title: N1+/- + XCT790 Replicate 3

first: Christina

last: Theodoris

address: 1650 Owens Street

institute: Gladstone Institutes, University of California, San Francisco

data_processing:
Sequencing quality was assessed with FASTQC
Reads were aligned to the hg19 (Homo sapiens assembly February 2009) transcriptome and genome using the Spliced Transcripts Alignment to a Reference (STAR) Aligner
Differential expression was analyzed using Cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: test file that includes the FPKM value for each gene, separated by replicate, calculated by CuffDiff

source_name: iPSC-derived Ecs_N1+/- + XCT790

growth_protocol: cells derived, differentiated, and cultured as in Theodoris et al., Cell, 2015

extract_protocol:
Qiagen RNeasy Micro purification kit per kit protocol
Clontech SMRTer Stranded RNA-seq Library Prep Kit for Illumina per kit protocol

treatment_protocol: Starting on day 15 of differentiation, WT ECs were exposed to 10μM DMSO while isogenic N1+/- ECs were exposed to either 10μM DMSO or one of the small molecules. DMSO or small molecules were renewed with EC media (ScienCell #1001) changes on alternating days until the cells were ultimately collected for analysis on day 21

value: iPSC-derived ECs


title: RNAseq_KO_rep2

status: Public on Jan 01 2021

type: SRA

city: San Francisco

first: Eric

middle: Joseph

last: Wigton

state: CA

address: 500 Parnassus Ave.

department: Immunology

country: USA

institute: UCSF

description: ready for alignment to genome

library_source: transcriptomic

data_processing:
Raw Fastqs were binned based on barcode using python bst  and perl fastx_barcode_splitter.pl
barcodes and adapters were trimmed using parallel -j3 'cutadapt -e 0.2 -a GTGTCTTTACACAGCTACGGCGTCG -m 19 --cut 11
The fastq files were then aligned to the mm9 genome and combined into single BAM using bowtie2 and samtools
BAM files were intersected to exclude miRNA reads using miRBASE bam filed and samtools BAM files converted to SAM files using samtools for downstream use on dCLIP
For RNAseq fastq files were aligned using STAR and compared using DESeq2 to give All_genes text files
Genome_build: mm9
Supplementary_files_format_and_content: read count and DESeq analysis for RNA-seq data. dCLIP analysis produces dCLIP_output.txt and dCLIP_summary.bed files containing the results (WT file 1 input KO file 2 input) IGV tool TDF files for peak viewing of individual library samples.

molecule: total RNA

organism: Mus musculus

source_name: activated splenic B cells

growth_protocol: Cells were grown in 96 well plates sitmulated with aCD40 (500ng/ml) IL4 (25ng/ml) and IL21 (10ng/ml) for 4 days

extract_protocol:
RNA was extracted by Trizol for RNAseq or by Ago2 immunoprecipitation for Ago2-HITS-CLIP
RNAseq library multiplexed for HISEQ4000.  Ago2-HITS-CLIP custom library design for HISEQ2500 (see Gagnon JD, et al 2019 and Loeb, et al 2012)

tag: strain

tag: tissue

value: spleen

tag: cell type

value: B cell

tag: rna fraction

value: total RNA


title: 00 hour rep 1

city: Seattle

first: Christine

last: Queitsch

state: WA

address: 3720 15th Ave NE, Foege Hall

department: Genome Sciences

institute: University of Washington

description:
single cell RNA-seq data from 00 hour experiment
matrix.mtx
barcodes.tsv
genes.tsv

data_processing:
Illumina Nextseq 500 base caller is used
cellranger mkfastq was run on the nextseq output to generate fastq files
cellranger counts was run on output fastq files from each sample, to identify barcodes with sufficient reads for analysis, and to align reads to the Arabdiopsis genome using the Araport annotation.
cellranger aggr was then used to combine samples into one matrix and barcode set
Genome_build: TAIR10/ARAPORT
Supplementary_files_format_and_content: matrix.mtx is the UMI count matrix for the number of UMIs, each barcode (cell) had associated with each gene; barcodes.tsv contains barcode info, as well as experiment of origin and cell type label; genes.tsv

organism: Arabidopsis thaliana

source_name: root tissue

growth_protocol: For all plant experiments, Arabidopsis seeds were sown on 0.5× LS 0.8% agar plates, stratified at 4°C for 2 days, and grown in continuous light conditions at 22°C for respective experimental design.

extract_protocol:
Protoplast isolation was done according to Bargmann and Birnbaum (2010), with slight modifications.
10X genomics protocol

treatment_protocol: Seeds were placed on 0.5 LS+0.8% bacto-agar plate following a specific pattern to avoid seedling collision during the lateral root bend essay.  The plate was stratified during 120 hours, grown vertically for 96 hours at 22°C, rotated 90°C while keeping vertically and grown for an additional 20 hours.

value: root tissue

tag: experiment

value: 00 hour


title: 08 hour rep 1

value: 08 hour


title: N1+/- + XCT790 Replicate 2

state: California

organism: Homo sapiens

tag: genotype/variation

tag: treatment


title: YAMATseq, H.vulgare seedling

city: Tianjin

first: Xuan

last: Ma

address: Binshui West Road

department: College of Life Sciences

country: China

institute: Tianjin Normal University

description: pretreated RNA

data_processing:
Library strategy: YAMAT-seq
tRNA-seq data were first processed to remove the 5’ and 3’ adaptor sequences using cutadapt with the parameters “-m 17 --trim-n -f fastq -a AGATCGGAAGAGCAC -A GATCGTCGGACTGTA -g TACAGTCCGACGATC -G GTGCTCTTCCGATCT -n 2”. Then, the trimmed data were analyzed by a self-designed pipeline for quantifications of tRFs and tRNAs.
YAMAT-seq data were first processed to trim the 5’ and 3’ adaptor sequences using Cutadapt, and the 5’ nucleotide complementary to the discriminator base was also trimmed. Then, the adaptor-free sequences that have perfect match to annotated mature tRNAs were counted and normalized against total tRNA reads to measure mature tRNA expression levels.
Genome_build: TAIR10, Phytozome
Supplementary_files_format_and_content: The file tRNAseq_tRNA.xlsx summarizes tRNA expressions in various plants. The YAMATseq files are tRNA count data.

organism: Hordeum vulgare

source_name: H.vulgare seedling

growth_protocol: Arabidopsis thaliana, Glycine max, Hordeum vulgare, Setaria italica, Sorghum bicolor, Triticum aestivum, Zea mays plants were germinated in the soil and grown at 23 ºC under the standard long-day condition (16 hours of light followed by 8 hours of darkness). The 10-day old seedlings were collected for tRNA-seq or YAMAT-seq analysis.

extract_protocol:
RNA extraction was conducted using TRIzol reagent (Invitrogen). Ethanol precipitation was performed overnight at -20ºC to maximize sRNA yield.
RNA pretreatment was conducted using rtStar tRF&tiRNA pretreatment kit (Arraystar). Pretreated RNAs were purified by Phenol:Chloroform extraction and ethanol precipitation. tRNA-seq library was constructed using VAHTS Small RNA Library Prep Kit for Illumina (Vazyme). Purification of PCR amplified cDNAs were conducted using VAHTS DNA Clean Beads (Vazyme). YAMAT-seq was performed as previously described (Shigematsu et al Nucleic Acids Res. 2017) with some modifications. The design of Y-shaped adapters followed previous study. 2 µl of 3’ adaptor (10 µM) and 2 µl of 5’ adaptor mix (10 µM) were incubated at 70ºC for 2 min and cooled at room temperature to allow 5’ and 3’ adaptors to fully anneal. Then, the Y-shaped adaptor was mixed with 2 µg pretreated RNA, 4 unit T4 Rnl2 (New England Biolabs) and 2 µl ligation buffer with total reaction of 20 µl, and incubated at 37 ºC for 2 h. Next, 1 µl RNA RT Primer (RTP, Illumina) was added to the reaction and incubated at 70 ºC for 3 min, and then immediately chilled on ice. Subsequently, reverse transcription and cDNA amplification reactions were performed using VAHTS Small RNA Library Prep Kit for Illumina (Vazyme). A Universal Primer and RNA PCR Index Primers (Illumina) were used for amplifying cDNAs with 12 PCR cycles. The PCR products were purified using VAHTS DNA Clean Beads (Vazyme).

value: seedling


title: N1het AV Stenosis + XCT790 Replicate 3

data_processing:
Sequencing quality was assessed with FASTQC
Reads were aligned to the mm9 transcriptome and genome using hisat2
Unmapped (-F 4) and low-quality reads with MAPQ score below 30 (-q 30) were removed using Samtools
Duplicate reads were removed using Picard MarkDuplicates
Differential expression was analyzed using Useq
Genome_build: mm9
Supplementary_files_format_and_content: FPKMs

source_name: aortic valve

growth_protocol: mouse valves collected as in Theodoris et al., JCI, 2017 and directly lysed for RNA isolation

extract_protocol:
Qiagen RNeasy Micro purification kit per kit protocol
NUGEN Ovation RNA-Seq System V2 per kit protocol

treatment_protocol: mice were treated by daily intraperitoneal injection with control solvent or XCT790 (5mg/kg/day) for four weeks starting at four weeks of age

tag: genotype

value: N1+/-, generation 2 Terc-/-

tag: agent

tag: disease state

value: AV stenosis

value: aortic valve


title: Blood QC44

type: genomic

first: huanxin

last: chen

address: No.61, third avenue, tianjin economic and technolo

institute: Teda International Cardiovascular Hospital

description: Hybridized to Affymetrix SNP 6.0

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The overall hybridization quality was estimated by the call rate obtained from Genotyping Console Software 4.2 (birdseed algorithm with default parameter settings). Partek Genomics Suite (version 6.5, Partek Inc., St. Louis, MO) was used for copy number analysis. Regions of CNV were detected using a Hidden Markov Model (HMM) algorithm in the Partek workflow for unpaired samples.

