title: Control-Lymph-AH015-Full ROI-AH015_rescan-010

description: Lymph


title: MM_14

status: Public on Apr 04 2024

type: SRA

city: Nantes

first: David

last: Chiron

address: 8 quai Moncousu

country: France

institute: CRCI2NA, INSERM_U1307, CNRS_6075, Nantes_Université

library_source: transcriptomic

data_processing:
Samples demultiplexing is performed with a python script. It will transform the raw paired-end fastq.gz files into a single-end fastq.gz file for each sample
Alignment on refseq reference transcriptome is performed using bwa
Aligned reads are parsed and UMI are counted for each gene in each sample to create an expression matrix
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: CD138+ sorted cells

extract_protocol:
RNA was extracted with RNeasy Mini Kit (Qiagen) and sequenced on 3’ends
The libraries are prepared from 10 ng of total RNA in 4µl. The mRNA poly(A) tails are tagged with universal adapters, well-specific barcodes and unique molecular identifiers (UMIs) during template-switching reverse transcriptase. Barcoded cDNAs from multiple samples are then pooled, amplified and tagmented using a transposon-fragmentation approach which enriches for 3′ends of cDNA. A library of 350–800 bp length is run on an Illumina NovaSeq 6000 using NovaSeq 6000 SP Reagent Kit 100 cycles (ref #20027464)

tag: cell type

value: CD138+ sorted cells

tag: disease

value: MM

tag: batch

value: C


title: colorectal cancer tissue sample AUS2_818_T

type: RNA

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

description: Gene expression estimates as RMA values on log2-scale.

hyb_protocol: Samples were hybridized onto Affymetrix Human Transcriptome 2.0 Arrays according to the manufacturer's protocol (Affymetrix).

scan_protocol: Array scanning was performed according to the manufacturer's protocol (Affymetrix).

data_processing: Gene level expression values were estimated according to the robust multi-array average (RMA) approach implemented with the justRMA function in the R package affy and using custom CDF files from Brainarray. A batch effect from different lot numbers of the GeneChip™ WT Plus Reagent Kit was corrected with ComBat in the R package sva using default parameters (the batch of each sample is indicated as analysis batch.

label: biotin

source_name: Colorectal cancer patient

label_protocol: 100 ng total RNA was amplified, fragmented and labelled according to the Affymetrix GeneChip HT WT User Guide.

extract_protocol: Total RNA was isolated from colorectal cancer tissue samples using the Qiagen Allprep DNA/RNA/miRNA Universal kit, according to the manufacturer's protocol (Qiagen).

tag: tissue

value: colorectal cancer tissue sample

value: no

value: T


title: Control-Intima+Media-AH015-Full ROI-AH015_rescan-007

city: Aurora

first: Rubin

middle: M

last: Tuder

state: CO

address: 12700 East 19th Avenue

department: Medicine

country: USA

institute: University of Colorado

description: Intima+Media

scan_protocol: GeoMx Digital Spatial Profiler

data_processing: Gene expression was normalised with RUVIII (Molania et al. 2019) (v0.9.7.1, k=5). The set of control genes with lowest variation across pseudobiological replicates was identified in a two-step approach, first running RUVIII across log2 transformed counts with all genes as controls, then choosing the 100 genes with the least variation to use for the normalisation.

source_name: Control Lung

extract_protocol: rna kit

tag: individuial


title: Control-Intima+Media-AH015-Full ROI-AH015_rescan-008

description: Intima+Media


title: colorectal cancer tissue sample AUS2_816_INV

value: INV


title: Control-Adventitia-AH015-Full ROI-AH015_rescan-006

description: Adventitia


title: Mouse, kidney, E2, M, H3K4me3

city: Bethesda

first: Jakub

last: Jankowski

state: MD

address: 8 Center DR.

department: NIDDK

institute: NIH

library_source: genomic

data_processing:
first, samples were processed with trimmomatic (Bolger et al., Bioinformatics, 2014) in order to filter low quality reads
next, samples were aligned to mm10 genome with bowtie2  (Langmead et al., Nature methods, 2012)
next, MASC2 was used to visualize peaks (Zhang et al., Genome Biology, 2008)
next,  .tdf files were generated using IGV and IGVTools (Robinson et al., Nature Biotechnology 2011)
Assembly: mm10
Supplementary files format and content: .tdf files containing tracks with respective histone modification peak heights and locations, .bedgraph files containing tracks with respective histone modification peak heights and locations

molecule: genomic DNA

organism: Mus musculus

source_name: Kidney

extract_protocol:
Snap-frozen kidneys of 12-14 weeks old mice were ground into powder in liquid nitrogen. After 15 min Chromatin cross-linking in 1% formaldehyde at room temperature the reaction was quenched with 0.125M Glycine. Cells were then lysed using Farnham Lysis Buffer and homogenized on ice. After filtering through a 70um filter, chromatin was sonicated until majority of the fragments were below 1000bp length as assessed by electrophoresis of small aliquots.
Sheared chromatin (>600ug per sample) was incubated with H3K27ac (Active Motif, 39133), H3K4me3 (Millipore, CS200580), and HNF1b (Invitrogen, 720259) antibodies. Libraries for next generation sequencing were prepared with NEBNext Ultra II DNA Library Prep Kit (New England BioLabs, E7645) and sequenced on a NovaSeq 6000 or HiSeq 3000 machine (Illumina).

value: Kidney

tag: genotype

value: Klotho E2 KO

tag: Sex

value: male

tag: antibody

value: Millipore, CS200580


title: Mouse, kidney, WT, F, H3K27ac

value: Klotho E1 WT

value: female

value: Active Motif, 39133


title: MM_10

value: B


title: colorectal cancer tissue sample AUS2_815_T2


title: MM_9


title: Mouse, kidney, WT, F, H3K4me3


title: colorectal cancer tissue sample AUS2_815_T


title: MM_13


title: Mouse, kidney, WT, M, H3K27ac


title: Mouse, kidney, E2, M, H3K27ac


title: colorectal cancer tissue sample AUS2_812_T2


title: Control-Intima+Media-AH015-Full ROI-AH015_rescan-005

description: Intima+Media


title: Mouse, kidney, E1+2, M, H3K27ac

value: Klotho E1+2 KO


title: Control-Adventitia-AH015-Full ROI-AH015_rescan-002

description: Adventitia


title: Control-Intima+Media-AH015-Full ROI-AH015_rescan-004

description: Intima+Media


title: Control-Intima+Media-AH015-Full ROI-AH015_rescan-001

description: Intima+Media


title: colorectal cancer tissue sample AUS2_812_T3


title: Control-Intima+Media-AH006-Full ROI-AH006-009

description: Intima+Media


title: WSU-DLCL2 MAK683 H3K4me3

city: Shanghai

first: Wei

last: Qi

state: Shanghai

address: B514, L Building

department: School of Life Science and Technology

country: China

institute: ShanghaiTech University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trim-galore (version 0.4.4_dev) and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Bowtie2(version v1.3.0).
ChIP-seq sample depleted repeat sequences by Picard (version 2.23.6) and normalized by drosophila histone modification.
These reads were used to generate binding site with MACS2 (version 2.2.7.1).
Assembly: hg38
Supplementary files format and content: bigwig files were generated using deeptools(version 3.4.3).

growth_protocol: WSU-DLCL2 cell lines were cultured in RPMI1640 (Gibco) supplemented with 15% fetal bovine serum (Lonsera # S711-001S), 100 U ml-1 penicillin and 100 μg ml-1 streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
A total amount of 50 ng DNA per sample was used as input material for the ChIP sample preparations. Sequencing libraries were generated using NEBNext Ultratm DNA Library PrepKit for Illumina(NEB USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly,the Chip DNA was purified using AMPure XP system (Beckman Coulter Beverly,USA). After adenylation of 3'ends of DNA fragments, the NEB Next Adaptor with hairpin loop structure were ligated to prepare for hybridization. Then electrophoresis was used to select DNA fragments specified in length. 3 uL USER Enzyme(NEB，USA) was used with size-selected,adaptor-ligated DNA at 37C for15 min followed by5 min at 95C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index(X) Primer. At last. PCRproducts were purified(AMPure XP system) and library quality was assessed on the AgilentBioanalyzer 2100 system.

treatment_protocol: All samples were DMSO or MAK683 treated for 3 days.

tag: cell line

tag: chip antibody

value: wild type

tag: treatment


title: Mouse, kidney, E1, M, H3K4me3

value: Klotho E1 KO


title: Control-Intima+Media-AH015-Full ROI-AH015_rescan-003

description: Intima+Media


title: MM_5

value: CD138+ sorted cells

value: MM

value: A


title: Mouse, kidney, E1, F, H3K4me3

data_processing:
first, samples were processed with trimmomatic (Bolger et al., Bioinformatics, 2014) in order to filter low quality reads
next, samples were aligned to mm10 genome with bowtie2  (Langmead et al., Nature methods, 2012)
next, MASC2 was used to visualize peaks (Zhang et al., Genome Biology, 2008)
next,  .tdf files were generated using IGV and IGVTools (Robinson et al., Nature Biotechnology 2011)
Assembly: mm10
Supplementary files format and content: .tdf files containing tracks with respective histone modification peak heights and locations

extract_protocol:
Snap-frozen kidneys of 12-14 weeks old mice were ground into powder in liquid nitrogen. After 15 min Chromatin cross-linking in 1% formaldehyde at room temperature the reaction was quenched with 0.125M Glycine. Cells were then lysed using Farnham Lysis Buffer and homogenized on ice. After filtering through a 70um filter, chromatin was sonicated until majority of the fragments were below 1000bp length as assessed by electrophoresis of small aliquots.
Sheared chromatin (>600ug per sample) was incubated with H3K27ac (Active Motif, 39133) and H3K4me3 (Millipore, CS200580) antibodies. Libraries for next generation sequencing were prepared with NEBNext Ultra II DNA Library Prep Kit (New England BioLabs, E7645) and sequenced on a NovaSeq 6000 machine (Illumina).


