title: IFNg_Ezh2i_rep3

data_processing:
Bulk RNA-seq samples were preprocessed for adapter/quality trimming and then aligned to the transcriptome using STAR with EnsEMBLv75 annotations. Filtered fastq files were used in Salmon 0.8.2 to recover raw reads counts and transcripts per million (TPM) values per transcript and gene. The differential gene expression analysis was performed from the estimated gene counts with Deseq2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: P13159_100*_quant.sf: Contains the tab-separated table of normalized abundance measurements output from Salmon at transcript level. With EnsEMBL75 mm10 annotation, for each of the 12 samples. Including transcript length, estimated number of counts and TPM.
Supplementary_files_format_and_content: Ctrl_Ezh2i_DGE_deseq2.Gene.res: Differential gene expression output from Deseq2 using as reference the 3 replicates of the Ctrl samples compared to the 3 replicates of the 1.5 uM Ezh2i treated samples.
Supplementary_files_format_and_content: Ifng_Ezh2i_DGE_deseq2.Gene.res: Differential gene expression output from Deseq2 using as reference the 3 replicates of the IFNg samples compared to the 3 replicates of the 1.5 uM Ezh2i treated samples.

extract_protocol:
Cells were collected with qiazol (Qiagen) and stored at -80°C until further processing. RNA was extracted with the miRNeasy mini kit (Qiagen) according to manufacturer’s instructions. Contaminating DNA was degraded by treatment of the samples with RNase-free DNase (Qiagen) in column.
0.1-1ug of RNA was used to make RNA-seq libraries with the TruSeq Stranded Total RNA Library Prep Gold kit (Illumina) according to manufacturer's instructions. Three replicates per condition were performed with primary OPCs obtained from different litters. Libraries were sequenced on an Illumina Novaseq 6000 with a 150-8-8-150 read set-up.

treatment_protocol: Cells were treated with EZH2 inhibitor (EPZ011989, 1.5uM, S7805, Selleckchem) for 4 days, renewing the inhibitor every 48 hours. After 4 days IFN-gamma (100ng/ml) was added for 6 hours together with new EZH2 inhibitor.

value: Sox10GFP+ OPCs

tag: treatment

value: 1.5uM Ezh2i


title: 190426Mk1_Ctr

status: Public on Jan 28 2022

type: SRA

city: Stockholm

first: Eneritz

last: Agirre

address: Solnavägen 9

department: MBB

country: Sweden

institute: Karolinska Institutet

description: ATACseq (Buenrostro et al., 2013)

library_source: genomic

data_processing:
Bulk ATAC-seq reads were trimmed and aligned with Bowtie2 with TN5 shifted tagAlign for ATAC pipeline. Aligned reads were filtered and duplicates removes (CutAdapt mark duplicates), more detail Kundaje Lab pipeline. Peaks were called with MACS2, with specific parameters for ATAC-seq peak calling (TN5 shifted tagAlign for ATAC pipeline). Peaks signal files, the wig files, were normalize to total number of reads per sample with DeepTools in order to visualize them.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: ATAC-seq peaks signal in wig files normalized to total read count.

molecule: genomic DNA

organism: Mus musculus

source_name: Sox10GFP+ OPCs

growth_protocol: Brains from P4-P6 mouse pups were collected and dissociated with the neural tissue dissociation kit (P; 130-092-628, Miltenyi). OPCs were obtained by either FACS with Sox10GFP+ selection or by MACS with CD140a microbeads (Cd140a microbead kit, 130-101-547, Miltenyi). For each experiment, multiple brains were pooled to obtain a sufficient number of cells. Cells were seeded on poly-L-lysine (P4707, Sigma) coated plates and grown with OPC proliferation media consisting of DMEM/F12, GlutaMAX (10565018, ThermoFisher Scientific), N2 supplement (17502001, ThermoFisher Scientific) NeuroBrew 21 (130-097-263, Miltenyi), penicillin-streptomycin (15140122, ThermoFisher Scientific), PDGFaa (10ng/ml, 315-17, PeproTech) and bFGF (20ng/ml, 100-18B, PeproTech).

extract_protocol:
Cells were harvested by TrypLE incubation at 37°C for 5 minutes, collection in cell culture medium and washing in PBS.
ATAC-seq was performed as previously described (Buenrostro et al., 2013) with minor adaptations. Primary OPCs were incubated with TrypLE () at 37°C for 5 minutes and collected in cell culture media. 60,000 cells per condition were washed with PBS and lysed with lysis buffer (containing 0.1% IGEPAL (CA-630), 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) and centrifuged for 20 minutes at 500xg and 4°C. Cells were then resuspended in tagmentation mix (dH2O, 2x TD buffer (Wang et al., 2013) and Tn5 enzyme (Picelli et al., 2014)) for 30 minutes at 37°C. The DNA was purified pre- and post-PCR with the MinElute purification kit (Qiagen) and then PAGE purified to remove adapter dimers. Three replicates per condition were performed with primary OPCs obtained from different litters. Libraries were sequenced on an Illumina Novaseq 6000 with a 50-8-8-50 read set-up.

treatment_protocol: Cells were treated with either dexamethasone (1uM, D4902, Sigma) or IFN-gamma (100ng/ml, 485-MI-100, R&D) for 48 hours.

tag: mouse model

value: EAE

tag: age

tag: cell type

tag: condition

value: Ctr

tag: replicate


title: rosa26cre_batch3_sample_28

type: RNA

city: Münster

first: Kornelius

last: Kerl

address: Albert-Schweitzer-Campus 1

department: Department of Pediatric Hematology and Oncology

country: Germany

institute: University Children's Hospital Münster

hyb_protocol: 3.8 µg fragmented and labeled sense-strand single-stranded cDNA were hybridized to Affymetrix GeneChip Mouse Gene 2.0 ST arrays for 16 h at 45 °C and 60 rpm in an Affymetrix GeneChip hybridization oven 640.

scan_protocol: GeneChips were washed and stained in an Affymetrix GeneChip Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G System. Fluidics and scan functions were controlled by the Affymetrix GeneChip Command Console v4.1.3 software.

data_processing: The .CEL files were read into R (version 3.5.1) using the package oligo. Data normalization was performed per batch, with the RMA algorithm. Samples from the three batches were then combined and batch effect was corrected using the ComBat function from the sva package.

label: Biotin

molecule: total RNA

label_protocol: The Affymetrix GeneChip Whole Transcript (WT) PLUS Reagent Kit Protocol was used for the preparation of biotinylated sense-strand single-stranded cDNA from 200ng of total RNA, followed by an enzymatic fragmentation and terminal labeling with biotin.

extract_protocol: Fresh tumor tissues were isolated and fresh frozen. Afterwards, total RNA was extracted using  RNeasy Mini Kit (Quiagen) following the manufacturer’s suggested protocol. Genomic DNA was removed using a gDNA eraser step.