label: biotin

molecule: genomic DNA

source_name: healthy control_blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from peripheral blood for each patient and control subject, using QIAamp® DNA blood mini kit according to the manufacturer’s instruction

tag: group

value: healthy control

value: blood


title: N1+/- + XCT790 Replicate 1


title: N1+/- + Putrescine Replicate 3

source_name: iPSC-derived Ecs_N1+/- + Putrescine

value: Putrescine


title: Blood QC46

description: Hybridized to Affymetrix SNP 6.0


title: tRNAseq, H.vulgare seedling

description:
pretreated RNA
tRNAseq_tRNA.xlsx

data_processing:
tRNA-seq data were first processed to remove the 5’ and 3’ adaptor sequences using cutadapt with the parameters “-m 17 --trim-n -f fastq -a AGATCGGAAGAGCAC -A GATCGTCGGACTGTA -g TACAGTCCGACGATC -G GTGCTCTTCCGATCT -n 2”. Then, the trimmed data were analyzed by a self-designed pipeline for quantifications of tRFs and tRNAs.
YAMAT-seq data were first processed to trim the 5’ and 3’ adaptor sequences using Cutadapt, and the 5’ nucleotide complementary to the discriminator base was also trimmed. Then, the adaptor-free sequences that have perfect match to annotated mature tRNAs were counted and normalized against total tRNA reads to measure mature tRNA expression levels.
Genome_build: TAIR10, Phytozome
Supplementary_files_format_and_content: The file tRNAseq_tRNA.xlsx summarizes tRNA expressions in various plants. The YAMATseq files are tRNA count data.


title: tRNAseq, S.bicolor seedling

description:
pretreated RNA
tRNAseq_tRNA.xlsx

organism: Sorghum bicolor

source_name: S.bicolor seedling


title: N1het AV Stenosis + XCT790 Replicate 2


title: Blood QC43

description: Hybridized to Affymetrix SNP 6.0


title: N1+/- + Putrescine Replicate 2


title: N1+/- + Putrescine Replicate 1


title: N1het AV Stenosis + XCT790 Replicate 1


title: SUNE1-shWIPI-1 rep2

city: Guangzhou

first: Yin

last: Zhao

state: Guangdong

address: 651 Dongfeng Road East

department: State Key Laboratory of Oncology in South China

institute: Sun Yat-sen University Cancer Center

data_processing:
RNAseq libraries were loaded on the cBot (automated cluster generation system) (Illumina), and sequenced using the Illumina NovaSeq 6000 platform. Sequencing reads were mapped to the human (hg38) reference genome with HiSat2 (version 2.1.0).
FPKM (Fragments Per Kilobase of exon modelper Million mapped fragments) was used to calculate relative transcript level of genes.
Subsequently, genes which did not have at least 10 reads were discarded. Differential expression analysis was conducted by the Bioconductor packages edgeR (version 3.12) and limma (version 3.12).
Genome_build: Homo sapiens GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

growth_protocol: SUNE1 cells were grown in RPMI-1640 with 10% fetal bovine serum.

extract_protocol:
RNA from SUNE1 cells was extracted by TRIzol reagent. Truseq RNA Sample Preparation v2 Kit (Illumina) with 1 ug of total RNA was applied to construct RNA sequencing libraries.
RNA sequencing libraries were prepared based on the standard Illumina instruction.

treatment_protocol: SUNE1 cells were transfected with control shRNA or WIPI-1 shRNA for 48h.

value: nasopharyngeal carcinoma

tag: cell line

tag: transfection


title: Blood QC42

description: Hybridized to Affymetrix SNP 6.0


title: N1het AV Stenosis + Control Solvent Replicate 3


title: N1+/- + TG003 Replicate 3

source_name: iPSC-derived Ecs_N1+/- + TG003


title: SUNE1-shWIPI-1 rep1


title: RNAseq_KO_rep1

description: ready for alignment to genome


title: N1het AV Stenosis + Control Solvent Replicate 2


title: Blood QC41

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC40

description: Hybridized to Affymetrix SNP 6.0


title: SUNE1-NC rep2

value: shCtrl


title: N1+/- + TG003 Replicate 2


title: N1het AV Stenosis + Control Solvent Replicate 1


title: Blood QC45

description: Hybridized to Affymetrix SNP 6.0


title: N1+/- + TG003 Replicate 1


title: SUNE1-NC rep1


title: N1het Healthy AV + XCT790 Replicate 5

value: healthy AV


title: Blood QC39

description: Hybridized to Affymetrix SNP 6.0


title: N1het Healthy AV + XCT790 Replicate 4


title: N1+/- + Biperiden Replicate 3

source_name: iPSC-derived Ecs_N1+/- + Biperiden

value: iPSC-derived ECs

value: Biperiden


title: Blood QC37

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC38

description: Hybridized to Affymetrix SNP 6.0


title: N1het Healthy AV + XCT790 Replicate 3

value: control solvent


title: N1+/- + Biperiden Replicate 2


title: hSAEC-KD24 h-replicate 2 ATAC

city: Madison

first: Allan

last: Brasier

state: WI

address: 715 Highland

department: ICTR

institute: university of Wissconsin

description: SMARCA4 depleted hSAECs

library_source: genomic

data_processing:
Nextera adapters were trimmed with cutadapt (version 2.0)(32) with option “-q 30 --minimum-length 36”
Paired-end ATAC-seq reads were aligned to the human genome assembly (hg19) with bowtie2 (version 2.3.4.1) with option “-X 800 --no-mixed --no-discordant”
unmapped reads and mitochondrial sequences were filtered out by using SAMtools view (version 1.8)(34) with option “-F 4”
Peaks were called for pooled and individual samples by MACS2
Genome_build: hg19

source_name: hSAEC- SMARCA4 knockdown

growth_protocol: hSAECs were grown in SAGM small airway epithelial cell growth medium (Lonza, cc-3118).

extract_protocol: 50,000 cells (>95% viability) were trypsinized and washed.  Cell pellets were re-suspended in 300ul of cold lysis buffer (10mM Tris-HCl, pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630) and incubate on ice for 10 min. Nuclei were pelleted, re-suspended in 50 µl of transposition mixture (25 µl 2x TD buffer (Illumina, 15027866), 2.5 µl TDE1 (Illumina Nextera Tn5 transposase,15027865), 22.5 µl nuclease-free water) and incubate for 30 min at 37oC water bath with gentle mixing.  After cleaning with Qiagen MinElute PCR purification kit (Qiagen, 28204), eluted DNA was pre-amplified for 5 cycles in PCR mix (30 µl NEBNext High-Fidelity 2x master mix (NEB, M054 1S), 10 µl primer mix (Illumina, NEXtera DNA UD indexes20026121), 20 µl purified DNA) for 5 cycles. Additional 3 amplification cycles were added based on QPCR amplification.  PCR reactions were then purified with Qiagen PCR purification kit and sent to University of Wisconsin Biotechnology Center. Libraries were further purified, quantified and analyzed on a bioanalyzer and sequenced on a NovaSeq 6000 with 50 million reads per sample.

treatment_protocol: SMARCA4 KD cells (“723”) with short hairpin RNA (shRNA) were generated using lentiviral particles (Sigma, TRCN0000380723 for SMARCA4 KD and SHC001V for control).  The human RSV Long strain was grown in Hep-2 cells and prepared by sucrose cushion

value: human small airway epithelial cells (hSAEC)

value: SMARCA4 depleted

value: RSV infected 24 h

tag: replicate

value: replicate 2


title: hSAEC-KD-0-replicate 2 ATAC

description: SMARCA4 depleted hSAECs

value: uninfected (0h)


title: hSAEC-KD24 h-replicate 1 ATAC

description: SMARCA4 depleted hSAECs

value: replicate 1


title: N1het Healthy AV + XCT790 Replicate 2

value: N1+/-, generation 2 Terc-/-


title: Blood QC36

description: Hybridized to Affymetrix SNP 6.0


title: N1+/- + Biperiden Replicate 1


title: N1het Healthy AV + XCT790 Replicate 1

value: aortic valve


title: Blood QC35

description: Hybridized to Affymetrix SNP 6.0

value: healthy control


title: N1+/- + CB1954 Replicate 3

source_name: iPSC-derived Ecs_N1+/- + CB1954


title: N1het Healthy AV + Control Solvent Replicate 6


title: Blood QC33

description: Hybridized to Affymetrix SNP 6.0

value: blood


title: N1+/- + CB1954 Replicate 2


title: hSAEC-WT-24 h-replicate 1 ATAC

description: Wild type small airway epithelial cells

source_name: hSAEC wild type

value: Wild type


title: N1+/- + GSK837149A Replicate 3

source_name: iPSC-derived Ecs_N1+/- + GSK837149A


title: hSAEC-WT-0-replicate 2 ATAC

description: Wild type small airway epithelial cells


title: N1het Healthy AV + Control Solvent Replicate 4


title: Blood QC32

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC31

description: Hybridized to Affymetrix SNP 6.0


title: N1het Healthy AV + Control Solvent Replicate 3


title: Blood QC30

description: Hybridized to Affymetrix SNP 6.0


title: KD-24 h-replicate 4

description: SMARCA4 depleted hSAECs

data_processing:
bar codes were removed by skewer
alignment and quantification were performed using Salmon
differential analysis was using DESeq2

extract_protocol: Cells were harvested for RNA isolation using RNeasy kit with on-column DNase digestion (Qiagen). Synthesis of complementary DNAs (cDNAs) was done with First Strand cDNA Synthesis Kit (Thermo Scientific).