title: MM_3


title: colorectal cancer tissue sample AUS2_812_INV

value: colorectal cancer tissue sample

value: no


title: colorectal cancer tissue sample AUS2_809_INV

value: INV


title: WSU-DLCL2 MAK683 H3K27me3


title: Mouse, kidney, E1+2, M, H3K4me3

value: Kidney


title: colorectal cancer tissue sample AUS2_812_T

value: T


title: colorectal cancer tissue sample AUS2_809_T2


title: colorectal cancer tissue sample AUS2_807_INV


title: colorectal cancer tissue sample AUS2_807_T2


title: WSU-DLCL2 MAK683 Input

value: Input


title: RNA_RA_24h_dTAG13

city: Berlin

first: Pavel

last: Tsaytler

address: Ihnestrasse  63-73

country: Germany

institute: MPI Molecular Genetics

data_processing:
Reads were subjected to quality control using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed using cutadapt (version 2.9) (Martin, https://doi.org/10.14806/ej.17.1.200) to remove adapter sequences. Alignment was performed using Hisat2 (version 2.1.0) (Kim, 2019) with the following arguments: --no-mixed --no-discordant. The index files for Hisat2 were built using mm10 reference genome containing chromosomes 1-19, X, Y and M, and splice sites and exon data from refSeq annotations. The resulting sam format files were then converted to bam format, sorted and indexed using samtools (version 1.9) (Li, 2009). FPKM values were calculated using Cuffdiff (version 2.2.1) (Trapnell, 2018) with the following arguments: -u -no-effective-length-correction -b.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596036) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 23 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).

value: embryonic stem cells

value: Sox2 KO

value: neural differentiation


title: colorectal cancer tissue sample AUS2_809_T


title: Mouse, kidney, E1, M, H3K27ac

value: male

value: Active Motif, 39133


title: WSU-DLCL2 DMSO Input

value: DMSO


title: RNA_RA_6h_dTAG13

data_processing:
Reads were subjected to quality control using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed using cutadapt (version 2.9) (Martin, https://doi.org/10.14806/ej.17.1.200) to remove adapter sequences. Alignment was performed using Hisat2 (version 2.1.0) (Kim, 2019) with the following arguments: --no-mixed --no-discordant. The index files for Hisat2 were built using mm10 reference genome containing chromosomes 1-19, X, Y and M, and splice sites and exon data from refSeq annotations. The resulting sam format files were then converted to bam format, sorted and indexed using samtools (version 1.9) (Li, 2009). FPKM values were calculated using Cuffdiff (version 2.2.1) (Trapnell, 2016) with the following arguments: -u -no-effective-length-correction -b.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596036) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 21 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).


title: WSU-DLCL2 DMSO H3K27me3

value: wild type


title: RNA_RA_12h_dTAG13

data_processing:
Reads were subjected to quality control using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed using cutadapt (version 2.9) (Martin, https://doi.org/10.14806/ej.17.1.200) to remove adapter sequences. Alignment was performed using Hisat2 (version 2.1.0) (Kim, 2019) with the following arguments: --no-mixed --no-discordant. The index files for Hisat2 were built using mm10 reference genome containing chromosomes 1-19, X, Y and M, and splice sites and exon data from refSeq annotations. The resulting sam format files were then converted to bam format, sorted and indexed using samtools (version 1.9) (Li, 2009). FPKM values were calculated using Cuffdiff (version 2.2.1) (Trapnell, 2017) with the following arguments: -u -no-effective-length-correction -b.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596036) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 22 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).


title: WSU-DLCL2 invivo ACVR1KO MAK683 rep3

data_processing:
Illumina PE150 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trim-galore (version 0.4.4_dev) and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2(version 2.2.0).
The number of reads falling in the exons were calculated using featureCounts (version v1.5.3) and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: comma-delimited text files include FPKM values for each Sample

source_name: WSU-DLCL2-derived Xenogrft  tissue

growth_protocol: Cells were maintained in a humidified incubator at 37 °C, 5% (vol/vol) CO2. WSU-DLCL2 were cultured in RPMI1640 (Gibco) supplemented with 15% fetal bovine serum (Lonsera # S711-001S), 100 U ml-1 penicillin and 100 μg ml-1 streptomycin.WSU-DLCL2 cells were implanted subcutaneously in female BALB/c nude mice.

extract_protocol:
RNA samples were harvested with Trizol reagent.
Total RNA was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Next First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEB Next Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beverly, USA). Then 3 µL USER Enzyme (NEB, USA) was used with size selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent 5400 system（Agilent，USA） and quantified by QPCR (1.5 nM).

treatment_protocol: Cell lines were treated with 3 μM MAK683 for 6 days. WSU-DLCL2-derived xenograft carrying mice were given vehicle or 100 mg/kg MAK683 orally for 28 consecutive days before the xenograft tumor tissues were harvested.

value: WSU-DLCL2-derived Xenogrft  tissue

value: ACVR1 -/-


title: Mouse, kidney, E1,  F, H3K27ac

value: Klotho E1 KO

value: female


title: RNA_RA_3h_dTAG13

data_processing:
Reads were subjected to quality control using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed using cutadapt (version 2.9) (Martin, https://doi.org/10.14806/ej.17.1.200) to remove adapter sequences. Alignment was performed using Hisat2 (version 2.1.0) (Kim, 2019) with the following arguments: --no-mixed --no-discordant. The index files for Hisat2 were built using mm10 reference genome containing chromosomes 1-19, X, Y and M, and splice sites and exon data from refSeq annotations. The resulting sam format files were then converted to bam format, sorted and indexed using samtools (version 1.9) (Li, 2009). FPKM values were calculated using Cuffdiff (version 2.2.1) (Trapnell, 2015) with the following arguments: -u -no-effective-length-correction -b.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596036) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 20 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).


title: colorectal cancer tissue sample AUS2_805_T3

value: colorectal cancer tissue sample


title: WSU-DLCL2 invivo ACVR1KO MAK683 rep1


title: RNA_RA_24h_DMSO

data_processing:
Reads were subjected to quality control using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed using cutadapt (version 2.9) (Martin, https://doi.org/10.14806/ej.17.1.200) to remove adapter sequences. Alignment was performed using Hisat2 (version 2.1.0) (Kim, 2019) with the following arguments: --no-mixed --no-discordant. The index files for Hisat2 were built using mm10 reference genome containing chromosomes 1-19, X, Y and M, and splice sites and exon data from refSeq annotations. The resulting sam format files were then converted to bam format, sorted and indexed using samtools (version 1.9) (Li, 2009). FPKM values were calculated using Cuffdiff (version 2.2.1) (Trapnell, 2014) with the following arguments: -u -no-effective-length-correction -b.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596036) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 19 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).

value: WT


title: WSU-DLCL2 invivo ACVR1KO MAK683 rep2


title: RNA_RA_12h_DMSO

data_processing:
Reads were subjected to quality control using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed using cutadapt (version 2.9) (Martin, https://doi.org/10.14806/ej.17.1.200) to remove adapter sequences. Alignment was performed using Hisat2 (version 2.1.0) (Kim, 2019) with the following arguments: --no-mixed --no-discordant. The index files for Hisat2 were built using mm10 reference genome containing chromosomes 1-19, X, Y and M, and splice sites and exon data from refSeq annotations. The resulting sam format files were then converted to bam format, sorted and indexed using samtools (version 1.9) (Li, 2009). FPKM values were calculated using Cuffdiff (version 2.2.1) (Trapnell, 2013) with the following arguments: -u -no-effective-length-correction -b.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596036) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 18 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).


title: RNA_RA_6h_DMSO

data_processing:
Reads were subjected to quality control using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed using cutadapt (version 2.9) (Martin, https://doi.org/10.14806/ej.17.1.200) to remove adapter sequences. Alignment was performed using Hisat2 (version 2.1.0) (Kim, 2019) with the following arguments: --no-mixed --no-discordant. The index files for Hisat2 were built using mm10 reference genome containing chromosomes 1-19, X, Y and M, and splice sites and exon data from refSeq annotations. The resulting sam format files were then converted to bam format, sorted and indexed using samtools (version 1.9) (Li, 2009). FPKM values were calculated using Cuffdiff (version 2.2.1) (Trapnell, 2012) with the following arguments: -u -no-effective-length-correction -b.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596036) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 17 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).


title: colorectal cancer tissue sample AUS2_807_T

value: no


title: WSU-DLCL2 invivo ACVR1KO DMSO rep2


title: colorectal cancer tissue sample AUS2_805_T2


title: WSU-DLCL2 invivo ACVR1KO DMSO rep3


title: WSU-DLCL2 invivo ACVR1KO DMSO rep1


title: RNA_RA_3h_DMSO

data_processing:
Reads were subjected to quality control using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed using cutadapt (version 2.9) (Martin, https://doi.org/10.14806/ej.17.1.200) to remove adapter sequences. Alignment was performed using Hisat2 (version 2.1.0) (Kim, 2019) with the following arguments: --no-mixed --no-discordant. The index files for Hisat2 were built using mm10 reference genome containing chromosomes 1-19, X, Y and M, and splice sites and exon data from refSeq annotations. The resulting sam format files were then converted to bam format, sorted and indexed using samtools (version 1.9) (Li, 2009). FPKM values were calculated using Cuffdiff (version 2.2.1) (Trapnell, 2011) with the following arguments: -u -no-effective-length-correction -b.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596036) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 16 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).


title: WSU-DLCL2 DMSO H3K4me3


title: colorectal cancer tissue sample AUS2_805_T


title: RNA_UT

data_processing:
Reads were subjected to quality control using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed using cutadapt (version 2.9) (Martin, https://doi.org/10.14806/ej.17.1.200) to remove adapter sequences. Alignment was performed using Hisat2 (version 2.1.0) (Kim, 2019) with the following arguments: --no-mixed --no-discordant. The index files for Hisat2 were built using mm10 reference genome containing chromosomes 1-19, X, Y and M, and splice sites and exon data from refSeq annotations. The resulting sam format files were then converted to bam format, sorted and indexed using samtools (version 1.9) (Li, 2009). FPKM values were calculated using Cuffdiff (version 2.2.1) (Trapnell, 2010) with the following arguments: -u -no-effective-length-correction -b.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
Total RNA was extracted from 40,000 mESCs or differentiated cells using Trizol reagent (ThermoFisher; 15596036) following the manufacturer’s instructions and purified using the RNeasy Micro kit (Qiagen). Residual genomic DNA was digested on a column.
Strand-specific RNA-seq libraries were generated from 100 ng of total RNA using the ScriptSeq v2 (Epicentre) low input library preparation kit according to manufacturer’s instructions. The library was amplified using 15 PCR cycles. RNA-seq libraries were quantified using the Qubit HS DNA assay (Life Technologies) and the size distribution was assessed using the DNA HS Bioanalyzer chips (Agilent).