tag: batch

tag: localization

value: intracranial

tag: localization details

value: brain, lateral to the cerebellum

tag: age (weeks)

tag: tumor classification

value: MYC


title: rosa26cre_batch3_sample_29

value: spinal

value: spinal tumor


title: 190419Mk3_Ifng

description: ATACseq (Buenrostro et al., 2013)

value: IFNg


title: P12_PD_1

city: Ann Arbor

first: Malcolm

last: Low

state: MI

address: 1000 wall street

department: Molecular & Integrative Physiology

country: USA

institute: University of Michigan

library_source: transcriptomic

data_processing:
We checked the quality of the raw reads data for each sample using FastQC (version v0.11.3) to identify features of the data that may indicate quality problems (e.g. low quality scores, over-represented sequences, inappropriate GC content).
We aligned reads to the reference genome (UCSC mm10) , using TopHat (version 2.0.13) and Bowtie2 (version 2.2.1.).
We used FastQC for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis
We ran differential expression analysis using HTSeq/DESeq2, with UCSC mm10.fa as the reference genome sequence
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: hypothalamus

extract_protocol:
Mice (Pomc-CreER; ROSA26eGFP-L10a) were euthanized and decapitated. Brain was removed from the skull and the arcuate nucleus was isolated from a 2-mm thick coronal slices using a brain matrix. Tissues were then homogenized and the subsequent tissue lysate was subjected to immunopurification steps
The ribo-depletion kit (RiboGone, Takara, CA) and SMARTer Stranded total RNA sample prep kit were used to remove excess ribosomal RNA and synthesize cDNA library.

tag: strain

tag: tissue

value: hypothalamus

value: postnatal day 12

tag: molecule subtype

value: ribo-depleted mRNA


title: TWCM-13-17

city: Saint Louis

first: Kory

last: Lavine

state: Missouri

address: 660 S. Euclid Ave

department: Internal Medicine - Cardiology

institute: Washington University School of Medicine

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj

data_processing:
Alignment: Cell Ranger V3, aligned to GRCh38 transcriptome, or custom pre-mrna reference.
QC and Filtering: Seurat V3/V4
Unsupervised Clustering: Seurat V3/V4
Genome_build: GRCh38 V3.0.0
Supplementary_files_format_and_content: Seurat V4 R Objects
Supplementary_files_format_and_content: I*Counts.csv: Comma-separated expression matrices.

organism: Homo sapiens

source_name: Transmural LV Apex

extract_protocol:
Transmural tissue samples were removed from the left ventricle apex during LVAD implantation or after whole heart explantation. Samples for single cell were processed fresh by enzymatic digestion while samples for single nuclei were frozen in liquid nitrogen and stored at -80C until use and processed by mechanical homogenization. All single cell/nuclei suspensions were sorted by FACS to remove debris and dead cells.
10X Genomics Chromium Single Cell 5’ Reagent V1.1.

value: Transmural LV Apex

tag: storage condition

tag: technology

value: Single Nuclei

tag: disease state

value: Dilated cardiomyopathy


title: Ctrl_Ezh2i_rep3

tag: treatment


title: IFNg_Ctrl_rep3

tag: mouse model

value: 0uM Ezh2i


title: TWCM-13-132

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj

value: Non-diseased


title: RNA_ERHoxB8_WT_rep2

city: La Jolla

first: Christopher

middle: K

last: Glass

state: CA

address: 9500 Gilman Drive

department: CMM

institute: University of California, San Diego

data_processing:
FASTQ files from sequencing experiments were mapped to the mm10 genome using STAR with default parameters (Dobin et al., 2013). HOMER was used to convert aligned reads into “tag directories” for downstream analysis (Heinz et al., 2010).
Transcripts were quantified by TPM values generated by the “analyzeRepeats” script of HOMER with the parameters -condenseGenes -count exons -tpm.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file: table of TPM values

growth_protocol: Bone marrow cells were isolated from femurs and tibias of Cas9-expressiong transgenic mice (Jackson Laboratory, No.028555). Murine stem cell virus-based expression vector for ER-Hoxb8 was gifted from Dr. David Sykes (Massachusetts General Hospital, Boston, MA). Cas9-expressing ER-HoxB8 conditionally immortalized myoid progenitor cells were generated following established protocols (Wang et al., 2006). In brief, bone marrow cells were purified with a Ficoll gradient (Ficoll-Paque-Plus, Sigma-Aldrich) and resuspended in RPMI 1640 containing 10% FBS, 1% penicillin/streptomycin and 10 ng/ml each of SCF, IL-3 and IL-6 (PeproTech). After 48 hours culture, 2.5x10e5 cells in 1 ml were transduced with 2 ml of ER-HoxB8 retrovirus (in DMEM with 30% FBS) containing 0.5 ul/ml lentiblast A (OZ Biosciences), 2.5 ul/ml lentiblast B (OZ Biosciences) and 8 ug/ml polybrene (Sigma-Aldrich) in a well of fibronectin (Sigma-Aldrich)-coated 6-well culture plates and centrifuged at 1000g for 90 min at 22°C. After transduction, 6 ml of ER-HoxB8 cell culture media (RPMI 1640 supplemented with 10% FBS, 1% penicillin/streptomycin, 0.5 uM β-estradiol (Sigma-Aldrich), and 20 ng/ml GM-CSF (PeproTech)) were added and an additional half-media exchange with ER-Hoxb8 media performed the next day. Transduced cells were selected with G418 (Thermo Fisher) at 1 mg/ml for 48 hours. Thereafter, cells were maintained in ER-HoxB8 cell culture media. ER-HoxB8 cells were washed twice with PBS, plated at a density of 3x10e6 cells per 10 cm culture plate, and differentiated into macrophages in DMEM with 10% FBS, 1% pencillin/streptomycin, and 17 ng/ml M-CSF (Shenandoah) for 7 days with 2 culture media exchanges. Differentiated cells were washed twice with PBS and collected for sequencing experiments.

extract_protocol:
Total RNA was isolated from in vitro culture cells and purified using a Direct-zol RNA MicroPrep Kit (Zymo Research) according to the manufacturer’s instructions (Zymo Research).
Poly A enriched mRNA was fragmented, in 2x Superscript III first-strand buffer with 10mM DTT (Thermo Fisher Scientific), by incubation at 94°C for 9 minutes, then immediately chilled on ice before the next step. The 10 µL of fragmented mRNA, 0.5 µL of Random primers (3 µg/µL) (Thermo Fisher Scientific), 0.5 µL of Oligo dT primer (50 µM) (Thermo Fisher Scientific), 0.5 µL of SUPERase-In (Ambion), 1 µL of dNTPs (10 mM) and 1 µL of DTT (10 mM) were heated at 50°C for one minute. At the end of incubation, 5.8 µL of water, 1 µL of DTT (100 mM), 0.1 µL Actinomycin D (2 µg/µL), 0.2 µL of 1% Tween-20 (Sigma) and 0.5 µL of Superscript III (Thermo Fisher Scientific) were added and incubated in a PCR machine using the following conditions: 25°C for 10 minutes, 50°C for 50 minutes, and a 4°C hold. The product was then purified with RNAClean XP beads (Beckman Coulter) according to manufacturer's instruction and eluted with 10 µL nuclease-free water. The RNA/cDNA double-stranded hybrid was then added to 1.5 µL of Blue Buffer (Enzymatics), 1.1 µL of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 µL of RNAse H (5 U/µL), 1.05 µL of water, 1 µL of DNA polymerase I (Enzymatics) and 0.15 µL of 1% Tween-20. The mixture was incubated at 16°C for 2.5 hours. The resulting dUTP-marked dsDNA was purified using 28 µL of SpeedBeads (GE Healthcare), diluted with 20% PEG8000, 2.5M NaCl to final of 13% PEG, eluted with 40 µL EB buffer (10 mM Tris-Cl, pH 8.5) and frozen at -80°C. The purified dsDNA (40 µL) underwent end repair by blunting, A-tailing and adapter ligation using barcoded adapters (NextFlex, Bioo Scientific). Libraries were PCR-amplified for 16 cycles, size selected by gel extraction.