title: N1het Healthy AV + Control Solvent Replicate 2


title: N1+/- + GSK837149A Replicate 1


title: hSAEC-KD-0-replicate 1 ATAC

description: SMARCA4 depleted hSAECs


title: N1het Healthy AV + Control Solvent Replicate 1


title: hSAEC-WT-0-replicate 1 ATAC

description: Wild type small airway epithelial cells


title: N1+/- + Cytochalasin Replicate 2

source_name: iPSC-derived Ecs_N1+/- + Cytochalasin

value: Cytochalasin


title: N1+/- + Cytochalasin Replicate 3


title: hSAEC-WT-24 h-replicate 2 ATAC

description: Wild type small airway epithelial cells


title: KD-24 h-replicate 2

description: SMARCA4 depleted hSAECs


title: Blood QC29

description: Hybridized to Affymetrix SNP 6.0


title: KD-24 h-replicate 3

description: SMARCA4 depleted hSAECs


title: Blood QC34

description: Hybridized to Affymetrix SNP 6.0


title: N1het Healthy AV + Control Solvent Replicate 5


title: N1+/- + Cytochalasin Replicate 1


title: KD-24 h-replicate 1

description: SMARCA4 depleted hSAECs


title: N1+/- + GSK837149A Replicate 2


title: WT Healthy AV + Control Solvent Replicate 4

value: N1+/+, generation 2 Terc-/-


title: WT Healthy AV + Control Solvent Replicate 2

value: healthy AV


title: N1+/- + RO4929097 Replicate 3

source_name: iPSC-derived Ecs_N1+/- + RO4929097

value: iPSC-derived ECs


title: N1+/- + CB1954 Replicate 1


title: Blood QC28

description: Hybridized to Affymetrix SNP 6.0


title: WT Healthy AV + Control Solvent Replicate 3


title: N1+/- + RO4929097 Replicate 2


title: Blood QC25

description: Hybridized to Affymetrix SNP 6.0


title: N1+/- + RO4929097 Replicate 1


title: KD-16 h-replicate 3

description: SMARCA4 depleted hSAECs

value: RSV infected 16 h


title: KD-16 h-replicate 2

description: SMARCA4 depleted hSAECs


title: Blood QC26

description: Hybridized to Affymetrix SNP 6.0


title: WT Healthy AV + Control Solvent Replicate 1

value: control solvent


title: GoF_3

city: MARSEILLE

first: Sonia

last: Stefanovic

address: 27 BD JEAN MOULIN

country: France

institute: INSERM U1251

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
RNA-Seq reads were aligned using the STAR aligner version 2.5.2
Transcripts abundance was computed using HTSEQ-count 0.9.12 and the background was estimated through read counts from intergenic regions using windows of 5 kb length
Normalisation and differential gene expression analysis between conditions were performed using R (R version 3.3.4) and DESEQ2
Genome_build: mm10
Supplementary_files_format_and_content: The final processed data files is the output of the DESEQ2 package. This file contains the gene name, the base mean , the log2foldchange, the test value, the p-value, the adjusted p-value and the normalized count foreach sample.

molecule: polyA RNA

source_name: Amplified ds cDNA with Ovation V2 Nugen kit

extract_protocol:
SHF was microdissected, flash frozen on dry ice, and RNA was harvested using the NucleoSpin® RNA XS kit
Amplified cDNA was prepared from 2 ng of total RNA using the Ovation RNA-seq system V2 (NuGEN Technologies, Inc.) following manufacturer's instructions. Briefly, first-strand cDNA was prepared from total RNA using a combination of random and poly-T DNA/RNA chimeric SPIA primers and reverse transcriptase, resulting in a cDNA/mRNA hybrid molecule. Priming sites created by a heating fragmentation of the mRNA within the cDNA/mRNA complex were used to synthesize the second strand cDNA using a DNA polymerase. The resulting double-stranded cDNA with a unique RNA/DNA heteroduplex at one end was purified using Agencourt RNAClean XP beads (Beckman Coulter Inc.). The purified product was then used as the substrate of a linear amplification process, SPIA (single primer isothermal amplification). During the amplification step, RNase H degrades RNA in DNA/RNA heteroduplex at the 5'end of the first cDNA strand, creating a binding site for the DNA/RNA SPIA chimeric primer, then DNA polymerase starts replication at the 3'end of the primer displacing the existing forward strand. The process including SPIA DNA/RNA primer binding, DNA replication, strand displacement and RNA degradation is repeated and results in rapid generation of microgram quantities of amplified cDNA. Amplified cDNA was purified using AMPure XP beads (Beckman Coulter Inc.) and 500 ng was fragmented by sonication using a Covaris E210 instrument (with duty cycle: 10X, intensity: 5 and cycle/burst: 200 for 180 seconds).    The next steps of RNA-Seq Library preparation were performed using Ovation Ultralow Library System kit (NuGEN Technologies, Inc.) according to manufacturer's instructions. Briefly, in this system 100 ng of amplified cDNA were blunted, phosphorylated and ligated to indexed adapter dimers. The libraries were then enriched by PCR amplification (2 min at 72 degrees Celsius; [30 sec at 94 degrees Celsius, 30 sec at 60 degrees Celsius, 1 min at 72 degrees Celsius] x 6 cycles; 5 min at 72 degrees Celsius) and surplus PCR primers were removed by purification using AMPure XP beads. DNA libraries were checked for quality using 2100 Bioanalyzer (Agilent) and quantified using Kapa Sybr Fast Light Cycler 480 qPCR Kit  (Kapa Biosystems) following manufacturer's instructions.

value: second heart field region

tag: Stage


title: N1+/- + Fmoc-leu Replicate 3

source_name: iPSC-derived Ecs_N1+/- + Fmoc-leu

value: Fmoc-leu


title: Blood QC24

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC27

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC23

description: Hybridized to Affymetrix SNP 6.0


title: GoF_2


title: GoF_1


title: Blood QC22

description: Hybridized to Affymetrix SNP 6.0


title: KD-16 h-replicate 1

description: SMARCA4 depleted hSAECs

value: human small airway epithelial cells (hSAEC)

value: SMARCA4 depleted


title: KD-0-replicate 4

description: SMARCA4 depleted hSAECs

value: uninfected (0h)


title: N1+/- + Fmoc-leu Replicate 2


title: N1+/- + Fmoc-leu Replicate 1


title: KD-16 h-replicate 4

description: SMARCA4 depleted hSAECs


title: KD-0-replicate 3

description: SMARCA4 depleted hSAECs


title: CTRL_3

value: CTRL Mef2c-Cre


title: N1+/- + DMSO Replicate 3

source_name: iPSC-derived Ecs_N1+/- + DMSO

value: DMSO


title: Blood QC21

description: Hybridized to Affymetrix SNP 6.0


title: CTRL_2


title: KD-0-replicate 2

description: SMARCA4 depleted hSAECs


title: Blood QC20

description: Hybridized to Affymetrix SNP 6.0


title: N1+/- + DMSO Replicate 2


title: KD-0-replicate 1

description: SMARCA4 depleted hSAECs


title: Blood QC19

description: Hybridized to Affymetrix SNP 6.0


title: Kit- Macrophage Progenitor3

city: La Jolla

first: Judy

last: Varner

address: 3855 Health Sciences DR

department: Pathology

institute: Moores UCSD Cancer Center

data_processing:
Base calling used Illumina's  Real-Time Analysis software called RTA2
Quality assessment used FASTQC, then mapped to mm10 whole genome using STAR 2.5.3a.
Quantification used RSEM 1.3.0. Annotation used Mus_musculus.GRCm38.68.gtf.
MultiQC was used to aggregate QC results into a single report
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene count, TPM, and FPKM values for each Sample.

source_name: tumor macrophages

growth_protocol: Lewis lung carcinoma tumors grown in mice were used to isolate tissue resident CD45+CD11b+Gr1-F4/80hi and bone marrow derived CD45+CD11b+Gr1+F4/80lo macrophages for RNA sequencing. These cells were also used to generate macrophage progenitors by culture in methycellulose + stem cell growth factors. Resulting Colony cells were then sorted for Kit expression and sequenced.

extract_protocol:
RNA was isolated from sorted cells using Qiagen RNA Easy Kits
Whole transcriptome analysis was performed using TruSeq Stranded RNA Kit (Illumina)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tumors were dissociated with collegenase and sorted into macrophage subpoulations by flow cytometry and RNA was prepared. Macrophage subsets were also cultured in methylcellulose containing SCF, IL3, and IL6, and colony cells were isolated RNA was prepared and sequenced.

value: lung tumor

value: progenitor/Kit-

tag: cell type isolation

value: Sorted Gr1-F4/80hi cells cultured in methylcellulose + SCF,IL3, IL6 and sorted for cKit- cells


title: Blood QC18

description: Hybridized to Affymetrix SNP 6.0

value: healthy control

value: blood


title: Blood QC17

description: Hybridized to Affymetrix SNP 6.0


title: Kit- Macrophage Progenitor 1


title: Blood QC16

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC15

description: Hybridized to Affymetrix SNP 6.0


title: Macrophage Progenitor 2

description: 8_StemCell_F480hiGr1neg_2_S8_L008_R1_001

value: total progenitor

value: Sorted Gr1-F4/80hi cells cultured in methylcellulose + SCF,IL3, IL6


title: WT + DMSO Replicate 1

source_name: iPSC-derived Ecs_WT + DMSO

value: iPSC-derived ECs

value: WT


title: Macrophage Progenitor 3

description: 9_StemCell_F480hiGr1neg_3_S9_L008_R1_001


title: Macrophage Progenitor 1

description: 7_StemCell_F480hiGr1neg_1_S7_L008_R1_001


title: WT-16 h-replicate 4

description: Wild type small airway epithelial cells

value: Wild type

value: RSV infected 16 h


title: 12h-4

city: Groningen

first: Bart

last: Eggen

state: Groningen

address: Antonius Deusinglaan 1

department: Department of Biomedical Sciences

country: Netherlands

institute: UMCG Groningen

data_processing:
Sequenced reads were trimmed for adaptor and low-quality sequences using trimgalore, with additional parameter max_length = 70
Trimmed reads were aligned to the reference genome from Ensembl: Mus musculus (GRCm38.92) using HISAT2 (version 2.1.0)
Aligned data was processed with the following functions of picard (version 1.140): SortSam, AddOrReplaceReadGroups (), FixMateInformation, MergeSamFiles and MarkDuplicates
Processed data was then subjected to sort function of the SAMtools package (version 1.9), followed by and gene level quantification which was performed using featurecounts (version 1.6.2)
Genome_build: Mus musculus (GRCm38.92)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Brain

extract_protocol:
Microglia were isolated from mouse brain by mechanical tissue dissociation and Percoll gradient centrifugation at 4°C followed by flow cytometry of viable (DAPI-), CD45+, CD11b+, Ly6c- cells.
RNA libraries were prepared for sequencing using standard Lexogen protocols.