value: untreated


title: WSU-DLCL2 invivo MAK683 rep2


title: ATAC_RA_24h_dTAG13

data_processing:
Reads were trimmed to 40 bp length and adapter sequences were removed using cutadapt. The trimmed reads were aligned to the reference genome using bowtie (version 1.1.2) (Langmead, 2009) with the following arguments: -y -v 2 --best --strata -m 3 -k 1 -S -X 2000 --allow-contain. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. Reads mapped to chr M and Y or known ATAC artifact regions (ENCODE) were removed using samtools. Possible PCR duplicates were removed using Picard (version 1.103, https://broadinstitute.github.io/picard). For visualization, the reads from replicates were combined, and the data were normalized and converted to bigWig format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing RPCG --effectiveGenomeSize 2652783500 --extendReads 200 --smoothLength 9 -bs 19 -ignore chrY chrM.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
The cells were lysed in 50 μl of cold lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged at 500g, 4°C for 10 min. The pellet was resuspended in the transposition reaction mix (25 μl 2x TD buffer, 2.5 μl Tn5 transposase, 22.5 μl H2O) and incubated at 37°C for 30 minutes. After incubation, the reaction was stopped with the addition of PB buffer (Qiagen) and the tagmented DNA was purified using the MinElute kit (Qiagen).
The DNA was combined with the ATAC index PCR primers and 2x Kapa HiFi Hotstart Ready Mix and pre-amplified (98°C 30 seconds, 5x [98°C 10 seconds, 63°C 30 seconds, 72°C 1 minute] in a 50 μl volume. To determine the remaining cycles to avoid potential over-amplification, 5 μl of the pre-amplification mix was combined with the primers, 1x Evagreen SYBR green (Jena Biosciences) and 2x Kapa HiFi Hotstart Ready Mix in a 15 μl total volume and run for 30 cycles on a StepOne Plus. The remaining 45 μl of pre-amplified samples were amplified for a further 6-23 cycles and the libraries were purified using MinElute column (Qiagen). The libraries were quantified using the Qubit DNA HS assay and the library sizes were validated using DNA HS Bioanalyzer chips.


title: WSU-DLCL2 invivo MAK683 rep3


title: ATAC_RA_48h_dTAG13

data_processing:
Reads were trimmed to 40 bp length and adapter sequences were removed using cutadapt. The trimmed reads were aligned to the reference genome using bowtie (version 1.1.2) (Langmead, 2009) with the following arguments: -y -v 2 --best --strata -m 3 -k 1 -S -X 2000 --allow-contain. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. Reads mapped to chr M and Y or known ATAC artifact regions (ENCODE) were removed using samtools. Possible PCR duplicates were removed using Picard (version 1.103, https://broadinstitute.github.io/picard). For visualization, the reads from replicates were combined, and the data were normalized and converted to bigWig format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing RPCG --effectiveGenomeSize 2652783500 --extendReads 200 --smoothLength 9 -bs 20 -ignore chrY chrM.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
The cells were lysed in 50 μl of cold lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged at 500g, 4°C for 10 min. The pellet was resuspended in the transposition reaction mix (25 μl 2x TD buffer, 2.5 μl Tn5 transposase, 22.5 μl H2O) and incubated at 37°C for 30 minutes. After incubation, the reaction was stopped with the addition of PB buffer (Qiagen) and the tagmented DNA was purified using the MinElute kit (Qiagen).
The DNA was combined with the ATAC index PCR primers and 2x Kapa HiFi Hotstart Ready Mix and pre-amplified (98°C 30 seconds, 5x [98°C 10 seconds, 63°C 30 seconds, 72°C 1 minute] in a 50 μl volume. To determine the remaining cycles to avoid potential over-amplification, 5 μl of the pre-amplification mix was combined with the primers, 1x Evagreen SYBR green (Jena Biosciences) and 2x Kapa HiFi Hotstart Ready Mix in a 15 μl total volume and run for 30 cycles on a StepOne Plus. The remaining 45 μl of pre-amplified samples were amplified for a further 6-24 cycles and the libraries were purified using MinElute column (Qiagen). The libraries were quantified using the Qubit DNA HS assay and the library sizes were validated using DNA HS Bioanalyzer chips.


title: colorectal cancer tissue sample AUS2_804_T3

data_processing: Gene level expression values were estimated according to the robust multi-array average (RMA) approach implemented with the justRMA function in the R package affy and using custom CDF files from Brainarray. A batch effect from different lot numbers of the GeneChip™ WT Plus Reagent Kit was corrected with ComBat in the R package sva using default parameters (the batch of each sample is indicated as analysis batch.

extract_protocol: Total RNA was isolated from colorectal cancer tissue samples using the Qiagen Allprep DNA/RNA/miRNA Universal kit, according to the manufacturer's protocol (Qiagen).


title: ATAC_RA_12h_dTAG13

data_processing:
Reads were trimmed to 40 bp length and adapter sequences were removed using cutadapt. The trimmed reads were aligned to the reference genome using bowtie (version 1.1.2) (Langmead, 2009) with the following arguments: -y -v 2 --best --strata -m 3 -k 1 -S -X 2000 --allow-contain. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. Reads mapped to chr M and Y or known ATAC artifact regions (ENCODE) were removed using samtools. Possible PCR duplicates were removed using Picard (version 1.103, https://broadinstitute.github.io/picard). For visualization, the reads from replicates were combined, and the data were normalized and converted to bigWig format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing RPCG --effectiveGenomeSize 2652783500 --extendReads 200 --smoothLength 9 -bs 18 -ignore chrY chrM.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
The cells were lysed in 50 μl of cold lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged at 500g, 4°C for 10 min. The pellet was resuspended in the transposition reaction mix (25 μl 2x TD buffer, 2.5 μl Tn5 transposase, 22.5 μl H2O) and incubated at 37°C for 30 minutes. After incubation, the reaction was stopped with the addition of PB buffer (Qiagen) and the tagmented DNA was purified using the MinElute kit (Qiagen).
The DNA was combined with the ATAC index PCR primers and 2x Kapa HiFi Hotstart Ready Mix and pre-amplified (98°C 30 seconds, 5x [98°C 10 seconds, 63°C 30 seconds, 72°C 1 minute] in a 50 μl volume. To determine the remaining cycles to avoid potential over-amplification, 5 μl of the pre-amplification mix was combined with the primers, 1x Evagreen SYBR green (Jena Biosciences) and 2x Kapa HiFi Hotstart Ready Mix in a 15 μl total volume and run for 30 cycles on a StepOne Plus. The remaining 45 μl of pre-amplified samples were amplified for a further 6-22 cycles and the libraries were purified using MinElute column (Qiagen). The libraries were quantified using the Qubit DNA HS assay and the library sizes were validated using DNA HS Bioanalyzer chips.


title: WSU-DLCL2 invivo MAK683 rep1


title: WSU-DLCL2 invivo DMSO rep3


title: colorectal cancer tissue sample AUS2_804_INV

value: INV


title: ATAC_RA_6h_dTAG13

data_processing:
Reads were trimmed to 40 bp length and adapter sequences were removed using cutadapt. The trimmed reads were aligned to the reference genome using bowtie (version 1.1.2) (Langmead, 2009) with the following arguments: -y -v 2 --best --strata -m 3 -k 1 -S -X 2000 --allow-contain. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. Reads mapped to chr M and Y or known ATAC artifact regions (ENCODE) were removed using samtools. Possible PCR duplicates were removed using Picard (version 1.103, https://broadinstitute.github.io/picard). For visualization, the reads from replicates were combined, and the data were normalized and converted to bigWig format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing RPCG --effectiveGenomeSize 2652783500 --extendReads 200 --smoothLength 9 -bs 17 -ignore chrY chrM.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
The cells were lysed in 50 μl of cold lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged at 500g, 4°C for 10 min. The pellet was resuspended in the transposition reaction mix (25 μl 2x TD buffer, 2.5 μl Tn5 transposase, 22.5 μl H2O) and incubated at 37°C for 30 minutes. After incubation, the reaction was stopped with the addition of PB buffer (Qiagen) and the tagmented DNA was purified using the MinElute kit (Qiagen).
The DNA was combined with the ATAC index PCR primers and 2x Kapa HiFi Hotstart Ready Mix and pre-amplified (98°C 30 seconds, 5x [98°C 10 seconds, 63°C 30 seconds, 72°C 1 minute] in a 50 μl volume. To determine the remaining cycles to avoid potential over-amplification, 5 μl of the pre-amplification mix was combined with the primers, 1x Evagreen SYBR green (Jena Biosciences) and 2x Kapa HiFi Hotstart Ready Mix in a 15 μl total volume and run for 30 cycles on a StepOne Plus. The remaining 45 μl of pre-amplified samples were amplified for a further 6-21 cycles and the libraries were purified using MinElute column (Qiagen). The libraries were quantified using the Qubit DNA HS assay and the library sizes were validated using DNA HS Bioanalyzer chips.


title: ATAC_RA_2h_dTAG13

data_processing:
Reads were trimmed to 40 bp length and adapter sequences were removed using cutadapt. The trimmed reads were aligned to the reference genome using bowtie (version 1.1.2) (Langmead, 2009) with the following arguments: -y -v 2 --best --strata -m 3 -k 1 -S -X 2000 --allow-contain. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. Reads mapped to chr M and Y or known ATAC artifact regions (ENCODE) were removed using samtools. Possible PCR duplicates were removed using Picard (version 1.103, https://broadinstitute.github.io/picard). For visualization, the reads from replicates were combined, and the data were normalized and converted to bigWig format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing RPCG --effectiveGenomeSize 2652783500 --extendReads 200 --smoothLength 9 -bs 16 -ignore chrY chrM.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
The cells were lysed in 50 μl of cold lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged at 500g, 4°C for 10 min. The pellet was resuspended in the transposition reaction mix (25 μl 2x TD buffer, 2.5 μl Tn5 transposase, 22.5 μl H2O) and incubated at 37°C for 30 minutes. After incubation, the reaction was stopped with the addition of PB buffer (Qiagen) and the tagmented DNA was purified using the MinElute kit (Qiagen).
The DNA was combined with the ATAC index PCR primers and 2x Kapa HiFi Hotstart Ready Mix and pre-amplified (98°C 30 seconds, 5x [98°C 10 seconds, 63°C 30 seconds, 72°C 1 minute] in a 50 μl volume. To determine the remaining cycles to avoid potential over-amplification, 5 μl of the pre-amplification mix was combined with the primers, 1x Evagreen SYBR green (Jena Biosciences) and 2x Kapa HiFi Hotstart Ready Mix in a 15 μl total volume and run for 30 cycles on a StepOne Plus. The remaining 45 μl of pre-amplified samples were amplified for a further 6-20 cycles and the libraries were purified using MinElute column (Qiagen). The libraries were quantified using the Qubit DNA HS assay and the library sizes were validated using DNA HS Bioanalyzer chips.