tag: strain background

value: wild-type ER-HoxB8 cells


title: Ctrl_Ctrl_rep3

value: EAE

tag: age

tag: cell type

value: Sox10GFP+ OPCs


title: RNA_ERHoxB8_WT_rep1


title: TWCM-13-84

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj


title: rosa26cre_batch2_sample_25

value: intracranial

value: lateral to the cerebellum


title: IFNg_Ezh2i_rep2

value: 1.5uM Ezh2i

tag: condition

tag: replicate


title: TWCM-11-103

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj


title: ChIP_H3K27ac_ERHoxB8_WT

data_processing:
FASTQ files from sequencing experiments were mapped to the mm10 genome using Bowtie2 (Langmead and Salzberg, 2012). Wild-type data were mapped using default parameters whereas CRISPR data were mapped using "--local --rdg 10,1 --rfg 10,1" to allow different sizes of gaps/InDels. HOMER was used to convert aligned reads into “tag directories” for downstream analysis (Heinz et al., 2010).
The enriched regions (i.e. peaks) were identified using HOMER (Heinz et al., 2010) to call 200-bp peaks (command “findPeaks -style factor -size 200”).
H3K27ac tag counts were computated within +/- 500 bp around ATAC peaks using HOMER annotatePeaks.pl script with parameter "-norm 1e7 -size -500,500".
The CRISPR mapped reads were grouped based on the InDel size and whether the InDel overlaps with any of the PU.1 and C/EBP motifs. In processed file "ChIP_ERHoxB8_CRISPR_tagCounts.tsv", each column represents an InDel group.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file containing called peaks in the HOMER peak file format

extract_protocol:
Culture media was removed, and plates were washed once with PBS and then fixed for 10 minutes with 1% formaldehyde (Thermo Fisher Scientific) in PBS at room temperature. Reaction was then quenched by adding glycine (Thermo Fisher Scientific) to 0.125M. After fixation, cells were washed once with cold PBS and then scraped into supernatant using a rubber policeman, pelleted for 5 minutes at 400xg at 4°C. Cells were transferred to Eppendorf DNA LoBind tubes and pelleted at 700xg for 5 minutes at 4°C, snap-frozen in liquid nitrogen and stored at -80°C until ready for ChIP-seq protocol preparation. Chromatin immunoprecipitation (ChIP) was performed in biological replicates as described previously (Hoeksema et al., 2020). Samples were sonicated using a probe sonicator in 500 µl lysis buffer (10 mM Tris/HCl pH 7.5, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% deoxycholate, 0.5% sarkozyl, 1x protease inhibitor cocktail). After sonication, 10% Triton X-100 was added to 1% final concentration and lysates were spun at full speed for 10 minutes. 1% was taken as input DNA, and immunoprecipitation was carried out overnight with 20 µl Protein A Dynabeads (Invitrogen) and 2 µg specific antibodies for C/EBPβ (Santa Cruz, sc-150), PU.1 (Cell Signaling, #2258), and H3K27ac (Active Motif, 39135). Beads were washed three times each with wash buffer I (20 mM Tris/HCl, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA), wash buffer II (10 mM Tris/HCl, 250 mM LiCl, 1% IGEPAL CA-630, 0.7% Na-deoxycholate, 1 mM EDTA), TE 0.2% Triton X-100 and TE 50 mM NaCl and subsequently resuspended 25 µl 10 mM Tris/HCl pH 8.0 and 0.05% Tween-20. ChIP-seq libraries were prepared on the Dynabeads as described below. For locus specific enrichment ChIP-seq, bead complex was resuspended in 50 µl 1% SDS-TE. 4 µl ProtK, 4 µl RNase A, 3 µl 5 M NaCl was added to these and the input samples and incubated at 50℃ for 1 hour, reverse crosslinked at 65℃ overnight and then eluted from the beads.
For wild-type cells, ChIP libraries were prepared while bound to Dynabeads using NEBNext Ultra II Library preparation kit (NEB) using half reactions. DNA was polished, polyA-tailed and ligated after which dual UDI (IDT) or single (Bioo Scientific) barcodes were ligated to it. Libraries were eluted and crosslinks reversed by adding to the 46.5 µl NEB reaction 16 µl water, 4 µl 10% SDS, 4.5 µl 5 M NaCl, 3 µl 0.5 M EDTA, 4 µl 0.2 M EGTA, 1 µl RNAse (10 mg/ml) and 1 µl 20 mg/ml proteinase K, followed by incubation at 55℃ for 1 hour and 75℃ for 30 minutes in a thermal cycler. Dynabeads were removed from the library using a magnet and libraries were cleaned up by adding 2 µl SpeedBeads 3 EDAC (Thermo) in 124 µl 20% PEG 8000/1.5 M NaCl, mixing well, then incubating at room temperature for 10 minutes. SpeedBeads were collected on a magnet and washed two times with 150 µl 80% ethanol for 30 seconds. Beads were collected and ethanol removed following each wash. After the second ethanol wash, beads were air dried and DNA eluted in 12.25 µl 10 mM Tris/HCl pH 8.0 and 0.05% Tween-20. DNA was amplified by PCR for 14 cycles in a 25 µl reaction volume using NEBNext Ultra II PCR master mix and 0.5 µM each Solexa 1GA and Solexa 1GB primers. Libraries were size selected using TBE gels for 200 – 500 bp and DNA eluted using gel diffusion buffer (500 mM ammonium acetate, pH 8.0, 0.1% SDS, 1 mM EDTA, 10 mM magnesium acetate) and purified using ChIP DNA Clean & Concentrator (Zymo Research).    For CRISPR/Cas9-mutated cells, after performing the target-specific ChIPs, we performed an initial PCR for locus-specific amplicon enrichment using NEBNext 2X High Fidelity PCR MM (NEB) and 5’-biotinylated stub adapter primers specific to appropriate genomic regions to be interrogated (Figure 5-table supplement 1). Initial hotstart/denaturation at 98℃ for 30 sec was followed by 10 cycles of amplification (98℃ for 15 sec, 65-67℃ for 15 sec, 72oC for 30 sec) and then a final elongation at 72℃ for 5 min. After this, we performed a 0.7X AmpureXP clean-up and eluted in 20 µl 0.5x TT (5 mM Tris pH 8.0 + 0.025% Tween20). Dynabeads MyOne Streptavidin T1 beads were then washed in 1x Wash Binding Buffer (WBB, 2X WBB: 10 mM Tris-HCl (pH 7.5), 1 mM EDTA, 2 M NaCl, 0.1% Tween) and resuspended beads at 20 µl per sample in 2x WBB. 20 µl prepared Dynabeads MyOne Streptavidin T1 beads (in 2x WBB) were then added to cleaned up 20 µl 0.5x TT PCR fragments, mixed and incubated for 60min at RT with mild shaking. After this, beads were collected on a magnet and washed twice with 150 µl 1x WBB and once with 180 µl TET (TE + 0.05% Tween-20). Finally, beads were resuspended in 25 µl 0.5x TT and on bead PCR for addition of Illumina-specific adapters and 10-bp Unique Dual Indexes (UDIs) using NEBNext 2X High Fidelity PCR MM (NEB) and 25 PCR cycles was performed (Figure 5-table supplement 2). Libraries were size selected using TBE gels for 300-500 bp and DNA eluted using gel diffusion buffer and purified using ChIP DNA Clean & Concentrator (Zymo Research).