treatment_protocol: Mice were terminated by cervical dislocation and left at room temperature for 0, 4, 6, 12 h.

value: Microglia

tag: postmortem delay (h)


title: Blood QC14

description: Hybridized to Affymetrix SNP 6.0

source_name: healthy control_blood


title: 12h-3

tag: strain


title: 12h-2


title: ChIP-Seq:TR WT rep3

city: Philadelphia

first: Mitchell

last: Lazar

state: PA

address: 3400 Civic Center Blvd

department: Perelman School of Medicine

institute: University of Pennsylvania

description: both_OldInput_Union.fully_annotated.peaks

data_processing:
RNA-Seq alignment: STAR v.2.7.3a with parameters --outSAMstrandField intronMotif –outFilterMultimapNmax 1
Gene expression quantification: featureCounts v.2.0.0 from Subread package
Differential gene expression: edgeR v.3.28.1
ChIP-Seq alignment: bowtie2 v.2.4.1 with parameters “-N 1 -t”. Duplicate reads dropped and uniquely mapped reads are selected using samtools 1.3.1
ChIP-Seq coverage calculation: Homer v4.11.1. Tag directories are created with makeTagDirectory, bigWig files are created with makeUCSCfile
ChIP-Seq peak calling: Homer  v4.11.1 findPeaks, using corresponding input experiment as background
TR ChIP-Seq was additionally filtered against the WT experiment (no HA tag)
Genome_build: mm9
Supplementary_files_format_and_content: peak: Homer format peak files with additional annotations
Supplementary_files_format_and_content: bigWig: coverage tracks for ChIP-Seq data
Supplementary_files_format_and_content: tsv: edgeR results for two-conditions differential gene expression
Supplementary_files_format_and_content: tsv: featureCounts output for RNA-Seq data

source_name: Mouse liver

growth_protocol: For PTU treatment, mice were provided with drinking water containing 1% perchlorate and 0.05% propylthiouracil for 3 wk. In the last five days all animals were intraperitoneally injected with vehicle (0.9% saline in 100 μl volume) for hypothyroid group or 40 μg/100 g T4 with 4μg/100g T3 for hyperthyroid group. For MMI treatment, mice were provided with 0.05% methimazole and 1% potassium perchlorate in the drinking water for 4 weeks inducing hypothyroidism, adapted from established methods (Amma et al., 2001). To induce hyperthyroidism, half of the groups were given T3 at 5 μg/ml in the same drinking water (MMI+T3).

extract_protocol:
HA-TRβ and H3K27ac ChIP-seq were performed as previously described (Armour et al., 2017). Magnetic beads (Pierce) were used to perform the immunoprecipitation with H3K27ac antibody (Active Motif, Cat #: 39133) or HA aagnetic beads (Pierce) . For ChIP-seq of HA-TRβ, 3 biological replicates were used for sequencing, and WT mice were used as negative control.
The ChIP-seq library has been performed as previously described (Armour et al., 2017)

tag: tissue

value: Liver

tag: chip antibody

value: Pierce™ Anti-HA Magnetic Beads #88836


title: Tumor bone marrow deriived macrophage 3

tag: cell type

value: bone marrow derived

value: CD45+CD11b+Gr1+F4/80lo cells were isolated by Facs sorting from LLC tumors


title: CTRL_1

value: second heart field region

value: CTRL Mef2c-Cre


title: WT-16 h-replicate 3

description: Wild type small airway epithelial cells

value: human small airway epithelial cells (hSAEC)


title: WT-16 h-replicate 2

description: Wild type small airway epithelial cells


title: Blood QC13

description: Hybridized to Affymetrix SNP 6.0


title: Kit-Macrophage Progenitor 2

value: lung tumor

value: progenitor/Kit-

value: Sorted Gr1-F4/80hi cells cultured in methylcellulose + SCF,IL3, IL6 and sorted for cKit- cells


title: N1+/- + DMSO Replicate 1

value: DMSO


title: 12h-1


title: WT-16 h-replicate 1

description: Wild type small airway epithelial cells


title: WT + DMSO Replicate 3


title: WT + DMSO Replicate 2


title: Blood QC11

description: Hybridized to Affymetrix SNP 6.0

value: healthy control

value: blood


title: Tumor bone marrow deriived macrophage 2


title: ChIP-Seq:TR WT rep2

value: WT


title: Tumor bone marrow deriived macrophage 1


title: 6h-3


title: Blood QC10

description: Hybridized to Affymetrix SNP 6.0


title: 6h-4


title: Tumor tissue resident macrophage 3

value: tissue resident

value: CD45+CD11b+Gr1-F4/80hi cells were isolated by Facs sorting from LLC tumors


title: Blood QC9

description: Hybridized to Affymetrix SNP 6.0


title: 6h-2

value: Microglia


title: Blood QC8

description: Hybridized to Affymetrix SNP 6.0


title: Tumor tissue resident macrophage 2


title: 6h-1


title: Blood QC7

description: Hybridized to Affymetrix SNP 6.0


title: 4h-4


title: HMLER XIST-KO clone#2

city: Paris

first: Laia

last: Richart

address: 13 Rue Pierre et Marie Curie

department: Developmental Biology

institute: Institut Curie

data_processing:
The human reference genome hg19 was masked with a list of informative heterozygous SNPs on the X chromosome using BEDtools maskfasta (v2.2.2).
Fastq files were aligned to the human reference genome hg19, using the gene annotation from GENCODE and the aligner STAR (v2.7.0a) with the following parameters: --outFilterMultimapNmax 1 --outSAMattributes NH HI NM MD --alignEndsType EndToEnd.
For gene expression analyses, reads overlapping exons or genes (GENCODE annotation) were counted using FeatureCounts (Subread v1.5.1) with the following parameters: -t exon -g gene_name -p -B -C.
For allele-specific analyses, PCR duplicates were removed from mapped reads using Picard tools (v1.97) with the following parameters: REMOVE_DUPLICATES=true ASSUME_SORTED=true.
Remaining reads were then split by allele using SNPsplit (v0.3.2) (options: --paired) and reads overlapping informative SNPs were quantified using SAMtools (v1.9) mpileup.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data file "raw.counts.txt" contains raw counts overlapping exons and genes for non-transformed HMLE samples. VCF files contain the read counts overlapping heterozygous SNPs on the X chromosome.

source_name: HMLE

growth_protocol: HMLE/HMLER cells were cultured in DMEM:F-12/GlutaMAX supplemented with 10% FBS, 1% MEM Non-Essential Amino Acids, 1% Pen/Strep, 10 µg/ml insulin, 1 µg/mL hydrocortisone, and 10 ng/mL human epidermal growth factor (EGF).

extract_protocol:
RNA was isolated with Trizol-Chloroform followed by isopropanol precipitation.
RNA-Seq Libraries for HMLE cells were prepared by the Institut Curie Next Generation Sequencing Core Facility using the TruSeq Stranded mRNA kit (Illumina, ref. 20020594-5) according to manufacturer’s instructions and sequenced on an Illumina HiSeq 2500 (PE100). RNA-Seq libraries for HMLER cells were prepared using the Swift RNA Library Kit (Swift Biosciences, ref. R1024 and R1096) according to manufacturer’s instructions and sequenced on an Illumina NovaSeq 6000 (PE100).

treatment_protocol: Cells were tripsinized, resuspended in FACS buffer (PBS 1X, 1% BSA, 5mM EDTA), and stained with FACS-grade primary antibodies against ESA or a combination of CD44 and CD24. HMLE were FACS-sorted into two populations according to their ESA positivity. In the case of HMLER, only CD44+/CD24- cells (corresponding to CSCs) were selected for subsequent analyses.

value: HMLE transformed with oncogenic HRASG12V

value: XIST-KO

tag: cell compartment

value: Cancer Stem Cells


title: Blood QC12

description: Hybridized to Affymetrix SNP 6.0


title: Tumor tissue resident macrophage 1


title: Blood QC6

description: Hybridized to Affymetrix SNP 6.0


title: 4h-3


title: HMLER XIST-KO clone#1


title: 4h-2


title: 4h-1


title: HMLER WT


title: Blood QC5

description: Hybridized to Affymetrix SNP 6.0


title: HMLE WT ML No antibody CTRL

description: HMLE.WT.ML.no.Ab.bw

data_processing:
Library strategy: Cut&Run
Trimmed fastq files were aligned to the human reference genome hg19 using the Bowtie2 aligner (v2.2.5) with default parameters.
PCR duplicates were discarded using Picard tools (v1.97) with the option REMOVE_DUPLICATES=true.
bigWig files were created using deepTools bamCoverage (v3.0.2) with the following parameters: --normalizeUsingRPKM --ignoreForNormalization chrX chrY --samFlagInclude 64 --binSize 10 (H3K4me3/H3K4me1/H3K27Ac) / 30 (H3K27me3/H2AUb) --extendReads. Reads overlapping problematic, blacklisted regions from the Encode Consortium (wgEncodeDacMapabilityConsensusExcludable.bed) were excluded from the computation of coverage with the option ----blackListFileName.
bigWig files from biological replicates were merged with the UCSC tools (v2017.05.03) bigWigMerge and bedGraphToBigWig.
Peak calling for H3K4me1 and H3K27Ac Cut&Run-Seq data was done on bam files without PCR duplicates using MACS2 (v2.0.10) callpeak and the following parameters: -p 1e-05 --broad --broad-cutoff 1e-03. As control, cells processed as in the Cut&Run protocol but without primary antibody were used (option -c).
To map enhancers, consensus lists of H3K4me1 and H3K27Ac peaks were generated by pooling together data from all compartments and genotypes analyzed. Overlapping peaks were merged using BEDtools merge (v2.2.2) and the consensus lists for H3K27Ac and H3K4me1 were intersected using BEDtools intersect (v2.2.2).
Peaks were annotated using HOMER annotatePeaks.pl (v4.3) and those within +/- 3kb windows around TSS were discarded.
For the allele-specific analysis of H3K27Ac and H3K4me3 Cut&Run-Seq data, trimmed fastq files were aligned to an N-masked version of the human reference genome (hg19) at positions of heterozygous SNPs on the X chromosome using the Bowtie2 aligner (v2.2.5) with the parameters -q -N 1 -L 22 --end-to-end.
PCR duplicates were discarded using Picard tools (v1.97) with the option REMOVE_DUPLICATES=true.
Remaining reads were then split by allele using SNPsplit (v0.3.2) (options: --paired), which uses SAMtools (v1.9).
Reads overlapping informative SNPs were quantified using SAMtools (v1.9) mpileup.
Genome_build: hg19
Supplementary_files_format_and_content: bigWigs result from the merging of 2 biological replicates. VCF files summaryze the number of counts overlapping each heterozygous SNP on the X chromosome.
Supplementary_files_format_and_content: broadPeak files map the genome-wide distribution of peaks for H3K4me1 and H3K27Ac. "isec.EH.bed" lists the genomic coordinates of enhancers based on H3K4me1 and H3K27Ac enrichment.