title: WSU-DLCL2 invivo DMSO rep2


title: MS_LCL7

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
Sequenced reads were aligned using RSEM along with Bowtie2 against the human genome (version: hg19)
DESeq2 was used to normalize the reads and obtain the differentially expressed genes

molecule: polyA RNA

source_name: blood

extract_protocol: Lexogen Quantseq

value: blood

value: lymphoblastoid cell lines

tag: condition

value: Healthy Control


title: colorectal cancer tissue sample AUS2_804_T2


title: colorectal cancer tissue sample AUS2_802_T3


title: colorectal cancer tissue sample AUS2_802_T

value: T


title: colorectal cancer tissue sample AUS2_800_T2


title: WSU-DLCL2 invivo DMSO rep1


title: colorectal cancer tissue sample AUS2_802_T2


title: HC_LCL8


title: colorectal cancer tissue sample AUS2_800_T3


title: colorectal cancer tissue sample AUS2_802_INV


title: colorectal cancer tissue sample AUS2_800_T


title: WSU-DLCL2 ACVR1KO MAK683 rep3


title: HC_LCL7

value: Multiple Sclerosis


title: colorectal cancer tissue sample AUS2_800_INV


title: ATAC_RA_24h_DMSO

data_processing:
Reads were trimmed to 40 bp length and adapter sequences were removed using cutadapt. The trimmed reads were aligned to the reference genome using bowtie (version 1.1.2) (Langmead, 2009) with the following arguments: -y -v 2 --best --strata -m 3 -k 1 -S -X 2000 --allow-contain. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. Reads mapped to chr M and Y or known ATAC artifact regions (ENCODE) were removed using samtools. Possible PCR duplicates were removed using Picard (version 1.103, https://broadinstitute.github.io/picard). For visualization, the reads from replicates were combined, and the data were normalized and converted to bigWig format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing RPCG --effectiveGenomeSize 2652783500 --extendReads 200 --smoothLength 9 -bs 14 -ignore chrY chrM.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
The cells were lysed in 50 μl of cold lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged at 500g, 4°C for 10 min. The pellet was resuspended in the transposition reaction mix (25 μl 2x TD buffer, 2.5 μl Tn5 transposase, 22.5 μl H2O) and incubated at 37°C for 30 minutes. After incubation, the reaction was stopped with the addition of PB buffer (Qiagen) and the tagmented DNA was purified using the MinElute kit (Qiagen).
The DNA was combined with the ATAC index PCR primers and 2x Kapa HiFi Hotstart Ready Mix and pre-amplified (98°C 30 seconds, 5x [98°C 10 seconds, 63°C 30 seconds, 72°C 1 minute] in a 50 μl volume. To determine the remaining cycles to avoid potential over-amplification, 5 μl of the pre-amplification mix was combined with the primers, 1x Evagreen SYBR green (Jena Biosciences) and 2x Kapa HiFi Hotstart Ready Mix in a 15 μl total volume and run for 30 cycles on a StepOne Plus. The remaining 45 μl of pre-amplified samples were amplified for a further 6-18 cycles and the libraries were purified using MinElute column (Qiagen). The libraries were quantified using the Qubit DNA HS assay and the library sizes were validated using DNA HS Bioanalyzer chips.

value: embryonic stem cells

value: neural differentiation


title: WSU-DLCL2 ACVR1KO MAK683 rep2


title: colorectal cancer tissue sample AUS2_799_T


title: MS_LCL1_3


title: ATAC_RA_2h_DMSO

data_processing:
Reads were trimmed to 40 bp length and adapter sequences were removed using cutadapt. The trimmed reads were aligned to the reference genome using bowtie (version 1.1.2) (Langmead, 2009) with the following arguments: -y -v 2 --best --strata -m 3 -k 1 -S -X 2000 --allow-contain. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. Reads mapped to chr M and Y or known ATAC artifact regions (ENCODE) were removed using samtools. Possible PCR duplicates were removed using Picard (version 1.103, https://broadinstitute.github.io/picard). For visualization, the reads from replicates were combined, and the data were normalized and converted to bigWig format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing RPCG --effectiveGenomeSize 2652783500 --extendReads 200 --smoothLength 9 -bs 11 -ignore chrY chrM.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
The cells were lysed in 50 μl of cold lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged at 500g, 4°C for 10 min. The pellet was resuspended in the transposition reaction mix (25 μl 2x TD buffer, 2.5 μl Tn5 transposase, 22.5 μl H2O) and incubated at 37°C for 30 minutes. After incubation, the reaction was stopped with the addition of PB buffer (Qiagen) and the tagmented DNA was purified using the MinElute kit (Qiagen).
The DNA was combined with the ATAC index PCR primers and 2x Kapa HiFi Hotstart Ready Mix and pre-amplified (98°C 30 seconds, 5x [98°C 10 seconds, 63°C 30 seconds, 72°C 1 minute] in a 50 μl volume. To determine the remaining cycles to avoid potential over-amplification, 5 μl of the pre-amplification mix was combined with the primers, 1x Evagreen SYBR green (Jena Biosciences) and 2x Kapa HiFi Hotstart Ready Mix in a 15 μl total volume and run for 30 cycles on a StepOne Plus. The remaining 45 μl of pre-amplified samples were amplified for a further 6-15 cycles and the libraries were purified using MinElute column (Qiagen). The libraries were quantified using the Qubit DNA HS assay and the library sizes were validated using DNA HS Bioanalyzer chips.


title: SLCL_HC2

value: spontaneous lymphoblastoid cell lines


title: ATAC_RA_12h_DMSO

data_processing:
Reads were trimmed to 40 bp length and adapter sequences were removed using cutadapt. The trimmed reads were aligned to the reference genome using bowtie (version 1.1.2) (Langmead, 2009) with the following arguments: -y -v 2 --best --strata -m 3 -k 1 -S -X 2000 --allow-contain. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. Reads mapped to chr M and Y or known ATAC artifact regions (ENCODE) were removed using samtools. Possible PCR duplicates were removed using Picard (version 1.103, https://broadinstitute.github.io/picard). For visualization, the reads from replicates were combined, and the data were normalized and converted to bigWig format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing RPCG --effectiveGenomeSize 2652783500 --extendReads 200 --smoothLength 9 -bs 13 -ignore chrY chrM.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
The cells were lysed in 50 μl of cold lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged at 500g, 4°C for 10 min. The pellet was resuspended in the transposition reaction mix (25 μl 2x TD buffer, 2.5 μl Tn5 transposase, 22.5 μl H2O) and incubated at 37°C for 30 minutes. After incubation, the reaction was stopped with the addition of PB buffer (Qiagen) and the tagmented DNA was purified using the MinElute kit (Qiagen).
The DNA was combined with the ATAC index PCR primers and 2x Kapa HiFi Hotstart Ready Mix and pre-amplified (98°C 30 seconds, 5x [98°C 10 seconds, 63°C 30 seconds, 72°C 1 minute] in a 50 μl volume. To determine the remaining cycles to avoid potential over-amplification, 5 μl of the pre-amplification mix was combined with the primers, 1x Evagreen SYBR green (Jena Biosciences) and 2x Kapa HiFi Hotstart Ready Mix in a 15 μl total volume and run for 30 cycles on a StepOne Plus. The remaining 45 μl of pre-amplified samples were amplified for a further 6-17 cycles and the libraries were purified using MinElute column (Qiagen). The libraries were quantified using the Qubit DNA HS assay and the library sizes were validated using DNA HS Bioanalyzer chips.


title: colorectal cancer tissue sample AUS2_797_T


title: ATAC_RA_48h_DMSO

data_processing:
Reads were trimmed to 40 bp length and adapter sequences were removed using cutadapt. The trimmed reads were aligned to the reference genome using bowtie (version 1.1.2) (Langmead, 2009) with the following arguments: -y -v 2 --best --strata -m 3 -k 1 -S -X 2000 --allow-contain. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. Reads mapped to chr M and Y or known ATAC artifact regions (ENCODE) were removed using samtools. Possible PCR duplicates were removed using Picard (version 1.103, https://broadinstitute.github.io/picard). For visualization, the reads from replicates were combined, and the data were normalized and converted to bigWig format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing RPCG --effectiveGenomeSize 2652783500 --extendReads 200 --smoothLength 9 -bs 15 -ignore chrY chrM.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
The cells were lysed in 50 μl of cold lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged at 500g, 4°C for 10 min. The pellet was resuspended in the transposition reaction mix (25 μl 2x TD buffer, 2.5 μl Tn5 transposase, 22.5 μl H2O) and incubated at 37°C for 30 minutes. After incubation, the reaction was stopped with the addition of PB buffer (Qiagen) and the tagmented DNA was purified using the MinElute kit (Qiagen).
The DNA was combined with the ATAC index PCR primers and 2x Kapa HiFi Hotstart Ready Mix and pre-amplified (98°C 30 seconds, 5x [98°C 10 seconds, 63°C 30 seconds, 72°C 1 minute] in a 50 μl volume. To determine the remaining cycles to avoid potential over-amplification, 5 μl of the pre-amplification mix was combined with the primers, 1x Evagreen SYBR green (Jena Biosciences) and 2x Kapa HiFi Hotstart Ready Mix in a 15 μl total volume and run for 30 cycles on a StepOne Plus. The remaining 45 μl of pre-amplified samples were amplified for a further 6-19 cycles and the libraries were purified using MinElute column (Qiagen). The libraries were quantified using the Qubit DNA HS assay and the library sizes were validated using DNA HS Bioanalyzer chips.


title: colorectal cancer tissue sample AUS2_799_T2


title: colorectal cancer tissue sample AUS2_804_T


title: colorectal cancer tissue sample AUS2_797_T2


title: WSU-DLCL2 ACVR1KO MAK683 rep1

data_processing:
Illumina PE150 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trim-galore (version 0.4.4_dev) and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2(version 2.2.0).
The number of reads falling in the exons were calculated using featureCounts (version v1.5.3) and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: comma-delimited text files include FPKM values for each Sample

extract_protocol:
RNA samples were harvested with Trizol reagent.
Total RNA was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Next First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEB Next Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beverly, USA). Then 3 µL USER Enzyme (NEB, USA) was used with size selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent 5400 system（Agilent，USA） and quantified by QPCR (1.5 nM).