tag: cell line

tag: chip antibody


title: rosa26cre_batch2_sample_24

tag: batch

tag: localization

tag: localization details

value: brain, trigeminal

tag: age (weeks)

value: MYC


title: TWCM-10-5

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj

tag: tissue


title: ChIP_PU1_ERHoxB8_WT

tag: strain

value: PU1 (Cell Signaling, #2258)


title: Ctrl_Ezh2i_rep2

value: Ctr


title: IFNg_Ctrl_rep2

value: IFNg


title: rosa26cre_batch2_sample_23

value: brain, subventricular zone

tag: tumor classification

value: SHH


title: Sox2cre_batch2_sample_22

value: extracranial

value: mouth


title: ChIP_CEBPb_ERHoxB8_WT

value: CEBPb (Santa Cruz, sc-150, lot G1814)


title: Ctrl_Ctrl_rep2

value: 0uM Ezh2i


title: rosa26cre_batch2_sample_21


title: ChIP_input_ERHoxB8_WT

value: input


title: IFNg_Ezh2i_rep1

value: EAE


title: ATAC_ERHoxB8_WT_rep1

data_processing:
FASTQ files from sequencing experiments were mapped to the mm10 genome using Bowtie2 with default parameters (Langmead and Salzberg, 2012). HOMER was used to convert aligned reads into “tag directories” for downstream analysis (Heinz et al., 2010).
The reproducible enriched regions (i.e. peaks) were identified by first using HOMER (Heinz et al., 2010) to call unfiltered 200-bp peaks (command “findPeaks -style factor -L 0 -C 0 -fdr 0.9 -size 200”) and then running IDR (Li et al., 2011) on replicates with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file containing called peaks in the HOMER peak file format

extract_protocol:
5x10e5 cells were lysed at room temperature in 50 µl ATAC lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and 2.5 µL DNA Tagmentation Enzyme mix (Nextera DNA Library Preparation Kit, Illumina) was added. The mixture was incubated at 37°C for 30 minutes and subsequently purified using the ChIP DNA purification kit (Zymo Research) as described by the manufacturer.
DNA was amplified using the Nextera Primer Ad1 and a unique Ad2.n barcoding primers using NEBNext High-Fidelity 2X PCR MM for 8-14 cycles. PCR reactions were size selected using TBE gels for 175 – 350 bp and DNA eluted using gel diffusion buffer (500 mM ammonium acetate, pH 8.0, 0.1% SDS, 1 mM EDTA, 10 mM magnesium acetate) and purified using ChIP DNA Clean & Concentrator (Zymo Research).

tag: genotype/cell type

value: wild-type ER-HoxB8 cells


title: ATAC_ERHoxB8_WT_rep2


title: rosa26cre_batch2_sample_20

value: intracranial


title: TWCM-13-47

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj

value: Transmural LV Apex

tag: storage condition

tag: technology

value: Single Nuclei

tag: disease state

value: Dilated cardiomyopathy


title: rosa26cre_batch3_sample_27

value: brain, lateral to the cerebellum

value: MYC


title: IFNg_Ctrl_rep1

tag: mouse model

tag: age

value: Sox10GFP+ OPCs

tag: treatment


title: rosa26cre_batch2_sample_19

value: brain, basal


title: Sox2cre_batch3_sample_26


title: Ctrl_Ezh2i_rep1

tag: cell type

value: 1.5uM Ezh2i

tag: condition

value: Ctr

tag: replicate


title: Gcn-FLC-2

city: Nutley

first: Liang

last: Chen

state: NJ

address: 340 Kingsland Street

institute: Hackensack-Meridian Health Center for Discovery and Innovation

data_processing:
The reads data quality was examined using FastQC v.0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and reads were trimmed to remove low-quality bases (average quality per base < 20) using Trimmomatic v0.39.
The filtered reads were then aligned to the Candida glabrata CBS138/ATCC 2001 genome (www.candidagenome.org) using HISAT 2.2.1  and the raw read counts were obtained using HTSeq  v 0.12.3.
Genome_build: GCF_000002545.3
Supplementary_files_format_and_content: raw gene counts for every gene and every sample

organism: Nakaseomyces glabratus

growth_protocol: Cells were grown in liquid YPD at 37°C with shaking

extract_protocol: RNA was extracted using the Rneasy mini kit (Qiagen)  following the manufacturer's instructions. RNA was then treated with Rnase-free Dnase (ThermoFisher).

treatment_protocol: At OD600 of 0.6, cells were either untreated, or treated with fluconazole at 8 µg/ml or micafungin at 15ng/ml for 2h.

value: fluconazoel treated


title: TWCM-13-80

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj

value: Non-diseased


title: Ctrl_Ctrl_rep1


title: Gcn-FLC-1


title: TWCM-13-1

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj


title: WT-FLC-2

value: WT


title: Sox2cre_batch2_sample_16

tag: batch

value: extracranial

value: lip


title: Sox2cre_batch2_sample_17

tag: localization

value: gland thorax


title: TWCM-11-256

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj


title: WT-FLC-1


title: Sox2cre_batch2_sample_15

tag: localization details

value: SHH


title: TWCM-14-173

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj


title: 190315Mk2_Dexa

data_processing:
Bulk RNA-seq samples were preprocessed for adapter/quality trimming and then aligned to the transcriptome using STAR with EnsEMBLv75 annotations. Filtered fastq files were used in Salmon 0.8.2 to recover raw reads counts and transcripts per million (TPM) values per transcript and gene. The differential gene expression analysis was performed from the estimated gene counts with Deseq2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: P13154_100*_quant.sf: Contains the tab-separated table of normalized abundance measurements output from Salmon at transcript level. With EnsEMBL75 mm10 annotation, for each of the 12 samples. Including transcript length, estimated number of counts and TPM.
Supplementary_files_format_and_content: Dexa_DGE_deseq2.Gene.res.txt: Differential gene expression output from Deseq2 using as reference the 3 replicates of the Ctrl samples compared to the 3 replicates of the Dexa samples.
Supplementary_files_format_and_content: Ifng_Dexa_DGE_deseq2.Gene.res.txt: Differential gene expression output from Deseq2 using as reference the 3 replicates of the IFNg samples compared to the 3 replicates of the Dexa samples.
Supplementary_files_format_and_content: Ifng_DGE_deseq2.Gene.res.txt: Differential gene expression output from Deseq2 using as reference the 3 replicates of the Ctrl samples compared to the 3 replicates of the IFNg samples.