growth_protocol: HMLE cells were cultured in DMEM:F-12/GlutaMAX supplemented with 10% FBS, 1% MEM Non-Essential Amino Acids, 1% Pen/Strep, 10 µg/ml insulin, 1 µg/mL hydrocortisone, and 10 ng/mL human epidermal growth factor (EGF).

extract_protocol:
Cut&Run was performed as described previously (Skene et al. 2018). Briefly, 4-5*105 HMLE cells, together with 0.25*105 D. melanogaster Schneider 2 cells, were washed twice
with Wash buffer (20 mM HEPES pH=7.5, 150 mM NaCl, 0.5 mM spermidine) supplemented with protease inhibitors. Cells were then resuspended in Binding buffer (20 mM
HEPES pH=7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2) containing 10 µL of blocked BioMag®Plus Concanavalin A-coated beads (Polysciences, ref. 86057). After 10 min at RT, cells:beads were transferred to 50 µL of Antibody solution
(1:100 dilution of primary antibody in Wash buffer plus 0.1% digitonin [Millipore, ref. 300410-5GM]) and incubated for 1 h at RT on an end-to-end rotator. Cells:beads were washed three times with Wash buffer-0.1% digitonin and incubated for 10 min with pA-MNase diluted in Wash buffer-0.1% digitonin (produced by the Protein Expression and Purification Core Facility of Institut Curie). After three additional washes in Wash buffer-0.1% digitonin, tubes were placed in an ice/water bath and equilibrated to 0°C for 10 min. To trigger digestion of the DNA, CaCl2 was added (2 mM final concentration) for 30 min. Digestion was stopped by addition of 2X STOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.02% digitonin, 1:200 RNase A [50 μg/mL final concentration]). Digested DNA fragments were released from cells by incubating sample tubes on a heat block at 37 °C for 10 min. The supernatant was then recovered by placing tubes on a magnetic stand and DNA was purified using the NucleoSpin Gel and PCR Clean‑up kit (Macherey Nagel, ref. 740609).
Cut&Run-Seq libraries were prepared using the Accel-NGS 2S Plus DNA library kit (Swift Biosciences, ref. 21096) according to manufacturer’s instructions, and sequenced on an Illumina Novaseq 6000 (PE100) at the Institut Curie Next Generation Sequencing Core Facility.

treatment_protocol: Cells were tripsinized, resuspended in FACS buffer (PBS 1X, 1% BSA, 5mM EDTA), and stained with the FACS-grade primary antibody against ESA. HMLE were FACS-sorted into two populations according to their ESA positivity. FACS-sorted cells were expanded in culture for 48-72h and then processed for Cut&Run-Seq.

value: Immortalized human mammary epithelial cells

value: ML (ESA+)


title: Blood QC3

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC4

description: Hybridized to Affymetrix SNP 6.0


title: HMLE KO ML H2AUb rep2


title: Blood QC2

description: Hybridized to Affymetrix SNP 6.0


title: HMLE KO ML H2AUb rep1


title: Blood QC1

description: Hybridized to Affymetrix SNP 6.0


title: myoblasts-GREM1 stimulated repl 03

type: RNA

city: Lyon

first: Fabien

last: Le Grand

address: 8 avenue Rockefeller

department: Melis

institute: Institut Neuromyogene

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA was hybridized to GeneChip® Mouse Gene 2.0 ST (Affymetrix) at 45°C for 17 hours. After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix)

scan_protocol: GeneChips were scanned using the affymetrix GCS3000 7G system

data_processing: The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment. Affymetrix probe-set data were normalized using the robust multi-array average (RMA) method using R. Analysis done with custom CDF: mogene20st_Mm_ENTREZG_v19_9_2

source_name: GREM1-treated myoblasts

label_protocol: 2.5μg of Sens Target DNA were fragmented and biotin labelled using Encore Biotin Module kit (Nugen).

growth_protocol: Satellite cells-derived myoblasts were cultured on collagen-coated dishes in Ham's-F10 nutrient mix supplemented with 20% FBS and 2.5ng/ul basic FGF

extract_protocol: RNA extraction was performed by using the TRIzol Reagent (Life Technologies) according to manufacturer's instructions. 50 ng of total RNA was reverse transcribed following the Ovation PicoSL WTA System (Nugen). The resulting double strand cDNA was used for amplification based on SPIA technology. After purification according to Nugen protocol, 5ug of single strand DNA was used for generation of Sens Target DNA using Ovation Exon Module kit (Nugen).

treatment_protocol: Myoblasts were stimulated with 100ng/ml BMP4 protein, or 500ng/ml GREM1 protein in DMEM medium supplemented with 2% Horse serum.

value: skeletal muscle

value: satellite cells


title: 0h-2


title: myoblasts-GREM1 stimulated repl 02


title: HMLE KO MaSC H2AUb rep2

value: MaSC (ESA-)


title: 0h-1


title: myoblasts-BMP4 stimulated repl 03

source_name: BMP4-treated myoblasts


title: myoblasts-BMP4 stimulated repl 02


title: HMLE KO MaSC H2AUb rep1


title: HMLE WT ML H2AUb rep2


title: myoblasts-GREM1 stimulated repl 01


title: 0h-4


title: B-NC-YB1_1

city: Chongqing

first: Junyi

last: Yu

address: 10th Changjiangzhilu Road, Yuzhong District

department: Department of Cardiology

institute: Daping Hospital, The Third Military Medical University, Chongqing, P.R. China.

data_processing:
Fastqs were qualified by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and they were mapped to UCSC reference genome Rnor.6.0 using Bowtie2
SAMtools was used to manipulate SAM files into sorted BAM files
To capture ChIP signals, MACS2 was applied with the option qvalue cutoff = 0.05
Peaks were annotated by annotatePeaks.pl in Homer using Rat gtf files from ENSEMBL.
Genome_build: Rnor6

organism: Rattus norvegicus

source_name: A10 cell (ATCC CRL-1476)

growth_protocol: Rat thoracic aortic vascular smooth muscle A10 cells was purchased from ATCC (CRL-1476), and cultured in Dulbecco's Modified Eagle's Medium supplemented with 10% FBS, 100U/mL penicillin and 100g/mL streptomycin at 37 °C in a 95% air-5% CO2 atmosphere.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
NEBNext ChIP-seq library prep master mix set for Illumina was used to prepare the sequencing library with custom-synthesized primers (Wang et al., 2019). 50 nt single end reads (Arteridin ChIP-Seq) were generated on Illumina Hiseq 2500 platform and 150bp pair end reads (YBX1 ChIP-Seq) were generated on Illumina HiSeq X Ten.

treatment_protocol: Lipofactamine 3000 was used for plasmid transfection.

value: aorta, thoracic/medial layer

tag: passages

value: YBX1 (abcam ab12481, CST D299, MBL RN015P)


title: Apc Kras MYC Combo treated sample 3

city: Glasgow

first: Andrew

last: Campbell

address: Switchback Road

country: United Kingdom

institute: CRUK Beatson Institute

data_processing:
Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences and low-quality base calls, defined as those with a Phred score of less than 20, using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.98 using HISAT2 version 2.1.0
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Genome_build: GRCm38.98
Supplementary_files_format_and_content: Matrix of raw counts

source_name: Whole Intestine

extract_protocol:
1cm of proximal intestine was collected and dissociated using Precyllis homogeniser in b-ME in RLT buffer.  RNA was extracted using Qiagen RNA extraction kit following manufacturer's instructions.
Libraries for cluster generation and DNA sequencing were prepared following a previously described method (Fisher et al. 2011) using TruSeq RNA sample prep kit v2 (Illumina)
The libraries were run on Illumina Next Seq using the High Output 75 cycles kit (2x36 cycles, paired end reads, single index)

value: VillinCreER Apc fl/fl Kras G12D/+ Rosa26-lsl-MYC

tag: treatment


title: Apc Kras MYC Combo treated sample 4

tag: genotype


title: 0h-3


title: Apc Kras MYC Combo treated sample 2


title: B-YB1-INPUT


title: HMLE WT ML H2AUb rep1


title: myoblasts-BMP4 stimulated repl 01


title: Apc Kras MYC Combo treated sample 1


title: X-ART-YB1


title: myoblasts-control repl 03

source_name: mock-treated myoblasts


title: HMLE WT MaSC H2AUb rep2


title: myoblasts-control repl 02


title: Arabidopsis roots_KI

city: San Giuliano Terme

first: Pierdomenico

last: Perata

state: Pisa

address: Via Guidiccioni 8-10

department: Institute of Life Sciences

country: Italy

institute: Sant'Anna School of Advanced Studies

hyb_protocol: GeneChip Hybridization, Wash, and Stain Kit

scan_protocol: GeneChip Scanner 3000 7G

data_processing: Microarray Suite 5.0

source_name: Arabidopsis roots_KI

label_protocol: GeneChip  3' IVT PLUS Reagent Kit

growth_protocol: Arabidopsis plants grown in hydroponic system

extract_protocol: Total RNA was extracted as previously described (Perata et al., Plant Cell, 1997) with a minor modiﬁcation (omission of aurintricarboxylic acid)

treatment_protocol: Plants were hydroponically grown on the base nutrient solution (control plants; iodine concentration in the base nutrient solution was 8 nM, as a contaminant) or in the same medium to which 10 µM of KBr, NaI or KI was added. Sampling was performed 48 h after the beginning of the treatment.