title: WSU-DLCL2 ACVR1KO DMSO rep2

value: DMSO


title: ATAC_dTAG13_24h_rep2

data_processing:
Reads were trimmed to 40 bp length and adapter sequences were removed using cutadapt. The trimmed reads were aligned to the reference genome using bowtie (version 1.1.2) (Langmead, 2009) with the following arguments: -y -v 2 --best --strata -m 3 -k 1 -S -X 2000 --allow-contain. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. Reads mapped to chr M and Y or known ATAC artifact regions (ENCODE) were removed using samtools. Possible PCR duplicates were removed using Picard (version 1.103, https://broadinstitute.github.io/picard). For visualization, the reads from replicates were combined, and the data were normalized and converted to bigWig format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing RPCG --effectiveGenomeSize 2652783500 --extendReads 200 --smoothLength 9 -bs 10 -ignore chrY chrM.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
The cells were lysed in 50 μl of cold lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged at 500g, 4°C for 10 min. The pellet was resuspended in the transposition reaction mix (25 μl 2x TD buffer, 2.5 μl Tn5 transposase, 22.5 μl H2O) and incubated at 37°C for 30 minutes. After incubation, the reaction was stopped with the addition of PB buffer (Qiagen) and the tagmented DNA was purified using the MinElute kit (Qiagen).
The DNA was combined with the ATAC index PCR primers and 2x Kapa HiFi Hotstart Ready Mix and pre-amplified (98°C 30 seconds, 5x [98°C 10 seconds, 63°C 30 seconds, 72°C 1 minute] in a 50 μl volume. To determine the remaining cycles to avoid potential over-amplification, 5 μl of the pre-amplification mix was combined with the primers, 1x Evagreen SYBR green (Jena Biosciences) and 2x Kapa HiFi Hotstart Ready Mix in a 15 μl total volume and run for 30 cycles on a StepOne Plus. The remaining 45 μl of pre-amplified samples were amplified for a further 6-14 cycles and the libraries were purified using MinElute column (Qiagen). The libraries were quantified using the Qubit DNA HS assay and the library sizes were validated using DNA HS Bioanalyzer chips.

value: Sox2 KO


title: ATAC_RA_6h_DMSO

data_processing:
Reads were trimmed to 40 bp length and adapter sequences were removed using cutadapt. The trimmed reads were aligned to the reference genome using bowtie (version 1.1.2) (Langmead, 2009) with the following arguments: -y -v 2 --best --strata -m 3 -k 1 -S -X 2000 --allow-contain. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. Reads mapped to chr M and Y or known ATAC artifact regions (ENCODE) were removed using samtools. Possible PCR duplicates were removed using Picard (version 1.103, https://broadinstitute.github.io/picard). For visualization, the reads from replicates were combined, and the data were normalized and converted to bigWig format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing RPCG --effectiveGenomeSize 2652783500 --extendReads 200 --smoothLength 9 -bs 12 -ignore chrY chrM.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
The cells were lysed in 50 μl of cold lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged at 500g, 4°C for 10 min. The pellet was resuspended in the transposition reaction mix (25 μl 2x TD buffer, 2.5 μl Tn5 transposase, 22.5 μl H2O) and incubated at 37°C for 30 minutes. After incubation, the reaction was stopped with the addition of PB buffer (Qiagen) and the tagmented DNA was purified using the MinElute kit (Qiagen).
The DNA was combined with the ATAC index PCR primers and 2x Kapa HiFi Hotstart Ready Mix and pre-amplified (98°C 30 seconds, 5x [98°C 10 seconds, 63°C 30 seconds, 72°C 1 minute] in a 50 μl volume. To determine the remaining cycles to avoid potential over-amplification, 5 μl of the pre-amplification mix was combined with the primers, 1x Evagreen SYBR green (Jena Biosciences) and 2x Kapa HiFi Hotstart Ready Mix in a 15 μl total volume and run for 30 cycles on a StepOne Plus. The remaining 45 μl of pre-amplified samples were amplified for a further 6-16 cycles and the libraries were purified using MinElute column (Qiagen). The libraries were quantified using the Qubit DNA HS assay and the library sizes were validated using DNA HS Bioanalyzer chips.


title: WSU-DLCL2 ACVR1KO DMSO rep1

value: ACVR1 -/-


title: ATAC_dTAG13_24h_rep1

data_processing:
Reads were trimmed to 40 bp length and adapter sequences were removed using cutadapt. The trimmed reads were aligned to the reference genome using bowtie (version 1.1.2) (Langmead, 2009) with the following arguments: -y -v 2 --best --strata -m 3 -k 1 -S -X 2000 --allow-contain. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. Reads mapped to chr M and Y or known ATAC artifact regions (ENCODE) were removed using samtools. Possible PCR duplicates were removed using Picard (version 1.103, https://broadinstitute.github.io/picard). For visualization, the reads from replicates were combined, and the data were normalized and converted to bigWig format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing RPCG --effectiveGenomeSize 2652783500 --extendReads 200 --smoothLength 9 -bs 9 -ignore chrY chrM.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
The cells were lysed in 50 μl of cold lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged at 500g, 4°C for 10 min. The pellet was resuspended in the transposition reaction mix (25 μl 2x TD buffer, 2.5 μl Tn5 transposase, 22.5 μl H2O) and incubated at 37°C for 30 minutes. After incubation, the reaction was stopped with the addition of PB buffer (Qiagen) and the tagmented DNA was purified using the MinElute kit (Qiagen).
The DNA was combined with the ATAC index PCR primers and 2x Kapa HiFi Hotstart Ready Mix and pre-amplified (98°C 30 seconds, 5x [98°C 10 seconds, 63°C 30 seconds, 72°C 1 minute] in a 50 μl volume. To determine the remaining cycles to avoid potential over-amplification, 5 μl of the pre-amplification mix was combined with the primers, 1x Evagreen SYBR green (Jena Biosciences) and 2x Kapa HiFi Hotstart Ready Mix in a 15 μl total volume and run for 30 cycles on a StepOne Plus. The remaining 45 μl of pre-amplified samples were amplified for a further 6-13 cycles and the libraries were purified using MinElute column (Qiagen). The libraries were quantified using the Qubit DNA HS assay and the library sizes were validated using DNA HS Bioanalyzer chips.


title: HC_LCL5_3


title: WSU-DLCL2 MAK683 rep3

value: wild type


title: SLCL_SMS2


title: ATAC_dTAG13_12h_rep2

data_processing:
Reads were trimmed to 40 bp length and adapter sequences were removed using cutadapt. The trimmed reads were aligned to the reference genome using bowtie (version 1.1.2) (Langmead, 2009) with the following arguments: -y -v 2 --best --strata -m 3 -k 1 -S -X 2000 --allow-contain. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. Reads mapped to chr M and Y or known ATAC artifact regions (ENCODE) were removed using samtools. Possible PCR duplicates were removed using Picard (version 1.103, https://broadinstitute.github.io/picard). For visualization, the reads from replicates were combined, and the data were normalized and converted to bigWig format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing RPCG --effectiveGenomeSize 2652783500 --extendReads 200 --smoothLength 9 -bs 8 -ignore chrY chrM.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
The cells were lysed in 50 μl of cold lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged at 500g, 4°C for 10 min. The pellet was resuspended in the transposition reaction mix (25 μl 2x TD buffer, 2.5 μl Tn5 transposase, 22.5 μl H2O) and incubated at 37°C for 30 minutes. After incubation, the reaction was stopped with the addition of PB buffer (Qiagen) and the tagmented DNA was purified using the MinElute kit (Qiagen).
The DNA was combined with the ATAC index PCR primers and 2x Kapa HiFi Hotstart Ready Mix and pre-amplified (98°C 30 seconds, 5x [98°C 10 seconds, 63°C 30 seconds, 72°C 1 minute] in a 50 μl volume. To determine the remaining cycles to avoid potential over-amplification, 5 μl of the pre-amplification mix was combined with the primers, 1x Evagreen SYBR green (Jena Biosciences) and 2x Kapa HiFi Hotstart Ready Mix in a 15 μl total volume and run for 30 cycles on a StepOne Plus. The remaining 45 μl of pre-amplified samples were amplified for a further 6-12 cycles and the libraries were purified using MinElute column (Qiagen). The libraries were quantified using the Qubit DNA HS assay and the library sizes were validated using DNA HS Bioanalyzer chips.


title: SLCL_SMS3


title: WSU-DLCL2 ACVR1KO DMSO rep3


title: colorectal cancer tissue sample AUS2_796_T2

value: colorectal cancer tissue sample


title: WSU-DLCL2 MAK683 rep2


title: WSU-DLCL2 MAK683 rep1


title: SLCL_SMS1


title: ATAC_dTAG13_12h_rep1

data_processing:
Reads were trimmed to 40 bp length and adapter sequences were removed using cutadapt. The trimmed reads were aligned to the reference genome using bowtie (version 1.1.2) (Langmead, 2009) with the following arguments: -y -v 2 --best --strata -m 3 -k 1 -S -X 2000 --allow-contain. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. Reads mapped to chr M and Y or known ATAC artifact regions (ENCODE) were removed using samtools. Possible PCR duplicates were removed using Picard (version 1.103, https://broadinstitute.github.io/picard). For visualization, the reads from replicates were combined, and the data were normalized and converted to bigWig format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing RPCG --effectiveGenomeSize 2652783500 --extendReads 200 --smoothLength 9 -bs 7 -ignore chrY chrM.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
The cells were lysed in 50 μl of cold lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged at 500g, 4°C for 10 min. The pellet was resuspended in the transposition reaction mix (25 μl 2x TD buffer, 2.5 μl Tn5 transposase, 22.5 μl H2O) and incubated at 37°C for 30 minutes. After incubation, the reaction was stopped with the addition of PB buffer (Qiagen) and the tagmented DNA was purified using the MinElute kit (Qiagen).
The DNA was combined with the ATAC index PCR primers and 2x Kapa HiFi Hotstart Ready Mix and pre-amplified (98°C 30 seconds, 5x [98°C 10 seconds, 63°C 30 seconds, 72°C 1 minute] in a 50 μl volume. To determine the remaining cycles to avoid potential over-amplification, 5 μl of the pre-amplification mix was combined with the primers, 1x Evagreen SYBR green (Jena Biosciences) and 2x Kapa HiFi Hotstart Ready Mix in a 15 μl total volume and run for 30 cycles on a StepOne Plus. The remaining 45 μl of pre-amplified samples were amplified for a further 6-11 cycles and the libraries were purified using MinElute column (Qiagen). The libraries were quantified using the Qubit DNA HS assay and the library sizes were validated using DNA HS Bioanalyzer chips.