extract_protocol:
Cells were collected with qiazol (Qiagen) and stored at -80°C until further processing. RNA was extracted with the miRNeasy mini kit (Qiagen) according to manufacturer’s instructions. Contaminating DNA was degraded by treatment of the samples with RNase-free DNase (Qiagen) in column.
0.1-1ug of RNA was used to make RNA-seq libraries with the TruSeq Stranded Total RNA Library Prep Gold kit (Illumina) according to manufacturer's instructions. Four replicates per condition were performed with primary OPCs obtained from different litters. Libraries were sequenced on an Illumina Novaseq 6000 with a 150-8-8-150 read set-up.

value: EAE

value: Dexa


title: TWCM-11-192

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj

value: Transmural LV Apex

value: Single Nuclei


title: 190315Mk1_Ctr


title: TWCM-11-82

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj


title: Gcn-MCF-2

value: micafungin treated


title: TWCM-13-168

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj


title: 190315Mk9_Ifng

value: IFNg


title: TWCM-11-74

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj


title: TWCM-13-152

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj


title: rosa26cre_batch2_sample_13

value: intracranial

value: brain, subventricular zone

tag: age (weeks)


title: rosa26cre_batch2_sample_12

value: eye

value: MYC


title: WT-MCF-2


title: 190315Mk8_Dexa

value: Sox10GFP+ OPCs


title: TWCM-13-104

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj

tag: tissue

value: Non-diseased


title: Sox2cre_batch2_sample_14

value: spinal

value: spinal tumor


title: WT-MCF-1

tag: strain

value: WT


title: Sox2cre_batch2_sample_11

value: extracranial

value: facial tumor maxilar

tag: tumor classification


title: PD003 Expression

data_processing:
Single cell multiome human (10X Genomics) data samples were processed with default parameters with cellranger-arc (v2.0.0) count function. Reads were aligned to GRCh38 (refdata-cellranger-arc-GRCh38-2020-A-2.0.0) reference genome. Which resulted for each sample PD003 and PD004 of a median fragments per cell of 21422/22379, median UMI counts per cell of 7407/8189, median genes per cell of 2972/3268 and 5272/4513 cells.
Normalized single feature-barcode matrix combining the two individuals from both modalities was calculated with the parameter cellranger-arc aggr with default parameters, samples were normalized to depth for both ATAC and gene expression modalities. We used Cellranger-arc called peaks for preQC measurements. After QC we run macs2 whithin Seurat/Signac to call the peaks, to recover consistent peak set within the whole dataset. For downstrean analyses we combined Signac v1.4.0 and Seurat v4.0.0 joint RNA and ATAC analysis. We used as QC metrics nCount_ATAC < 100000 & nCount_RNA < 100000 & nCount_ATAC > 1000 & nCount_RNA > 1000 & nucleosome_signal < 2 & TSS.enrichment > 1, which resulted in a total 4194 and 3670 cells from each individual sample.
Dimension reduction and Findclusters was performed same as for single cell multiome mouse data. Samples were integrated using Harmony on the patient variable. Cells were annotated using a panel of canonical markers for main brain cell types; 'PLP1','MAG','MOG','OPALIN' for Oligocendrocytes. 'PDGFRA','SOX6','BCAN' for OPCs. 'FGFR3','GFAP','SLC14A1','AQP4' for Astrocytes. 'P2RY12','SPP1','CSF1R','IRF8' for Microglia. 'SLC17A7','FEZF2','RORB' for Excitatory Neurons. 'GAD1','ADARB2','LHX6' for Inhibitory Neurons. 'CLDN5','FLT1','EPAS1', 'EPS8','LAMA2' for Endothelial and Stromal cells. In order to get clear celltypes on the ATAC called peaks we discarded combinations of canonical markers from different main celltypes from the RNA expression. We then called peaks using MACS2 grouped by defined celltype.
Peak to gene interaction were predicted based on co-accessibility and expression from identified celltypes using R package ArchR.
Genome_build: hg38
Supplementary_files_format_and_content: Output files from cellranger-arc (v2.0.0), filtered feature matrix h5 file, filtered expression matrix h5 file,  called ATAC fragments for both samples.  Wig signal files for each identified celltype in each sample and both combined. Due to different number of cells in each celltype cluster, the wig files were built with a maximun of randomly selected 200 cells from each type. Predicted peak to gene interactions for each celltype, based on co-accessibility and expression as bedpe format. Bed file of identified celltype peaks. Processed data R object (.rds R.4.1.0) Signac 1.4.0/Seurat 4.0.5 used in the study.
Supplementary_files_format_and_content: Interactions pek2gene in .bedpe format.

source_name: Brain gray matter

extract_protocol: Nuclei were isolated from two 10mg fresh-frozen human grey matter brain samples (collected under the Imperial College Research Ethics Committee ICREC_14_2_11), using Nuclei Pure Prep Nuclei Isolation Kit (Sigma Aldrich) with the following modifications. The tissue was lysed in Nuclei Pure Lysis Solution with 0.1% Triton X, 1mM DTT and 0.4U/ul SUPERase-In™ RNase Inhibitor (ThermoFisher Scientific) freshly added before use, and homogenized with the help first of a 23G and then of a 29G syringe. Cold 1.8M Sucrose Cushion Solution, prepared immediately before use with the addition of1mM DTTand 0.4U/ul RNase Inhibitor, was added to the suspensions before they were filtered through a 30μm strainer. The lysates were then carefully and slowly layered on top of 1.8M Sucrose Cushion Solution previously added in new Eppendorf tubes. Samples were centrifuged for 45 minutes at 16000xg at 4°C. Pellets were re-suspended in Nuclei Storage Buffer with RNase Inhibitor, transferred in new Eppendorf tubes and centrifuged twice for 5 minutes at 500xg at 4°C. Finally purified nuclei were re-suspended in Nuclei Storage Buffer with RNase Inhibitor, stained with trypan blue and counted using Countess II (Life technology). After count, nuclei permeabilization was carried out following the demonstrated protocol for single cell multiome ATAC + Gene Expression sequencing from 10x Genomics. A total of 12,000 estimated nuclei from each sample was used for the transposition step and then loaded on the Chromium Next GEM Single Cell Chip J. ATAC library and gene expression library construction was performed using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit according to the manufacturer’s instructions. Libraries were sequenced using Illumina NovaSeq 6000 System and NovaSeq 6000 S2 Reagent Kit v1.5 (100 cycles), aiming at a minimum sequencing depth of 30K reads/nucleus.