value: Roots

tag: age

value: 3 weeks old

value: 10 µM of KI added to the base nutrient solution


title: HMLE KO ML H3K27me3 rep2


title: HMLE WT MaSC H2AUb rep1

value: WT


title: Apc Kras MYC sample 2

value: Untreated


title: Arabidopsis roots_NaI

source_name: Arabidopsis roots_NaI

value: 10 µM of NaI added to the base nutrient solution


title: Arabidopsis roots_Control

source_name: Arabidopsis roots_Control

value: Control_untreated plants


title: Arabidopsis roots_KBr

source_name: Arabidopsis roots_KBr

value: 10 µM of KBr added to the base nutrient solution


title: X-PSR-YB1


title: PAM_rep4

city: shanghai

first: jing

last: zhao

address: Qiuyue Road

institute: IRCBC

data_processing:
For RNA-Seq comparison, Sequencing reads were mapped to rat with STAR by default parameter. The read counts for each genes were calculated by featurecounts. The count files were used as input to DESeq2 for differential expression analysis.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: DESeq was used for calling differential expression.tab-delimited text files include normalized read counts,foldChange,pvalue

source_name: rat

extract_protocol:
Total RNA was extracted and purified using RNAiso Plus (TaKaRa)
RNA libraries were prepared according to instructions of Vazyme VAHTS mRNA-seq V3 Library Prep Kit for Illumina(NR611-01)

value: SD

value: brain

value: DIV 18

value: wild type


title: Arabidopsis leaves_NaI

source_name: Arabidopsis leaves_NaI

value: Leaves


title: myoblasts-control repl 01

value: skeletal muscle

value: satellite cells


title: Apc Kras sample 3

value: VillinCreER Apc fl/fl Kras G12D/+


title: Apc Kras MYC sample 1

value: VillinCreER Apc fl/fl Kras G12D/+ Rosa26-lsl-MYC


title: PAM_rep3


title: Apc Kras sample 2


title: PAM_rep2


title: Arabidopsis leaves_KBr

source_name: Arabidopsis leaves_KBr


title: Arabidopsis leaves_Control

source_name: Arabidopsis leaves_Control


title: HMLE WT ML H3K27me3 rep2

value: Immortalized human mammary epithelial cells

value: ML (ESA+)


title: PAM_rep1


title: veh_rep4


title: Apc Kras Combo treated sample 3


title: Arabidopsis leaves_KI

source_name: Arabidopsis leaves_KI

value: 3 weeks old

value: 10 µM of KI added to the base nutrient solution


title: HMLE WT ML H3K27me3 rep1

value: WT


title: HMLE WT MaSC H3K27me3 rep2

value: MaSC (ESA-)


title: Apc Kras Combo treated sample 2


title: HMLE KO ML H3K27me3 rep1

value: XIST-KO


title: Apc Kras Combo treated sample 1


title: HMLE WT MaSC H3K27me3 rep1


title: HMLE KO MaSC H3K27me3 rep2


title: veh_rep2


title: HMLE KO ML H3K4me3 rep2


title: Apc Kras Vehicle treated sample 4

value: Vehicle


title: veh_rep1

value: SD


title: TH17Ag_WT_rep_1 [re_analysis]

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

description: agTh17 cell cultures

hyb_protocol: Labeled RNA was dried and resuspended with Hybridization  Buffer and Blocking Agent, incubated 5 min at 100ºC and transferred to an ice water bath for 5 min. Samples were hybridized in a volume of 45ul to the Mouse miRNA Microarray, 8x15K (Agilent) for 20 hours at 55°C and 20rpm. Microarrays were then washed at room temperature for 5 min in Gene Expression Wash Buffer 1 and 5 min at 37ºC in Gene Expression Wash Buffer 2 (Agilent Technologies; Palo Alto, CA).

scan_protocol: Arrays were scanned on an Agilent G2565A microarray scanner under default settings recommended by Agilent Technologies for miRNA microarrays with 100% PMT and 5μm resolution. Data was extracted using Agilent Feature Extraction software 10.1.1.1.

data_processing: Data files were then imported into GeneSpring® GX software version 10. (Agilent Technologies) and quantile normalization was performed. Probes were flagged (Present, Marginal, Absent) using GeneSpring® default settings and filtered for further analysis according to expression (all miRNAs which raw expression levels are within the range 20%-100% of expression in 75% replicates of at least one condition were retained) and flags (all miRNAs flagged as Present or Marginal in 75% replicates of at least one condition were retained). To determine statistically significant differences between both conditions, moderated t-test using the limma package from Bioconductor was applied to the filtered data. Benjamini-Hochberg p-value correction was used for control of the False Discovery Rate (FDR or Corrected p-value)

source_name: Spleen and mesenteric lymph nodes

label_protocol: 100ng of total RNA from each sample was dephosphorylated with Calf Intestinal Alkaline Phosphatase (CIP) at 37ºC for 30’ following a denaturalization and then a ligation for 2h at 16ºC using Agilent miRNA Complete Labeling and Hyb Kit (Agilent Technologies; Palo Alto, CA). In this step a molecule of Cyanine3-pCp is incorporated to the 3’ end of RNA molecules.

extract_protocol: MicroRNA were extracted with miRNeasy minikit (Qiagen) as recommended by the manufacturer's. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Spleen and mesenteric lymph nodes were collected and incubated with mouse biotin conjugated antibodies against IgM, B220, CD19, MHCII, CD11c, CD11b, CD44, CD8a, Dx5a (Pharmingen, BD). Naive CD4+ T cells were purified by negative selection using Streptavidin Microbeads (Miltenyi Biotec) and LD columns (Miltenyi Biotec) as indicated by manufacturer. Cells were cultured with TGFbeta and IL-6 and in the presence of OVA.

tag: background

value: OTII mice

value: Spleen and mesenteric lymph nodes

value: WT Antigen specific Th17 cell culture


title: Apc Kras Vehicle treated sample 3


title: HMLE KO MaSC H3K27me3 rep1


title: Apc Kras sample 1

value: Untreated


title: CD4_WT_rep_1

scan_protocol: Arrays were scanned on an Agilent G2565A microarray scanner under default settings recommended by Agilent Technologies for miRNA microarrays with 100% PMT and 5μm resolution. Data was extracted using Agilent Feature Extraction software 10.7.3.1 (for raw files with Grid_Name = 019119_D_F_20091030) or 10.1.1.1 (for raw files with Grid_Name = 019119_D_20081121).

source_name: WT CD4+ Tcells

treatment_protocol: Spleen and mesenteric lymph nodes were collected and incubated with mouse biotin conjugated antibodies against IgM, B220, CD19, MHCII, CD11c, CD11b, CD44, CD8a, Dx5a (Pharmingen, BD). Naive CD4+ T cells were purified by negative selection using Streptavidin Microbeads (Miltenyi Biotec) and LD columns (Miltenyi Biotec) as indicated by manufacturer. Cells were cultured with TGFbeta and IL-6 and in the presence of OVA for the agTH17 cultures.

tag: strain background

value: wild type BALB/c

value: WT CD4+ Tcells


title: TH17Ag_WT_rep_5

source_name: Sorted WT Antigen specific Th17 cells

value: OTII BALB/c

value: Sorted WT Antigen specific Th17 cells


title: TH17Ag_WT_rep_4


title: TH17Ag_WT_rep_3


title: TH17Ag_cd69KO_rep_1

description: agTh17 cell cultures

value: cd69-/- OTII mice

value: cd69-/- Antigen specific Th17 cell culture


title: TH17poli_WT_rep_1

source_name: WT polyclonal Th17 cell culture

value: WT polyclonal Th17 cell culture


title: veh_rep3

value: brain

value: DIV 18

value: wild type


title: Apc Kras Vehicle treated sample 2

value: VillinCreER Apc fl/fl Kras G12D/+


title: Apc Kras Vehicle treated sample 1

value: Vehicle


title: HMLE KO MaSC H3K4me3 rep2

source_name: HMLE

value: Immortalized human mammary epithelial cells

value: XIST-KO

value: MaSC (ESA-)


title: HMLE KO MaSC H3K4me3 rep1


title: TH17Ag_WT_rep_2

value: Spleen and mesenteric lymph nodes


title: HMLE WT ML H3K4me3 rep2

value: WT

value: ML (ESA+)


title: Il4raF709_STAT6-KO_rep3

city: Boston

first: Talal

last: Chatila

state: MA

address: 1 Blackfan Circle

department: Division of Immunology

institute: Boston Children’s Hospital

data_processing:
Paired-end sequencing reads were aligned to the mouse  reference genome (mm10) using bowtie aligner version 2.2.9, followed by removal of reads with multiple alignments as well as reads mapping  to mitochondrial DNA.
De-duplication of reads was performed with picard (v2.8.0).  makeTagDirectory command of Homer package (v4.9) was used to create the tag  directory followed by identification of peaks using the ‘factor’ parameter in the findPeaks  command.
For visualization of ATAC-seq data, replicate specific bam output files from  picard were merged and converted into normalized bigwig format using the bamCoverage function in  deepTools with options  – fragmentLength 200 –normalizeUsingRPKM, and bigwig file was visualized on Integrative Genomics Viewer (IGV).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol:
MLNs were isolated and homogenized in PBS containing 2% FCS buffer. Cells were washed once with PBS containing 2% FCS stained and used for sorting. 20,000 live Treg cells were sorted and used for ATAC-seq experiments.
20,000 Treg cells/sample were used for preparation of ATAC-seq libraries  according to the protocol described previously; however, with few modifications  (Buenrostro et al., 2015). Briefly, cells were suspended in 100ul of cold hypotonic lysis  buffer [10mM Tris-HCl (pH 7.5), 10mM NaCl, 3mM MgCl2 and 0.5% NP40], followed by  immediate centrifugation at 550g for 30 min and re-suspension of the pellet in 5ul of  transposition reaction mix [1ul of Tagment DNA Enzyme and 2.5uL of Tagment DNA  Buffer from Nextera DNA Sample Prep Kit (Illumina), 1.5ul H2O]. The transposition  reaction was incubated for 60 min at 37°C which led to fragmentation and tagging of DNA.  For library preparation, 7-cycles of PCR were performed followed by selection of small  fragments (less than 600bp) using SPRI beads. A second round of PCR (7-cycles) with  similar conditions was performed in order to obtain the final library. Libraries were  sequenced on the NextSeq 500 instrument to generate paired-end short reads (50bp,  forward; 33bp, reverse).