title: SLCL_HC1


title: colorectal cancer tissue sample AUS2_796_T


title: colorectal cancer tissue sample AUS2_795_T


title: WSU-DLCL2 DMSO rep3


title: SLCL_AMS3


title: colorectal cancer tissue sample AUS2_795_T3


title: colorectal cancer tissue sample AUS2_795_T2


title: ATAC_DMSO_24h_rep1

data_processing:
Reads were trimmed to 40 bp length and adapter sequences were removed using cutadapt. The trimmed reads were aligned to the reference genome using bowtie (version 1.1.2) (Langmead, 2009) with the following arguments: -y -v 2 --best --strata -m 3 -k 1 -S -X 2000 --allow-contain. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. Reads mapped to chr M and Y or known ATAC artifact regions (ENCODE) were removed using samtools. Possible PCR duplicates were removed using Picard (version 1.103, https://broadinstitute.github.io/picard). For visualization, the reads from replicates were combined, and the data were normalized and converted to bigWig format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing RPCG --effectiveGenomeSize 2652783500 --extendReads 200 --smoothLength 9 -bs 5 -ignore chrY chrM.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
The cells were lysed in 50 μl of cold lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged at 500g, 4°C for 10 min. The pellet was resuspended in the transposition reaction mix (25 μl 2x TD buffer, 2.5 μl Tn5 transposase, 22.5 μl H2O) and incubated at 37°C for 30 minutes. After incubation, the reaction was stopped with the addition of PB buffer (Qiagen) and the tagmented DNA was purified using the MinElute kit (Qiagen).
The DNA was combined with the ATAC index PCR primers and 2x Kapa HiFi Hotstart Ready Mix and pre-amplified (98°C 30 seconds, 5x [98°C 10 seconds, 63°C 30 seconds, 72°C 1 minute] in a 50 μl volume. To determine the remaining cycles to avoid potential over-amplification, 5 μl of the pre-amplification mix was combined with the primers, 1x Evagreen SYBR green (Jena Biosciences) and 2x Kapa HiFi Hotstart Ready Mix in a 15 μl total volume and run for 30 cycles on a StepOne Plus. The remaining 45 μl of pre-amplified samples were amplified for a further 6-9 cycles and the libraries were purified using MinElute column (Qiagen). The libraries were quantified using the Qubit DNA HS assay and the library sizes were validated using DNA HS Bioanalyzer chips.

value: WT


title: WSU-DLCL2 DMSO rep2


title: SLCL_AMS2


title: ATAC_DMSO_12h_rep2

data_processing:
Reads were trimmed to 40 bp length and adapter sequences were removed using cutadapt. The trimmed reads were aligned to the reference genome using bowtie (version 1.1.2) (Langmead, 2009) with the following arguments: -y -v 2 --best --strata -m 3 -k 1 -S -X 2000 --allow-contain. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. Reads mapped to chr M and Y or known ATAC artifact regions (ENCODE) were removed using samtools. Possible PCR duplicates were removed using Picard (version 1.103, https://broadinstitute.github.io/picard). For visualization, the reads from replicates were combined, and the data were normalized and converted to bigWig format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing RPCG --effectiveGenomeSize 2652783500 --extendReads 200 --smoothLength 9 -bs 4 -ignore chrY chrM.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
The cells were lysed in 50 μl of cold lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged at 500g, 4°C for 10 min. The pellet was resuspended in the transposition reaction mix (25 μl 2x TD buffer, 2.5 μl Tn5 transposase, 22.5 μl H2O) and incubated at 37°C for 30 minutes. After incubation, the reaction was stopped with the addition of PB buffer (Qiagen) and the tagmented DNA was purified using the MinElute kit (Qiagen).
The DNA was combined with the ATAC index PCR primers and 2x Kapa HiFi Hotstart Ready Mix and pre-amplified (98°C 30 seconds, 5x [98°C 10 seconds, 63°C 30 seconds, 72°C 1 minute] in a 50 μl volume. To determine the remaining cycles to avoid potential over-amplification, 5 μl of the pre-amplification mix was combined with the primers, 1x Evagreen SYBR green (Jena Biosciences) and 2x Kapa HiFi Hotstart Ready Mix in a 15 μl total volume and run for 30 cycles on a StepOne Plus. The remaining 45 μl of pre-amplified samples were amplified for a further 6-8 cycles and the libraries were purified using MinElute column (Qiagen). The libraries were quantified using the Qubit DNA HS assay and the library sizes were validated using DNA HS Bioanalyzer chips.


title: colorectal cancer tissue sample AUS2_794_T3

data_processing: Gene level expression values were estimated according to the robust multi-array average (RMA) approach implemented with the justRMA function in the R package affy and using custom CDF files from Brainarray. A batch effect from different lot numbers of the GeneChip™ WT Plus Reagent Kit was corrected with ComBat in the R package sva using default parameters (the batch of each sample is indicated as analysis batch.

extract_protocol: Total RNA was isolated from colorectal cancer tissue samples using the Qiagen Allprep DNA/RNA/miRNA Universal kit, according to the manufacturer's protocol (Qiagen).

value: no


title: colorectal cancer tissue sample AUS2_794_T2


title: WSU-DLCL2 DMSO rep1


title: HC_LCL2_2


title: SLCL_AMS1


title: colorectal cancer tissue sample AUS2_794_T


title: SLCL_AMS4


title: Liver, anti-CSF1R

city: Liverpool

first: Michael

middle: C

last: Schmid

state: Merseyside

address: Ashton Street

department: Molecular and Clinical Cancer Medicine

country: United Kingdom

institute: University of Liverpool

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: features, cell barcodes and mtx files in tsv.gz and mtx.gz format

source_name: Liver

extract_protocol:
Freshly dissected livers were minced finely and incubated in digestion buffer (1mg/ml collgenase P in Ca2+/Mg2+ containing HBSS) in a shaking incubator at 37 degrees for 30 minutes. Cell extract was further digested with 0.25% trypsin-EDTA at 37 degrees for 5 minutes. After removal of RBCs, cells were then resuspended in PBS + 0.5% BSA and stained with viability dye and CD45, CD31,  and Epcam antibodies. Live, CD45-, CD31-, Epcam-, GFP+ cells were then isolated using FACS.
Library construction was performed using Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 and Chromium Next GEM Chip G Single Cell Kit v3.1, according to the manufacter’s instructions

treatment_protocol: Experimental liver metastasis was induced in 6 week old Pdgfrb-GFP mice. From day 7, to 14, metastasis-bearing mice were treated with IgG, or anti-CSF1R therapy.

value: Liver

value: Fibroblast

value: Pdgfrb-GFP

tag: time

value: Advanced metastasis

tag: location

value: tumor


title: ATAC_DMSO_24h_rep2

data_processing:
Reads were trimmed to 40 bp length and adapter sequences were removed using cutadapt. The trimmed reads were aligned to the reference genome using bowtie (version 1.1.2) (Langmead, 2009) with the following arguments: -y -v 2 --best --strata -m 3 -k 1 -S -X 2000 --allow-contain. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. Reads mapped to chr M and Y or known ATAC artifact regions (ENCODE) were removed using samtools. Possible PCR duplicates were removed using Picard (version 1.103, https://broadinstitute.github.io/picard). For visualization, the reads from replicates were combined, and the data were normalized and converted to bigWig format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing RPCG --effectiveGenomeSize 2652783500 --extendReads 200 --smoothLength 9 -bs 6 -ignore chrY chrM.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
The cells were lysed in 50 μl of cold lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged at 500g, 4°C for 10 min. The pellet was resuspended in the transposition reaction mix (25 μl 2x TD buffer, 2.5 μl Tn5 transposase, 22.5 μl H2O) and incubated at 37°C for 30 minutes. After incubation, the reaction was stopped with the addition of PB buffer (Qiagen) and the tagmented DNA was purified using the MinElute kit (Qiagen).
The DNA was combined with the ATAC index PCR primers and 2x Kapa HiFi Hotstart Ready Mix and pre-amplified (98°C 30 seconds, 5x [98°C 10 seconds, 63°C 30 seconds, 72°C 1 minute] in a 50 μl volume. To determine the remaining cycles to avoid potential over-amplification, 5 μl of the pre-amplification mix was combined with the primers, 1x Evagreen SYBR green (Jena Biosciences) and 2x Kapa HiFi Hotstart Ready Mix in a 15 μl total volume and run for 30 cycles on a StepOne Plus. The remaining 45 μl of pre-amplified samples were amplified for a further 6-10 cycles and the libraries were purified using MinElute column (Qiagen). The libraries were quantified using the Qubit DNA HS assay and the library sizes were validated using DNA HS Bioanalyzer chips.

value: untreated


title: colorectal cancer tissue sample AUS2_793_T2


title: HC_LCL2_1

value: blood

value: lymphoblastoid cell lines

value: Healthy Control


title: Liver, IgG

value: IgG control


title: Liver, Naïve

value: No tumor


title: colorectal cancer tissue sample AUS2_793_T

value: T


title: HC_LCL1_1


title: scRNA_E95_mCherry_and_GFP_mCherry_dual

first: Sara

last: Hetzel

address: Ihnestraße 63

department: Genome Regulation

institute: Max Planck Institute for Molecular Genetics

data_processing:
Raw base call (BCL) files generated by Illumina sequencers were demultiplexed into FASTQ files using 10X Genomics' Single-Cell Gene Expression Software Cell Ranger ("mkfastq" pipeline, version 6.0.1, default parameters).
FASTQ files were aligned, filtered, barcode and UMI counted using 10X Genomics' Single-Cell Gene Expression Software Cell Ranger ("count pipeline", version 6.0.1, default parameters).
mm10 (including mCherry and GFP transgenes)
The tar gz archive contains the raw gene-barcode matrix as produced by the Cell Ranger pipeline and the MEX-formatted UMI count matrix. 10x Genomics explains their MEX-formatted UMI counts as follows: "The cellranger pipeline generates a gene-barcode matrix... Each matrix is stored in Market Exchange Format (MEX). It also contains TSV files with genes and barcode sequences corresponding to row and column indices, respectively." More information on the formatting can be found at https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices.
Assembly: mm10 (including mCherry and GFP transgenes)

source_name: Sorted cells from pooled embryos

growth_protocol: GFP+ mESCs were cultured on mitotically inactive primary mouse embryo fibroblasts in serum/LIF condition for two days. Aggregated embryos, cultured in KSOM, that progressed to the expanded blastocyst stage were transferred to a pseudo-pregnant CD1 female. Post-implantation embryos were isolated at the indicated stage, including a 24-hour developmental delay due to the uterine transfer procedure.