value: Ctrl

value: Expression


title: Gcn-MCF-1


title: TWCM-13-101

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj

value: Transmural LV Apex


title: Sox2cre_batch2_sample_10

value: brain, basal


title: 190318Mk3_Ifng

value: EAE


title: Gcn2-2

value: untreated


title: Gcn2-1


title: TWCM-11-41

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj

value: Single Nuclei


title: rosa26cre_batch2_sample_18

value: Lip


title: rosa26cre_batch1_sample_3

value: intracranial

value: brain, subventricular zone

value: SHH


title: 190318Mk2_Dexa

value: Sox10GFP+ OPCs

value: Dexa


title: 190315Mk3_Ifng

value: IFNg


title: TWCM-11-42

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj

value: Non-diseased


title: WT2-2

value: WT


title: 190318Mk1_Ctr

value: Ctr


title: Sox2cre_batch1_sample_5

value: eye

value: MYC


title: WT2-1


title: TWCM-LVAD3

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj

value: Transmural LV Apex

value: Dilated cardiomyopathy


title: 190218Mk3_Ifng

value: EAE


title: 190218Mk2_Dexa


title: TWCM-LVAD2

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj


title: Sox2cre_batch1_sample_1

value: extracranial

value: mouth


title: TWCM-13-235

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj

value: Single Nuclei


title: 190218Mk1_Ctr


title: H3K27ac_HiChIP_IFN_mOPC_rep3

description:
replicate 3
P17103_1006
OPC_h3k27ac_hichip.hic
IFNg_5kb_EnhancerPredictions.txt
IFNg_5kb_EnhancerPredictions.bedpe
IFNg_5kb_EnhancerPredictionsFull.txt

data_processing:
Library strategy: HiChIP
Fastq files were aligned to the mm10 genome and filtered for duplicate reads using the HiC-Pro pipeline.
allValidPairs files from the HiC-Pro pipeline for each replicate were merged together
hicpro2juicebox.sh from HiC-Pro was used on the merged allValidPairs file to generate the .hic file in the Ctrl OPCs. Enhancer promoter interactions were called using ABC model with a 5Kb window size.
Genome_build: mm10
Supplementary_files_format_and_content: Juicebox compatible .hic file, contains contact matrix for Ctrl OPCs. Enhancer promoters interactions called with ABC model for Ctrl OPC and IFNg OPCs in bed format , bedpe. All the enhancer promoter interactions predicted with the ABC model in a tab separated file complementary of the bedpe files are provided.

source_name: Mouse brain

growth_protocol: Cells were cultured in OPC proliferation medium (DMEM/Glutamax, 1xN2 supplement, 1x Penicilin-streptomycin, 1x NeuroBrew, 20ng/mL bFGF, 20ng/mL mPDGF-AA)

extract_protocol:
Cells were harvested using TrypLE and fixed with 1% formaldehyde prior to processing for HiChIP
Libraries were prepared as specified in Mumbach et.al. (2016) and with 0.75uL Tn5 enzyme.
Samples were sequenced on a single-lane of an SP flowcell on the NovaSeq6000 with the 2x50bp read setup

treatment_protocol: 24hours after passaging the cells, cells were incubated in Control medium (OPC proliferation medium) or IFNg medium (OPC proliferation medium + 100ng/mL IFNg)

tag: genotype

tag: chip antibody

value: Abcam Ab177178

value: In-house Tn5

value: cultured primary mOPCs

value: IFN


title: Sox2cre_batch1_sample_8

value: intracranial

value: brain, basal


title: Sox2cre_batch1_sample__9


title: TWCM-13-208

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj

tag: storage condition

tag: technology


title: H3K27ac_HiChIP_Ctrl_mOPC_rep3

description:
replicate 3
P17103_1005
OPC_h3k27ac_hichip.hic
Ctrl_5kb_EnhancerPredictions.bedpe
Ctrl_5kb_EnhancerPredictionsFull.txt
Ctrl_5kb_EnhancerPredictions.txt

value: Ctrl


title: Sox2cre_batch1_sample_6


title: TWCM-13-198

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj

tag: disease state

value: Non-diseased


title: H3K27ac_HiChIP_IFN_mOPC_rep2

description:
replicate 2
P17103_1004
OPC_h3k27ac_hichip.hic
IFNg_5kb_EnhancerPredictions.txt
IFNg_5kb_EnhancerPredictions.bedpe
IFNg_5kb_EnhancerPredictionsFull.txt


title: Sox2cre_batch1_sample_2

value: subcutaneous fat tissue


title: Input_DNA

city: Tianjin

first: Hao

last: Wu

address: Jinnan District ,Yaguan Road No.135

country: China

institute: Tianjin University

data_processing:
Basecalls performed using Bcl2fastq version 2.17.1.14
Trimmomatic (version 0.38) was used to filter out low-quality reads.
ChIP-seq reads were aligned to the L.lactis F44  genome assembly using bwa version 0.7.15 with the following setting: bwa mem -M -k 48
Samtools (version 1.3.1) was used to remove potential PCR duplicates
peaks were called using MACS2 version 2.1.1.20160309 with the following setting:bandwidth,300 bp; model fold, 5, 50;q value, 0.05.
Genome_build: F44
Supplementary_files_format_and_content: xls files were generated using MACS2

organism: Lactococcus lactis

source_name: liquid culture in fermentation medium

growth_protocol: L. lactis F44 strains containing CodY-Flag overexpressing plasmid were  cultivated in the fermentation medium

extract_protocol:
Samples were lysed and chromatins were obtained on ice. Chromatins were sonicated to get soluble sheared chromatin (average DNA length of 200–500 bp). One part of the soluble chromatin was saved at –20°C for input DNA, and the remainder was used for immunoprecipitation by Flag antibodies.
Immunoprecipitated DNA was used to construct sequencing libraries following the protocol provided by the Illumina TruSeq ChIP Sample Prep Set A and sequenced on Illumina Xten with PE 150 method.

treatment_protocol: strains grow until mid-log phase and were cross-linked with formaldehyde at a final concentration of 1%.