tag: genotype/variation

value: regulatory T (Treg) cells


title: CrebA-GFP_sage-Gal4 input

city: Duluth

first: Matthew

last: Slattery

state: MINNESOTA

address: 1035 University Drive, SMed 219

institute: University of Minnesota Medical School

description: GFP-tagged CrebA transcription factor driven by sage-Gal4 driver

data_processing:
ChIP-seq reads were aligned to the dm6 genome assembly using BWA (Galaxy Tool Version 0.2.3) with default settings.
Replicates were merged using SamMerge (Galaxy Tool Version 1.1.2)
Peaks were called using MACS version 2.1.0.20140616 with a qvalue cutoff of 5.00e-02.
dm6
Genome_build: bed

organism: Drosophila melanogaster

source_name: Stage 11-16 embryos

growth_protocol: Embryos were collected for 8h at RT and allowed to age for 11 hours prior to their isloation.

extract_protocol:
Chromatin from two independent collections of stage 11-16 embryos were crosslinked at RT in 1.8% formaldehyde and homogenized for chromatin extraction. Anti-GFP antibody or anti-CrebA antiserum were used for immunoprecipitation.
Input and immunoprecipitated DNA were prepared for sequencing using the Illumina TruSeq ChIP Sample Preparation Kit per the manufacturer's instructions. Library construction was performed by the UCLA Technology Center for Genomics & Bioinformatics.

tag: antibody


title: CrebA-GFP_sage-Gal4 IP

value: anti-GFP


title: Il4raF709_STAT6-KO_rep2


title: CrebA-GFP_fkh-Gal4 input

description: GFP-tagged CrebA transcription factor driven by fkh-Gal4 driver


title: Il4raF709_STAT6-KO_rep1


title: HMLE WT MaSC H3K4me3 rep2


title: HMLE WT ML H3K4me3 rep1


title: HMLE KO ML H3K4me3 rep1


title: CrebA-GFP_fkh-Gal4 IP


title: CrebA_OregonR input

description: Untagged CrebA (Wild-type Oregon R embryos)

value: Oregon R


title: Il4raF709_rep2


title: HMLE WT MaSC H3K4me3 rep1


title: CrebA_OregonR IP

value: anti-CrebA


title: Control_rep3

value: Control


title: HMLE KO ML H3K27Ac rep2

description:
isec.EH.bed
HMLE.KO.ML.H3K27Ac.bw


title: HMLE KO ML H3K27Ac rep1

description:
isec.EH.bed
HMLE.KO.ML.H3K27Ac.bw


title: TH17Ag_WT_rep_1

source_name: WT Antigen specific Th17 cell culture

value: OTII BALB/c

value: WT Antigen specific Th17 cell culture


title: Control_rep2


title: Control_rep1


title: BEL7402 PRMT6 knockdown

city: Hong Kong

first: Stephanie

last: Ma

address: Rm 47, 1/F, Lab Block, Faculty of Medicine Bldg, 21 Sassoon Rd, Pok Fu Lam

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

description: Gene expression

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1 .

source_name: BEL7402 cells

label_protocol: Labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

growth_protocol: BEL7402 cells were grown in DMEM supplemented with 10% FBS and 1% penicillin and streptomycin.

extract_protocol: Total RNA extracted using Qiagen kit according to manufacturer's extraction.

treatment_protocol: Cells were transduced with lentivirus containing either non-target control (NTC) or shPRMT6 (clone 956) and stable pooled clones were selected by puromycin selection.

tag: cell line

value: HCC

tag: lentivirus

value: shPRMT6 (clone 956)


title: HMLE KO MaSC H3K27Ac rep2

description:
isec.EH.bed
HMLE.KO.MaSC.H3K27Ac.bw


title: BEL7402 control

description: Gene expression

value: non-target control


title: HMLE WT ML H3K27Ac rep2

description:
isec.EH.bed
HMLE.WT.ML.H3K27Ac.bw


title: 256402110010_b1 - 27_7WT(2684)_S+_rep3 vs 31_7Mut(2684)_S+_rep3

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Role of sulfur and of the sulfate store in leaf metabolism.

hyb_protocol: 31_7Mut_S+_rep3 Cy5 / 27_7WT_S+_rep3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Lathyrus oleraceus

source_name: 31_7Mut_S+_rep3 allele 2684

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, total RNA  .

growth_protocol: caulin leaf - Media:Perlite (2/3) and sand B3 (1L pot) Temperature: 18 °C Light:16h/day

treatment_protocol: Name:Sulfur efficiency - environmental treatment - sulfur concentration,sulfur:quantity 0.3mM .

value: cauline leaf

tag: cultivar

value: cameor

value: PsSultr4 mutant

tag: harvest date

source_name: 27_7WT_S+_rep3 allele 2684

value: wildtype


title: 256402110010_b2 - 31_7Mut(2684)_S+_rep3 vs 27_7WT(2684)_S+_rep3

hyb_protocol: 27_7WT_S+_rep3 Cy5 / 31_7Mut_S+_rep3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 256402110010_b3 - 28_8WT(2684)_S+_rep4 vs 32_8Mut(2684)_S+_rep4

hyb_protocol: 32_8Mut_S+_rep4 Cy5 / 28_8WT_S+_rep4 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 32_8Mut_S+_rep4 allele 2684

source_name: 28_8WT_S+_rep4 allele 2684


title: HMLE WT ML H3K27Ac rep1

description:
isec.EH.bed
HMLE.WT.ML.H3K27Ac.bw

value: Immortalized human mammary epithelial cells


title: 256402110010_b4 - 32_8Mut(2684)_S+_rep4 vs 28_8WT(2684)_S+_rep4

hyb_protocol: 28_8WT_S+_rep4 Cy5 / 32_8Mut_S+_rep4 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 256402110009_b4 - 28_8WT(2684)_S+_rep4 vs 12_8WT(2684)_S-_rep4

hyb_protocol: 12_8WT_S-_rep4 Cy5 / 28_8WT_S+_rep4 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 12_8WT_S-_rep4 allele 2684

treatment_protocol: Name:Sulfur deficiency - environmental treatment - sulfur concentration,sulfur:quantity 0mM .


title: HMLE KO MaSC H3K27Ac rep1

description:
isec.EH.bed
HMLE.KO.MaSC.H3K27Ac.bw

value: XIST-KO

value: MaSC (ESA-)


title: f81753, ko/ko

city: Heidelberg

first: Axel

last: Roers

address: Im Neuenheimer Feld 305

department: Institute of Immunology

country: Germany

institute: Heidelberg University Hospital

data_processing:
Alignment of the samples with GSNAP (version 2018-07-04) to the mm10 reference, and using Ensembl 87 for the support of splicesite detection
featureCounts (version1.6.2) was used to assign the reads to genes with the help of Ensembl 87 annotation
Genome_build: mm10
Supplementary_files_format_and_content: featureCounts.mm10.E87.csv.gz This is a "," separated text file, containing the following columns: GeneID, Chromosome, Start, End, Strand, Length, followed by the 9 samples

source_name: purified CD45- CD49f+ epidermal cells

extract_protocol:
epidermal cells were isolated accoring  to Ghouse et al., Cell Rep. 2018 Jan 2;22(1):27-35. doi: 10.1016/j.celrep.2017.12.010. CD45- CD49f+ cells were FACS-sorted for RNA extraction.
Polyadenylated RNA was reverse transcribed and amplified with 13 cycles using the SMARTseq2 protocol, before subjecting 3 ng of the cDNA to a tagmentation based library preparation (TruePrep DNA Library Prep Kit V2 for Illumina, Vazyme) followed by sequencing on a Nextseq500 to sequencing depth of 30 Mio. reads.

tag: flg genotype

value: ko/ko

value: purified CD45- CD49f+ epidermal cells


title: f82199, ko/ko


title: f81751, ko/ko


title: f81501, ko/ko


title: Il4raF709_rep1

tag: strain

value: regulatory T (Treg) cells


title: HMLE WT MaSC H3K27Ac rep2

description:
isec.EH.bed
HMLE.WT.MaSC.H3K27Ac.bw

value: WT


title: HMLE WT MaSC H3K27Ac rep1

description:
isec.EH.bed
HMLE.WT.MaSC.H3K27Ac.bw


title: f83039, wt/wt

value: wt/wt


title: 256402110009_b3 - 12_8WT(2684)_S-_rep4 vs 28_8WT(2684)_S+_rep4

hyb_protocol: 28_8WT_S+_rep4 Cy5 / 12_8WT_S-_rep4 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: tissue


title: HMLE KO ML H3K4me1 rep2

description:
isec.EH.bed
HMLE.KO.ML.H3K4me1.bw

tag: cell type

value: ML (ESA+)


title: f83038, wt/wt


title: 256402110009_b2 - 25_5WT(2684)_S+_rep1 vs 9_5WT(2684)_S-_rep1

hyb_protocol: 9_5WT_S-_rep1 Cy5 / 25_5WT_S+_rep1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 9_5WT_S-_rep1 allele 2684

source_name: 25_5WT_S+_rep1 allele 2684


title: 256402110008_b4 - 19_3WT(4693)_S+_rep3 vs 4_4WT(4693)_S-_rep4

hyb_protocol: 4_4WT_S-_rep4 Cy5 / 19_3WT_S+_rep3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 4_4WT_S-_rep4 allele 4693

source_name: 19_3WT_S+_rep3 allele 4693


title: 256402110008_b2 - 17_1WT(4693)_S+_rep1 vs 1_1WT(4693)_S-_rep1

hyb_protocol: 1_1WT_S-_rep1 Cy5 / 17_1WT_S+_rep1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 1_1WT_S-_rep1 allele 2684

