value: base

value: Responder

value: PMBC

value: Universal Human Reference (UHR)


title: TKO_RA_7D_H3K27me3_rep1

value: mESC-derived cell

value: Homemade


title: TKO_RA7D_GSK126_H3K27me3_rep2


title: Exp2_KGN_TGF_FOXL2_ChIP

value: Goat polyclonal antibody to  FOXL2 (Abcam Ab5096)


title: TKO_RA_7D_H3K27me3_rep2


title: TKO_RA7D_GSK126_H3K27me3_rep1


title: TKO_mES_H3K4me3_rep2


title: Exp2_KGN_FOXL2_ChIP


title: Exp2_KGN_SMAD2/3_ChIP


title: WT_13D_H3K27ac_rep2

value: Active Motif, Cat # 39133


title: Exp2_KGN_TGF_IgG_ChIP

value: KGN

value: Normal Goat IgG Control (R&D Systems AB-108-C)


title: Exp2_KGN_SMAD4_ChIP

value: KGN Cell-line is Heterozygous for FOXL2 C134W mutation


title: TKO_mES_H3K27me3_rep2

value: mESC


title: Exp2_KGN_IgG_ChIP


title: 48_54month_array

description:
48_54month_252800422212_1_3.txt
disease

value: Transplant

value: post


title: 48_38month_array

description:
48_38month_252800422212_1_1.txt
disease


title: 51_14month_array

description:
51_14month_252800422220_1_2.txt
disease

value: Non-responder


title: APw-1

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

description: Gene expression data from the myeloid leukemia cell line.

hyb_protocol: Standard Affymetrix/Applied Biosystems protocol.

data_processing: Normalize with SST-RMA by Applied Biosystems Transcriptome Analysis Console (TAC) v4.0.

label: biotin

source_name: mouse MLL/AF10 myeloid leukemia cells harboring wild-type PTPN11

growth_protocol: Cells were cultured in the RPMI 1640 medium containing 20% fetal bovine serum, 2 mM L-glutamine, 100 mM 2-mercaptoethanol, and 10 ng/ml interleukin-3, at 37℃ for 16h.

extract_protocol: Trizol reagent.

treatment_protocol: No treatment.

value: Myeloid leukemia cell line

value: Wild-type PTPN11


title: 48_Base_R_array

description:
48_Base_R_252800422020_1_3.txt
disease

value: SSc

value: base


title: TKO_mES_H3K27ac_rep2


title: 48_26month_array

description:
48_26month_252800421274_2_1.txt
disease

value: Responder

value: PMBC


title: 12G-H11

scan_protocol: Standard Affymetrix/Applied Biosystems protocol.

source_name: mouse MLL/AF10 myeloid leukemia cells harboring Hoxa11


title: AK3G

source_name: mouse MLL/AF10 myeloid leukemia cells harboring KRAS-G12C

label_protocol: Standard Affymetrix/Applied Biosystems protocol.


title: 5_base_array

description:
05_base_252800422380_2_2.txt
disease

value: Cyclophosphamide

value: Universal Human Reference (UHR)


title: 47_base_array

description:
47_base_252800421273_2_4.txt
disease


title: Exp2_HGrC1_C134W_TGF_FOXL2_ChIP

value: Goat polyclonal antibody to  FOXL2 (Abcam Ab5096)

value: HGrC1 cell-line transduced with C134W mutant (C134W) FOXL2 and stimulated with TGF


title: AKw1G

source_name: mouse MLL/AF10 myeloid leukemia cells harboring wild-type KRAS

value: Wild-type KRAS


title: 48_14month_array

description:
48_14month_252800420326_2_3.txt
disease


title: 12G-V

source_name: mouse MLL/AF10 myeloid leukemia cells negative control

value: No Hoxa11


title: TKO_13D_H3K4me3_rep2

value: mESC-derived cell

value: Homemade


title: PKO_RA_7D_H3K27me3_rep2


title: Exp2_HGrC1_WT_TGF_FOXL2_ChIP

value: HGrC1 cell-line transduced with wildtype (WT) FOXL2 and stimulated with TGF


title: 48_8month_array

description:
48_8month_252800420320_2_3.txt
disease

value: Transplant

value: post


title: PKO_RA_7D_GSK126_H3K27me3_rep2


title: PKO_RA_7D_H3K27me3_rep1


title: APm-1

source_name: mouse MLL/AF10 myeloid leukemia cells harboring PTPN11-G503A

value: Myeloid leukemia cell line


title: Exp2_HGrC1_WT_FOXL2_ChIP

value: HGrC1 cell-line transduced with wildtype (WT) FOXL2


title: Exp2_HGrC1_C134W_FOXL2_ChIP

value: HGrC1 cell-line transduced with C134W mutant (C134W) FOXL2


title: Exp2_HGrC1_EV_TGF_FOXL2_ChIP

value: HGrC1 cell-line transduced with empty vector (EV) control and stimulated with TGF