title: H3K27ac_HiChIP_Ctrl_mOPC_rep2

description:
replicate 2
P17103_1003
OPC_h3k27ac_hichip.hic
Ctrl_5kb_EnhancerPredictions.bedpe
Ctrl_5kb_EnhancerPredictionsFull.txt
Ctrl_5kb_EnhancerPredictions.txt


title: TWCM-13-192

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj


title: CodY_ChIPSeq

value: Anti-Flag


title: TWCM-13-181

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj


title: rosa26cre_batch1_sample_7

value: head extracranial

value: MYC


title: rosa26cre_batch1_sample4

value: gland thorax


title: H3K27ac_HiChIP_Ctrl_mOPC_rep1

description:
replicate 1
P17103_1001
OPC_h3k27ac_hichip.hic
Ctrl_5kb_EnhancerPredictions.bedpe
Ctrl_5kb_EnhancerPredictionsFull.txt
Ctrl_5kb_EnhancerPredictions.txt


title: TWCM-13-96

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj

value: Transmural LV Apex


title: TWCM-13-36

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj


title: H3K27me3_IFNg_Ezh2i_1.5uM_rep3

description:
processed data file: IFNg_15Ezh2i_H3K27me3_dupmark.bam_peaks.broadPeak
P15158_1045_S45

data_processing:
library strategy: Cut&Run (Skene&Henikoff, 2017)
Cut&Run samples were processed with the pipeline CUT&RUNTools that includes reads trimming, alignment (Bowtie2 mm10 reference genome) and peak calling with MACS2 https://bitbucket.org/qzhudfci/cutruntools/src/master/. For TF Cut&Run samples the narrow peaks  and for histone modifications broad peaks from all the fragments were used in downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Cut&Run peaks signal in wig files. Peaks coordenates for the merged replicates as a tab table for each condition.

extract_protocol:
Cut&Run was performed as previously described (Skene&Henikoff, 2017) with minor adaptations. Primary OPCs were incubated with TrypLE (Gibco #12605010) at 37°C for 5 minutes and collected in cell culture media. Cells were centrifuged for 5 minutes at 300xg and room temperature and then resuspended in wash buffer (20mM HEPES pH 7.5, 150 mM NaCl, 0.5mM Spermidine, 0.01%BSA, 1x Roche Complete Protease Inhibitor tablet). 250 000 cells per condition were centrifuged for 3 minutes at 600xg and room temperature and resuspended in wash buffer. Activated Concanavalin-A beads (Bangs Laboratories BP531) in binding buffer (20mM HEPES pH 7.5, 10mM KCl, 1mM CaCl2, 1mM MnCl2) was added to each condition and incubated for 10 minutes on a rotator at room temperature. Beads with nuclei were now kept on a magnetic stand and washed with Dig-wash buffer (0.05% digitonin in wash buffer). After discarding the liquid, beads were resuspended with primary antibody in antibody buffer (2mM EDTA in Dig-wash buffer) and incubated overnight at 4°C on a nutator. Then beads were washed with freshly prepared Dig-wash buffer and incubated with 2ug/mL Protein A-MNase (Schmid et al., 2004) in Dig-wash buffer for 1 hour at 4°C on a nutator. After two washes with Dig-wash buffer and one wash with low-salt rinse buffer (20mM HEPES pH 7.5, 0.5mM spermidine, 0.05% digitonin) ice-cold incubation buffer (3.5mM HEPES pH 7.5, 10mM CaCl2, 0.05% digitonin) was added to the beads which were subsequently placed in a metal block in an ice-water bath maintained at 0°C for 5 minutes. The beads were then placed on a magnet stand and liquid discarded. Stop buffer (170mM NaCl, 20mM EGTA, 0.05% digitonin, 50ug/mL RNase A, 25ug/mL glycogen, 2pg/mL Yeast spike-in DNA) was added to the beads and incubated for 30 minutes at 37°C. Beads were placed on a magnet stand and supernatant was collected. 2uL of 10% SDS and 2.5uL of 20mg/mL Proteinase K was added to the supernatant and incubated for 1 hour at 50°C. DNA from the samples was purified using the MinElute PCR purification kit (Qiagen) according to manufacturer’s instructions. Antibodies were used against H3K27me3 (Cell Signaling 9733S; rabbit; 1ug), H3K4me3 (Diagenode C15410003-50; rabbit; 1ug), H3K27ac (Abcam ab177178; rabbit; 1ug), CTCF (Cell Signaling 3418S; rabbit; 1:100).
Sequencing libraries were prepared using KAPA HyperPrep kit (Roche #07962363001) and KAPA Unique Dual-Indexed Adapters (Roche #08861919702) according to manufacturer’s instructions, but with the following adjustments. Two post-adapter ligation clean-ups were performed using 0.7x and 1.1x AMPure XP beads respectively. PAGE purification was performed on the post-amplification libraries to remove remaining adapter dimers. Three replicates were performed with primary OPCs obtained from different litters. Libraries were sequenced on the Illumina Novaseq 6000 with a 50-8-8-50 read setup.

value: Sox10GFP+ oligodendrocyte precursor cells (OPCs)

value: IFNg

tag: antibody

value: Cell Signaling 9733S; rabbit; 1ug


title: TWCM-11-3

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj

value: Single Nuclei

value: Dilated cardiomyopathy


title: Donor 6 T cells anti-BTLA

city: San Diego

first: John

last: Sedy

address: 10770 Wateridge Cir

institute: AnaptysBio

description: Total RNA was hybridized to Nanostring chips and analyzed for RNA counts

hyb_protocol: Frozen cell lysates were hybridized to Nanostring chips according to manufacture protocol

scan_protocol: Nanostring chips were analyzed on nCounter instrument

data_processing: RCC files were analyzed using nSolverAnalysisSoftware and differential expression analysis using the NanostringDiff package in R

source_name: PBMC

extract_protocol: Treated cells were resuspended in RLT buffer and frozen for later hybridization.

treatment_protocol: Human CD4+ T cells or B cells were purified from human PBMC. Cells were treated with anti-BTLA or control as indicated for 6 hours.

tag: cell

value: Purified CD4+ T cell

tag: donor

tag: treatment

value: anti-BTLA


title: Donor 6 T cells control

value: Control


title: Donor 5 T cells anti-BTLA


title: H3K27me3_Ctr_Ezh2i_1.5uM_rep3

description:
processed data file: Ctr_15Ezh2i_H3K27me3_dupmark.bam_peaks.broadPeak
P15158_1044_S44

source_name: Sox10GFP+ OPCs_H3K27me3_Ctr_Ezh2i_1.5uM

tag: cell type

tag: condition

value: Ctr


title: Donor 5 T cells control


title: H3K27me3_IFNg_Ezh2i_0uM_rep3

description:
processed data file: IFNg_0Ezh2i_H3K27me3_dupmark.bam_peaks.broadPeak
P15158_1043_S43

source_name: Sox10GFP+ OPCs_H3K27me3_IFNg_Ezh2i_0uM


title: Donor 4 T cells anti-BTLA


title: TWCM-11-78

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj


title: Patient 10 pretreatment biopsy [NS_CancerPath_C2535]

city: Houston

first: David

middle: S

last: Hong

state: Texas

address: Room FC8.3050, 1400 Holcombe Blvd.