source_name: 17_1WT_S+_rep1 allele 2684


title: 256402110007_b4 - 16_8Mut(2684)_S-_rep4 vs 12_8WT(2684)_S-_rep4

hyb_protocol: 12_8WT_S-_rep4 Cy5 / 16_8Mut_S-_rep4 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 16_8Mut_S-_rep4 allele 2684


title: 256402110008_b1 - 1_1WT(4693)_S-_rep1 vs 17_1WT(4693)_S+_rep1

hyb_protocol: 17_1WT_S+_rep1 Cy5 / 1_1WT_S-_rep1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 256402110009_b1 - 9_5WT(2684)_S-_rep1 vs 25v_5WT(2684)_S+_rep1

hyb_protocol: 25_5WT_S+_rep1 Cy5 / 9_5WT_S-_rep1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: HMLE KO ML H3K4me1 rep1

description:
isec.EH.bed
HMLE.KO.ML.H3K4me1.bw

source_name: HMLE

tag: cell compartment


title: 256402110008_b3 - 4_4WT(4693)_S-_rep4 vs 19_3WT(4693)_S+_rep3

hyb_protocol: 19_3WT_S+_rep3 Cy5 / 4_4WT_S-_rep4 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: HMLE KO MaSC H3K4me1 rep1

description:
isec.EH.bed
HMLE.KO.MaSC.H3K4me1.bw


title: f82649, wt/wt


title: f80726, wt/wt


title: HMLE KO MaSC H3K4me1 rep2

description:
isec.EH.bed
HMLE.KO.MaSC.H3K4me1.bw


title: Genomic DNA from FF breast tumor tissue_16823

city: Buffalo

first: Yao

last: Song

state: NY

address: Carlton House - A349, Elm and Carlton Streets

institute: Roswell Park Comprehensive Cancer Center

description: Tumor

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip (GPL13534) using standard Illumina protocol

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

data_processing:
The raw intensity IDAT files were extracted using GenomeStudio,and processed by the minfi R package. Only loci with a median detection p value <0.05 were retained for analysis, and only samples with detection p values < 1.0E-05 at more than 75% of CpG lici passed the performance criteria for inclusion. Probes containing SNPs and/or those that were ambiguously mapped were excluded from the analysis. The final dataset contained 276,108 CpG loci across 138 samples.
The signal_intensities.txt contains unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Flash frozen breast tumor tissue

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using a MasterPure DNA purification kit (Epicentre).

tag: gender

value: Female

value: Flash frozen breast tumor tissue


title: Genomic DNA from FF breast tumor tissue_19268

description: Tumor


title: Genomic DNA from FF breast tumor tissue_14944

description: Tumor


title: 256402110007_b3 - 12_8WT(2684)_S-_rep4 vs 16_8Mut(2684)_S-_rep4

hyb_protocol: 16_8Mut_S-_rep4 Cy5 / 12_8WT_S-_rep4 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: f80725, wt/wt


title: HMLE WT ML H3K4me1 rep2

description:
isec.EH.bed
HMLE.WT.ML.H3K4me1.bw


title: AMoh_TS

city: Columbia

first: Mitzi

last: Nagarkatti

state: SC

address: 6439 Garners Ferry Rd

department: PMI

institute: University of South Carolina School of Medicine

data_processing:
Base call files generated from the Illumina NextSeq 550 were demultiplexed using the cellranger mkfastq command. This pipeline uses bcl2fastq
Single cell feature counts files for each library were generated by running the cellranger count command on the demultiplexed fastq files.
The filtered gene matrices data output from the cellranger count pipeline were loaded into the Seurat package on R studio.
Cell qaulity was measured in Seurat using QC metrics that determined feature, count, and mitochondria read percentage per cell.
Data was scaled, normalized, clustered, and differential expression determined using the Seurat package in R studio.
Genome_build: mm10

source_name: lung single cell suspension

growth_protocol: Acute respiratory distress syndrome was induced in 6-8 week old mice by exposing mice to dual dose model of SEB. Mice were treated daily for 3 days with vehicle or 10 mg/kg each (i.p) of THC starting immediately after SEB exposure.

extract_protocol:
Single cell suspensions were processed for single-cell RNA by 10X Genomics Chromium Controller and 5' Gene Expression Kit.
Sequencing libraries were generated with 10X Genomics Chromium i7 Indexing Kit.
Paired-end sequencing of 26bp x 91bp was performed on an Illumina NextSeq 550.

treatment_protocol: Single cell suspension was prepared by mechanical and enzymatic breaking down the lung tissue and then the viability of isolated cells were evaluated by using trypan blue stain.

tag: s sex

value: female

tag: disease state

value: Treated group


title: HMLE WT ML H3K4me1 rep1

description:
isec.EH.bed
HMLE.WT.ML.H3K4me1.bw

tag: genotype


title: AMoh_S

value: Disease group


title: 256402110007_b2 - 15_7Mut(2684)_S-_rep3 vs 11_7WT(2684)_S-_rep3

hyb_protocol: 11_7WT_S-_rep3 Cy5 / 15_7Mut_S-_rep3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 11_7WT_S-_rep3 allele 2684

value: cauline leaf

value: cameor

source_name: 15_7Mut_S-_rep3 allele 2684


title: HMLE WT MaSC H3K4me1 rep2

description:
isec.EH.bed
HMLE.WT.MaSC.H3K4me1.bw


title: Genomic DNA from FF breast tumor tissue_17034

description: Tumor


title: Genomic DNA from FF breast tumor tissue_18800

description: Tumor


title: 4T1_ITGAV-gRNA4-UT-2

first: Archis

last: Bagati

state: MASSACHUSETTS

address: 450 brookline ave.

institute: Dana-Farber Cancer Institute

description:
ITGAV-gRNA-2 versus Control
20181220_4T1_ITGAV-gRNA4-UT-2_20181205_IDXH10_RV6429_S5

data_processing:
Statistics for differentially expressed genes were calculated using DESeq2 (version 3.5) (47) and Cufflinks (48).  Differential gene expression was analyzed using the DESeq2 (1.8.1) package in R using default settings (47). Principal component analyses were generated using the prcomp function in R and plotted with ggplot2. Human and mouse gene homologues were matched using the Mouse Genome Informatics annotation. Heatmaps were generated using the heatmap.2 function in R
Genome_build: hg19; mm9
Supplementary_files_format_and_content: Differential gene expression

growth_protocol: The base medium for this cell line is ATCC-formulated RPMI-1640 Medium, ATCC 30-2001. To make the complete growth medium, add the following components to the base medium: fetal bovine serum (ATCC 30-2020) to a final concentration of 10%.

extract_protocol:
Total RNA was extracted from control, SOX4 or ITGAV edited human BT549 and murine 4T1 cells cultured in complete RPMI media in biological triplicates.  RNA extraction was performed using the RNeasy Plus Mini Kit (Qiagen # 74134) following the manufacturer’s protocol. Total RNA was quality-checked using an Agilent BioAnalyzer 2000 instrument.  RNA with an integrity number of greater than 9.5 was used for subsequent analyses.
Libraries were prepared with TruSeq RNA Sample Prep Kit v2 (Illumina). Library concentrations were quantified by Qubit (Invitrogen) and mixed equally for single-end 75bp sequencing using an Illumina NextSeq 500 instrument.

value: murine TNBC cells

value: ITGAV-edited


title: HMLE WT MaSC H3K4me1 rep1

description:
isec.EH.bed
HMLE.WT.MaSC.H3K4me1.bw

value: Immortalized human mammary epithelial cells


title: Genomic DNA from FF breast tumor tissue_18793

description: Tumor


title: ES2 prexasertib-resistant cells replicate 2

first: Huy

last: Nguyen

state: Massachusetts

address: 450 Brookline Ave

department: Radiation Oncology

description:
ES2_prexR_P7_again_2
20191108_ES2_prexR_P7_again_2_KP7496_S20

data_processing:
RNAseq analysis was performed using the VIPER snakemake pipeline (Cornwell et al., 2018)
Sequenced reads were aligned to the UCSC hg19 reference genome assembly and gene counts were quantified using STAR (v2.7.3a)
Differential gene expression testing was performed by DESeq2 (v1.22.1), and limma (v3.38.3)
Genome_build: hg19
Supplementary_files_format_and_content: raw gene counts for every gene and every sample; DESeq2 and limma results

source_name: ES2 prexasertib-resistant cells

extract_protocol:
Total RNA was prepared using a Qiagen kit according to the manufacturer’s instructions
Libraries were prepared using Roche Kapa mRNA HyperPrep strand specific sample preparation kits from 200ng of purified total RNA according to the manufacturer’s protocol on a Beckman Coulter Biomek i7. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to the manufacturer’s protocols. Uniquely dual-indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NovaSeq 6000 with paired-end 50bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

value: ES-2 (ATCC CRL-1978)

tag: tissue source

value: ovary

tag: treatment

value: treated with prexasertib


title: 256402110006_b3 - 10_6WT(2684)_S-_rep2 vs 14_6Mut(2684)_S-_rep2

hyb_protocol: 14_6Mut_S-_rep2 Cy5 / 10_6WT_S-_rep2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 14_6Mut_S-_rep2 allele 2684

value: PsSultr4 mutant

source_name: 10_6WT_S-_rep2 allele 2684

value: wildtype


title: 256402110006_b4 - 14_6Mut(2684)_S-_rep2 vs 10_6WT(2684)_S-_rep2

hyb_protocol: 10_6WT_S-_rep2 Cy5 / 14_6Mut_S-_rep2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 256402110007_b1 - 11_7WT(2684)_S-_rep3 vs 15_7Mut(2684)_S-_rep3

hyb_protocol: 15_7Mut_S-_rep3 Cy5 / 11_7WT_S-_rep3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Genomic DNA from FF breast tumor tissue_17682

description: Tumor


title: ES2 prexasertib-resistant cells replicate 1

description:
ES2_prexR_P7_again_1
20191108_ES2_prexR_P7_again_1_KP7496_S19


title: 256402110006_b2 - 13_5Mut(2684)_S-_rep1 vs 9_5WT(2684)_S-_rep1

hyb_protocol: 9_5WT_S-_rep1 Cy5 / 13_5Mut_S-_rep1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: 13_5Mut_S-_rep1 allele 2684