extract_protocol:
Extraembryonic tissues were removed, and pooled embryos were dissociated using 0,25% Trypsin-EDTA, at 37 ºC for 10 minutes. The cells were washed with 10% FBS/DMEM, then stained with DAPI in 2% FBS/HBSS with 0,5 mM EDTA (FACS buffer) at 4 ºC for 8 minutes. Cells were resuspended in FACS buffer and the indicated populations were sorted into PBS using the BD FACSAria Fusion. The sorted populations were labelled with distinct MULTI-seq surface barcodes, and the cell suspension was filtered with Flowmi Cell Strainers 40 µM before subjected to single-cell RNA sequencing (10x Genomics, Chromium™ Single Cell 3’ v3.1).
Single-cell RNA-seq libraries were generated following the manual instructions of 10x Genomics, Chromium™ Single Cell 3’ v3.1, with the exception of fewer PCR cycles in the cDNA amplification step, where the MULTI-seq surface barcodes were also amplified. MULTI-seq libraries were generated parallel to the single-cell RNA-seq libraries.
scRNA-Seq

treatment_protocol: Embryos were generated by diploid complementation assay with aggregation. In each depression of the aggregation plate, one small GFP+ mESC colony of about 8-15 cells was added together with one zona pellucida-free mCherry+ pre-compaction morula.

value: Sorted cells from pooled embryos

tag: strain

value: mCherry+ morula (CD1/G4) aggregated with GFP+ mESCs (G4)

tag: developmental stage


title: UPF1_MOCK_INPUT

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Data was processed using the eCLIP pipeline and available at: http://github.com/yeolab/eclip
Unique Molecular Identifiers (UMIs) were extracted from raw sequencing reads with umi_tools extract
Post-umi-extracted reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using cutadapt.
Trimmed reads were mapped against RepBase with STAR to remove reads mapping to repetitive sequences (--outFilterMultimapNmax 30 --alignEndsType EndToEnd --outFilterMultimapScoreRange 1 --outSAMmode Full --outFilterType BySJout --outSAMtype BAM Unsorted --outFilterScoreMin 10 --outReadsUnmapped Fastx --outSAMattributes All)
Remaining reads were mapped to the appropriate genome build (mm10) using STAR aligner (--outFilterMultimapNmax 1 --alignEndsType EndToEnd --outFilterMultimapScoreRange 1 --outSAMmode Full --outFilterType BySJout --outSAMtype BAM Unsorted --outFilterScoreMin 10 --outReadsUnmapped Fastx --outSAMattributes All)
Uniquely mapped reads were removed of PCR duplicates with umi_tools
Peak clusters were identified with CLIPper, available at: https://github.com/YeoLab/clipper
Clusters enriched over corresponding size-matched input (SMInput) were identified using a custom Perl script, available in the main eCLIP repository as: overlap_peakfi_with_bam.pl
Overlapping enriched clusters (peaks) were merged with a custom perl script, available in the main eCLIP repository as: compress_l2foldenrpeakfi_for_replicate_overlapping_bedformat.pl
Assembly: mm10
Supplementary files format and content: bigwigs contain RPM-normalized read densities of uniquely-mapped reads
Supplementary files format and content: BED files contain CLIPper peak clusters. Columns 4 and 5 describe the -log10(p-value) and log2(fold) enrichment IP over corresponding SMInput.

source_name: Cortex

growth_protocol: Mouse NPCs were cultured in DMEM/F12 media with 1x B27 and 1x penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were lysed and and sonicated in eCLIP lysis buffer, and RNA was fragmented using RNase I (Ambion) and UPF1:RNA complexes were immunoprecipitated with UPF1-specific antibody (A301-902A)
RNA was reverse transcripted with Superscript III, and adaptor was ligated with T4 RNA Ligase 1, then libraries were constructed with Q5 High-Fidelity 2x Master Mix (NEB)

value: Cortex

value: neural progenitor cells


title: HC_LCL5_1

data_processing:
Sequenced reads were aligned using RSEM along with Bowtie2 against the human genome (version: hg19)
DESeq2 was used to normalize the reads and obtain the differentially expressed genes

extract_protocol: Lexogen Quantseq


title: HC_LCL5_2


title: colorectal cancer tissue sample AUS2_792_T3

value: colorectal cancer tissue sample

value: no


title: ATAC_DMSO_12h_rep1

data_processing:
Reads were trimmed to 40 bp length and adapter sequences were removed using cutadapt. The trimmed reads were aligned to the reference genome using bowtie (version 1.1.2) (Langmead, 2009) with the following arguments: -y -v 2 --best --strata -m 3 -k 1 -S -X 2000 --allow-contain. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. Reads mapped to chr M and Y or known ATAC artifact regions (ENCODE) were removed using samtools. Possible PCR duplicates were removed using Picard (version 1.103, https://broadinstitute.github.io/picard). For visualization, the reads from replicates were combined, and the data were normalized and converted to bigWig format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing RPCG --effectiveGenomeSize 2652783500 --extendReads 200 --smoothLength 9 -bs 3 -ignore chrY chrM.
genome build/assembly: mm10
processed data files format and content: bigWig files representing read density

extract_protocol:
The cells were lysed in 50 μl of cold lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged at 500g, 4°C for 10 min. The pellet was resuspended in the transposition reaction mix (25 μl 2x TD buffer, 2.5 μl Tn5 transposase, 22.5 μl H2O) and incubated at 37°C for 30 minutes. After incubation, the reaction was stopped with the addition of PB buffer (Qiagen) and the tagmented DNA was purified using the MinElute kit (Qiagen).
The DNA was combined with the ATAC index PCR primers and 2x Kapa HiFi Hotstart Ready Mix and pre-amplified (98°C 30 seconds, 5x [98°C 10 seconds, 63°C 30 seconds, 72°C 1 minute] in a 50 μl volume. To determine the remaining cycles to avoid potential over-amplification, 5 μl of the pre-amplification mix was combined with the primers, 1x Evagreen SYBR green (Jena Biosciences) and 2x Kapa HiFi Hotstart Ready Mix in a 15 μl total volume and run for 30 cycles on a StepOne Plus. The remaining 45 μl of pre-amplified samples were amplified for a further 6-7 cycles and the libraries were purified using MinElute column (Qiagen). The libraries were quantified using the Qubit DNA HS assay and the library sizes were validated using DNA HS Bioanalyzer chips.

value: embryonic stem cells

value: WT


title: colorectal cancer tissue sample AUS2_792_T2


title: saline treated Mybpc3R946X/R946X rep3

city: shanghai

first: wu

last: shuo

address: dongchuan road

institute: shanghai jiaotong university

description:
MUvsWT.csv
MUvsWT_DEG.csv
THvsMU.csv
THvsMU_DEG.csv

data_processing:
RNA-seq reads were aligned to mm10 genome assembly using hisat2.
Count  per Million mapped reads (CPM) were calculated using Htseq.
Differentially expressed genes were identified using DESeq2
Assembly: mm10
Supplementary files format and content: csv

source_name: Adult mouse heart

extract_protocol:
Hearts were removed from chests, 20-30mg hearts tissue from adult mice were flash frozen. Total RNA were extracted using RNAsimple Total RNA Kit (TIANGEN, DP419).
mRNA was enriched using oligo(dT)-attached magnetic beads. The complementary DNA (cDNA) was synthesized after mRNA fragmentation, constructed into barcoded library.

value: Adult mouse heart

value: saline


title: UPF1_MOCK


title: colorectal cancer tissue sample AUS2_792_T


title: HC_LCL6_2


title: saline treated Mybpc3R946X/R946X rep1


title: colorectal cancer tissue sample AUS2_791_T3


title: HC_LCL1_2


title: colorectal cancer tissue sample AUS2_792_INV

value: INV


title: HC_LCL4_1

value: blood


title: HC_LCL6_1

value: lymphoblastoid cell lines


title: HC_LCL4_2

value: Healthy Control


title: HC_LCL3_2


title: HC_LCL3_1


title: high-dose-exABE8e treated Mybpc3R946X/R946X rep1

description:
THvsWT.csv
THvsWT_DEG.csv
THvsMU.csv
THvsMU_DEG.csv


title: MS_LCL3_2

value: Multiple Sclerosis


title: high-dose-exABE8e treated Mybpc3R946X/R946X rep3


title: saline treated Mybpc3wt rep3

description:
MUvsWT.csv
MUvsWT_DEG.csv
THvsWT.csv
THvsWT_DEG.csv

value: wildtype


title: colorectal cancer tissue sample AUS2_791_T2


title: MS_LCL3_1


title: saline treated Mybpc3R946X/R946X rep2


title: colorectal cancer tissue sample AUS2_790_T3


title: colorectal cancer tissue sample AUS2_791_T

value: T


title: MS_LCL1_1


title: colorectal cancer tissue sample AUS2_790_T


title: colorectal cancer tissue sample AUS2_790_T2


title: saline treated Mybpc3wt rep2


title: MS_LCL1_2


title: SNU-484 parental-2 [shSOX13-5]

first: Ming

middle: zhe

last: Ma

email: mmz666@163.com, mmz666@shca.org.cn

address: Dongan Road 270

department: Department of gastric surgery

institute: Fudan university shanghai cancer center

description: raw counts

data_processing:
Bioinformatics data analysis was provided by NewCore BioTech. (Shanghai, China). Briefly, fastp  software (v0.20.0) was used to trim adaptor and remove low quality reads to get high quality clean  reads. STAR software (v2.7.9a) was used to align the high-quality clean reads to the human reference
genome (hg38). featureCounts software (v2.0) was used to get the raw gene level mRNA read counts  as the mRNA expression profile.
Assembly: hg38
Supplementary files format and content: raw counts within excel file

source_name: gastric cancer cell line SNU-484

growth_protocol: SNU-668 Erastin-resistant cells and SUN-484 RSL3-resistant cells were routinely generated by re-plating d 4 in DMEM supplemented with 10% FBS

extract_protocol:
Total RNA was extracted using Trizol Reagent (ThermoFisher, 15596026). rRNA was removed from total RNA. Then enriched with oligo dT.
KAPA Stranded RNA-Seq library Prep Kit (Roche) was used for library constructioin. Then Agilent 2100 Bioanalyzer was used to examine the library quality. And then library was sequenced on a DNBSEQ-T7 platerform.