title: Exp2_HGrC1_EV_FOXL2_ChIP

value: HGrC1 cell-line transduced with empty vector (EV) control


title: PKO_RA_7D_GSK126_H3K27me3_rep1


title: Exp1_HGrC1_C134W_TGF_FOXL2_ChIP


title: Exp1_HGrC1_WT_TGF_FOXL2_ChIP


title: 47_38month_array

description:
47_38month_252800422220_2_1.txt
disease

value: SSc

value: Non-responder

value: PMBC


title: PKO_mES_H3K4me3_rep2

value: mESC


title: 47_14month_array

description:
47_14month_252800420325_1_1.txt
disease

value: Cyclophosphamide

value: Universal Human Reference (UHR)


title: PKO_13D_H3K4me3_rep2


title: 45_base_R_array

description:
45_base_R_252800422020_1_1.txt
disease

value: base

value: Responder


title: Exp1_HGrC1_EV_TGF_FOXL2_ChIP

value: Goat polyclonal antibody to  FOXL2 (Abcam Ab5096)


title: 47_26month_array

description:
47_26month_252800420364_1_2.txt
disease


title: Exp1_HGrC1_C134W_FOXL2_ChIP


title: PKO_13D_H3K27me3_rep2

value: mESC-derived cell

value: Homemade


title: PKO_13D_H3K27ac_rep2

value: Active Motif, Cat # 39133


title: 45_8month_array

description:
45_8month_252800421275_2_1.txt
disease

value: Transplant

value: post


title: 45_26month_array

description:
45_26month_252800421274_2_2.txt
disease


title: 45_54month_array

description:
45_54month_252800422219_1_3.txt
disease


title: Exp1_HGrC1_WT_FOXL2_ChIP

value: HGrC1 cell-line transduced with wildtype (WT) FOXL2


title: Exp1_HGrC1_EV_FOXL2_ChIP


title: Exp0_KGN_FOXL2_mAb2_ChIP

value: KGN

value: Custom-made monoclonal mouse antibody to human FOXL2 Produced by Paul Cloos (Clone 1513)

value: KGN Cell-line is Heterozygous for FOXL2 C134W mutation


title: Exp0_KGN_FOXL2_polyAb_ChIP


title: 45_14month_array

description:
45_14month_252800420364_2_4.txt
disease

value: SSc


title: 47_8month_array

description:
47_8month_252800421275_1_3.txt
disease

value: Non-responder

value: PMBC


title: TTC_SC_451

city: Hangzhou

first: HONGWEI

last: OUYANG

state: Zhejiang

address: 866 Yu Hang Tang Road,Hangzhou, Zhejiang, P.R.China.

institute: Zhejiang University

data_processing:
Single-cell RNA sequence reads were evaluated by AfterQC. Bad reads were detected automatically and removed. Bases at 3' end of the read were further timmed by NGSQCToolkit if their PHRED quality score were less than.
The reads were mapped to the mouse genome(mm10) using bowtie2.
The mapped reads for genes were counted via featureCounts. Gene expression was represented by CPM (tags per million).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample

source_name: KO

extract_protocol:
Single-cell capture, RNA extraction and cDNA synthesis were performed following the methods described in the Fluidigm protocol(PN 100-9886)
The cDNA reaction products were quantified using the Qubit and were then diluted to a final concentration of 0.2 ng/ μl using C1 Harvest Reagent. The diluted cDNA reaction products were then converted into mRNA-seq libraries using the Nextera XT DNA Sample Preparation Kit (Illumina, FC-131-1096, -2001 and -2002) following the manufacturer’s instructions.

treatment_protocol: Tail tendons from 4-wk-old wild-type or Mkx-/- mice  was minced into desired pieces and digested in 0.2% collagenase I diluted in low-glucose Dulbecco’s modified Eagle’s medium solution at 37°C for 2 hours. Then the cell suspension was filtered using 40 μm strainer to remove the incompletely digested clumps and adjusted to a concentration of 4×10^5 cells/ml.

value: tail tendon

value: Mkx-/-

tag: age


title: TTC_SC_450

tag: genotype


title: TTC_SC_449

tag: strain


title: TTC_SC_447


title: TTC_SC_448