treatment_protocol: SNU-484 or SNU-668 cells (2 × 10^6) were inoculated in a 10-cm cell culture dish and exposed to low concentration of RSL3 (0.5 μM) or Erastin (2 μM) for 28 days, then these cells were exposed to high concentration of RSL3 (1 μM) or Erastin (5 μM) for another 28 days. The culture medium was routinely changed every other day, and the concentrations of the compounds were maintained at the indicated levels. The surviving clones were trypsinized, collected and expanded. A cell viability assay was utilized to assess the sensitivity of the surviving cells to Erastin or RSL3. The acquired ferroptosis-resistance was validated.

value: gastric cancer cell line SNU-484

value: gastric cancer cells

value: parental


title: colorectal cancer tissue sample AUS2_788_T2


title: colorectal cancer tissue sample AUS2_788_T3


title: colorectal cancer tissue sample AUS2_786_T


title: MS_LCL2_1


title: MS_LCL5_2


title: SNU-668 parental-3 [shSOX13-3]

description: raw counts

source_name: gastric cancer cell line SNU-668

value: gastric cancer cell line SNU-668


title: SNU-484 parental-3 [shSOX13-6]

description: raw counts


title: MS_LCL5_1


title: high-dose-exABE8e treated Mybpc3R946X/R946X rep2


title: MS_LCL2_2


title: colorectal cancer tissue sample AUS2_786_T3

value: colorectal cancer tissue sample


title: colorectal cancer tissue sample AUS2_785_T2

value: no


title: SNU-484 parental-1 [shSOX13-4]

description: raw counts


title: colorectal cancer tissue sample AUS2_785_T3


title: colorectal cancer tissue sample AUS2_788_T


title: MS_LCL6_2


title: colorectal cancer tissue sample AUS2_785_T


title: SNU-484 RSL3 resistant-3

description: raw counts

value: RSL3 resistant


title: saline treated Mybpc3wt rep1


title: SNU-668 parental-2 [shSOX13-2]

description: raw counts

value: WT


title: SNU-668 parental-1 [shSOX13-1]

description: raw counts


title: colorectal cancer tissue sample AUS2_785_INV


title: WSU-DLCL2 MAK683 CRISPR screen

data_processing:
Illumina HiSeq X10 software used for basecalling.
sgRNA counts were generated using MAGeCK (version 0.5.9.3)  count command using default parameters.
Statistical comparisons between DMSO and MAK683 for each genotype were computed using MAGeCK test command using default parameters
Assembly: hg38
Supplementary files format and content: tab-delimited text files include genes or sgRNAs count value, p value and rank for each sample.DMSO treatment served as the control group.MAK683 treatment served as the treatment group.
Library strategy: CRISPR screen

extract_protocol:
Genomic DNA of cells containing 800 coverage was harvested (Qiagen # 51192) on day 14 after drug treatment. sgRNAs were recovered by PCR amplification (New England Biolabs # M0530L ) in a single-step reaction of 27 cycles. PCR products from all reactions were pooled and purified by gel extraction (Omega # D2500-02).
For each sample, >50ng purified PCR fragment was used for library preparation. These PCR products were treated with End Prep Enzyme Mix for end repairing, 5’ Phosphorylation and dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Adaptor ligated DNA was then performed using DNA Clean Beads. A second PCR reaction was carried out with P5 and P7 primers carrying sequences which can anneal with flowcell to perform bridge PCR and index allowing for multiplexing. The final library product for sequencing were then purified by beads and was qualified. The qualified libraries were sequenced pair end 150bp on illumina Hiseq X10 System.

treatment_protocol: WSU-DLCL2 cells stably integrated with spCas9 were transduced with GeCKO v2 (A and B) human library , after seletion cells were treated with  0.2 μM MAK683 or DMSO for 14 days

value: wild type


title: colorectal cancer tissue sample AUS2_784_T


title: MS_LCL6_1


title: colorectal cancer tissue sample AUS2_784_T2


title: CD14+ monocytes patient D 3 month post-upadacitinib treatment

city: Madrid

first: Amaya

middle: Rocío

last: Puig Kröger

state: Madrid

address: Dr. Esquerdo 46

department: Immunology

country: Spain

data_processing:
BGISEQ platform
Low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) were filtered to get the clean reads.Sequences were mapped to GRCh38 genome using  Bowtie2 with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression levels were determined with software RSEM
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include Entrez Gene ID and FPKM values for each Sample

source_name: peripheral blood

growth_protocol: Blood was obtained in K2-EDTA tubes. Human Peripheral Blood Mononuclear Cells (PBMC) were isolated over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells) and total RNA was isolated.

extract_protocol:
Total RNA was extracted using the Rneasy Micro kit (QIAgen). RNA integrity was validated by LabChip RNA Analysis (Perkin Elmer).
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Three patients with rheumatoid arthritis (RA) and inadequate response to disease modifying anti-rheumatic drugs (DMARD) receiving upadacitinib as indicated by the treating rheumatologist were invited to participated in this study. Informed consent was obtained from these participants and the study was conducted in accordance with the Declaration of Helsinki, and approved by the Ethical Committee of Hospital General Universitario Gregorio Marañón (protocol code: JAKi-2022-v1). The three patients with seropositive RA were female with a mean (SD) age of 45 (15) years and moderate disease activity before initiating upadacitinib treatment (rinvoq 15 mg daily) with a mean (SD) CRP basedDisease Activity Score 28- joint counts (DAS28-CRP) of 4.1 (0.7). The three patients showed improvementatthree months follow-up with a mean (SD) DAS28-CRP of1.1 (0.2).

value: peripheral blood

value: monocytes

value: Peripheral blood monocytes

tag: subject status

value: rheumatoid arthritis patient

value: 3 month-Upadacitinib treatment


title: MS_LCL4_2

value: blood

tag: cell type

value: lymphoblastoid cell lines

value: Multiple Sclerosis


title: colorectal cancer tissue sample AUS2_781_T3


title: colorectal cancer tissue sample AUS2_780_T2


title: nh_inverted, st14, rep3

city: Princeton

first: Wenfan

last: Ke

state: New Jersey

address: 119 Lewis Thomas Laboratory

department: Department of Molecular Biology

institute: Princeton University

data_processing:
MicroC data for D. melanogaster were aligned to custom genomes edited from the Berkeley Drosophila Genome Project (BDGP) Release 6 reference assembly (dos Santos et al., 2015) with BWA-MEM (Li and Durbin, 2009) using parameters -S -P -5 -M.  Briefly, the custom genomes are simply insertions of the transgenic sequence into the –142kb integration site, as predicted from perfect integration.  These events were confirmed using PCR post-integration.  The resultant BAM files were parsed, sorted, de-duplicated, filtered, and split with Pairtools (https://github.com/mirnylab/pairtools).  We removed pairs where only half of the pair could be mapped, or where the MAPQ score was less than three.  The resultant files were indexed with Pairix (https://github.com/4dn-dcic/pairix).  The files from replicates were merged with Pairtools before generating 100bp contact matrices using Cooler (Abdennur and Mirny, 2020).  Finally, balancing and Mcool file generation was performed with Cooler’s Zoomify tool.
Assembly: dm6
Supplementary files format and content: mcool files generated by cooler for visualizing 3D genome organization
Library strategy: Micro-C

organism: Drosophila melanogaster

source_name: whole embryo, st14

growth_protocol: Embryos were collected on yeasted apple juice plates in population cages for 4 hours, incubated for 12 hours at 25℃, then subjected to fixation

extract_protocol:
Embryos were dechorionated for 2 mins in 3% sodium hypochlorite, rinsed with deionized water, and transferred to glass vials containing 5 mL PBST (0.1% Triton-X100 in PBS), 7.5 mL n-heptane, and 1.5mL fresh 16% formaldehyde.  Crosslinking was carried out at room temperature for exactly 15 mins on an orbital shaker at 250rpm, followed by addition of 3.7 mL 2M Tris-HCl pH7.5 and shaking for 5 mins to quench the reaction.  Embryos were washed twice with 15 mL PBST and subjected to secondary crosslinking.  Secondary crosslinking was done in 10mL of freshly prepared 3mM final DSG and ESG in PBST for 45 mins at room temperature with passive mixing.  The reaction was quenched by addition of 3.7mL 2M Tris-HCl pH7.5 for 5 mins, washed twice with PBST, snap-frozen, and stored at -80℃ until library construction.
Micro-C libraries were prepared as previously described (Batut et al., 2022) with the following modifications: 50uL of 12-16hr embryos were used for each biological replicate.  60U of MNase was used for each reaction to digest chromatin to a mononucleosome:dinucleosome ratio of 4.
Libraries were barcoded, pooled and subjected to paired-end sequencing on an Illumina Novaseq S1 100 nt Flowcell (read length 50 bases per mate, 6-base index read)

value: whole embryo, st14

tag: genetic modification

value: nhomie replaced by nhomie reversed


title: SNU-484 RSL3 resistant-2

description: raw counts

value: gastric cancer cell line SNU-484

value: gastric cancer cells


title: MS_LCL4_1

tag: batch


title: nh_forward, st14, rep2

tag: tissue

value: nhomie replaced by nhomie forward


title: SNU-484 RSL3 resistant-1

description: raw counts


title: colorectal cancer tissue sample AUS2_778_T2

value: colorectal cancer tissue sample

value: no


title: colorectal cancer tissue sample AUS2_776_T

value: T


title: SNU-668 Erastin resistant-3

description: raw counts

value: gastric cancer cell line SNU-668

value: WT

value: Erastin resistant


title: CD14+ monocytes patient C 3 month post-upadacitinib treatment

institute: Hospital General Universitario Gregorio Marañón

value: peripheral blood

value: monocytes

value: Peripheral blood monocytes


title: colorectal cancer tissue sample AUS2_781_T


title: nh_forward, st14, rep1


title: CD14+ monocytes patient D pre-upadacitinib

value: rheumatoid arthritis patient

value: Pre-treatment


title: SNU-668 Erastin resistant-2

description: raw counts


title: WSU-DLCL2 DMSO CRISPR screen

value: wild type

value: DMSO


title: colorectal cancer tissue sample AUS2_781_T2