department: Department of Investigational Cancer Therapeutics

institute: University of Texas M.D. Anderson Cancer Center

description:
100 ng of total RNA was hybridyzed with the NanoString nCounter panel of probes
08950279C

hyb_protocol: 65°C for 16-24 hours. Details are in user manual for nCounter Gene Expression CodeSet RNA hybridization protocol (Nanostring)

scan_protocol: nCounter® FLEX Analysis System (following the manufacturer's protocol)

data_processing:
Raw counts were exported using nSolver® Analysis Software (Nanostring) and analysed using custom R scripts (R v3.6.3). Background gene count levels were determined for each sample using mean plus two standard deviations of the included negative control counts. For data normalization, background-subtracted counts were then scaled using geometric means of 27 of 30 housekeeping genes shared between the two gene panels (excluding GPATHC3, CC2D1B and ZKSCAN5), with expected value set to 444.
Counts - number of molecules detected per 100 ng of total RNA

label: 6x fluorescent marker barcode

source_name: Metastatic Urothelial cancer

label_protocol: Detailed in user manual for nCounter Gene Expression CodeSet RNA hybridization protocol (Nanostring)

extract_protocol: Tumor tissue was macro-dissected from 4 μm sections of FFPE tissues and total RNA was extracted using the High Pure RNA FFPE Micro Kit (Roche), following the manufacturer’s protocol.

tag: timepoint

value: Baseline

tag: dose, bln cells

tag: cohort

tag: best overall response

value: Stable Disease


title: H3K27me3_Ctr_Ezh2i_0uM_rep3

description:
processed data file: Ctr_0Ezh2i_H3K27me3_dupmark.bam_peaks.broadPeak
P15158_1042_S42

source_name: Sox10GFP+ OPCs_H3K27me3_Ctr_Ezh2i_0uM


title: Donor 4 T cells control


title: H3K4me3_IFNg_Ezh2i_1.5uM_rep2

description:
processed data file: IFNg_15Ezh2i_H3K4me3_dupmark.bam_peaks.broadPeak
P15158_1041_S41

source_name: Sox10GFP+ OPCs_H3K4me3_IFNg_Ezh2i_1.5uM

value: Diagenode C15410003-50; rabbit; 1ug


title: Patient 9 pretreatment biopsy [NS_CancerPath_C2535]

description:
100 ng of total RNA was hybridyzed with the NanoString nCounter panel of probes
08950277C

source_name: Metastatic Melanoma cancer

value: Screening


title: H_ZC-LVAD-1

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj

tag: tissue


title: H3K4me3_Ctr_Ezh2i_1.5uM_rep2

description:
processed data file: Ctr_15Ezh2i_H3K4me3_dupmark.bam_peaks.broadPeak
P15158_1040_S40

source_name: Sox10GFP+ OPCs_H3K4me3_Ctr_Ezh2i_1.5uM


title: Donor 3 B cells anti-BTLA

value: Purified B cell


title: Patient 8 pretreatment biopsy [NS_CancerPath_C2535]

description:
100 ng of total RNA was hybridyzed with the NanoString nCounter panel of probes
07670152C

value: Progressive Disease


title: Donor 3 B cells control


title: H3K4me3_IFNg_Ezh2i_0uM_rep2

description:
processed data file: IFNg_0Ezh2i_H3K4me3_dupmark.bam_peaks.broadPeak
P15158_1039_S39

source_name: Sox10GFP+ OPCs_H3K4me3_IFNg_Ezh2i_0uM


title: TWCM-H8-lib1

description:
DCM_Cells.Robj
DCM_Integrated.Robj

value: Used fresh/not stored

value: Single Cell


title: H3K27ac_HiChIP_IFN_mOPC_rep1

description:
replicate 1
P17103_1002
OPC_h3k27ac_hichip.hic
IFNg_5kb_EnhancerPredictions.txt
IFNg_5kb_EnhancerPredictions.bedpe
IFNg_5kb_EnhancerPredictionsFull.txt

tag: strain

value: Abcam Ab177178

value: In-house Tn5

value: cultured primary mOPCs

value: IFN


title: Patient 6 pretreatment biopsy [NS_CancerPath_C2535]

description:
100 ng of total RNA was hybridyzed with the NanoString nCounter panel of probes
19_0053

source_name: Primary Urothelial cancer


title: Donor 2 B cells anti-BTLA


title: H3K4me3_Ctr_Ezh2i_0uM_rep2

description:
processed data file: Ctr_0Ezh2i_H3K4me3_dupmark.bam_peaks.broadPeak
P15158_1038_S38

source_name: Sox10GFP+ OPCs_H3K4me3_Ctr_Ezh2i_0uM

value: Sox10GFP+ oligodendrocyte precursor cells (OPCs)


title: TWCM-H7-lib1

description:
DCM_Cells.Robj
DCM_Integrated.Robj

value: Transmural LV Apex

value: Non-diseased


title: H3K27me3_IFNg_Ezh2i_1.5uM_rep2

description:
processed data file: IFNg_15Ezh2i_H3K27me3_dupmark.bam_peaks.broadPeak
P15158_1037_S37

value: IFNg

value: Cell Signaling 9733S; rabbit; 1ug


title: Donor 2 B cells control

value: Control


title: Donor 1 B cells anti-BTLA

value: anti-BTLA


title: 190315Mk7_Ctr

source_name: Sox10GFP+ OPCs

tag: mouse model

value: EAE

tag: age

value: Sox10GFP+ OPCs

value: Ctr

tag: replicate


title: TWCM-11-264

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj

tag: storage condition

tag: technology

value: Single Nuclei


title: Patient 3 pretreatment biopsy [NS_CancerPath_C2535]

description:
100 ng of total RNA was hybridyzed with the NanoString nCounter panel of probes
07670118C

value: Baseline

value: Progressive Disease


title: TWCM-H6-lib1

description:
DCM_Cells.Robj
DCM_Integrated.Robj

value: Used fresh/not stored

value: Single Cell

tag: disease state

value: Dilated cardiomyopathy


title: TWCM-11-104

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj


title: TWCM-H5

description:
DCM_Cells.Robj
DCM_Integrated.Robj


title: Patient 2 pretreatment biopsy [NS_CancerPath_C2535]

description:
100 ng of total RNA was hybridyzed with the NanoString nCounter panel of probes
2185

source_name: Metastatic Head&Neck cancer

value: Not Evaluable


title: TWCM-H4

description:
DCM_Cells.Robj
DCM_Integrated.Robj

source_name: Transmural LV Apex


title: Patient 1 pretreatment biopsy [NS_CancerPath_C2535]

description:
100 ng of total RNA was hybridyzed with the NanoString nCounter panel of probes
2186


title: TWCM-11-93

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj


title: HA-SOX4 in primary decidualized stromal cells repeat 2

city: Xiamen

first: Wenbo

last: Deng

state: Fujian

address: Xiang'an Road

department: School of Medicine

institute: Xiamen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Hg38 whole genome using STAR with default parameters
MACS2 was used to call the peaks of SOX4 binding using default parameters.
Genome_build: Hg38

source_name: decidualized primary human stromal cells

growth_protocol: Primary decidualized stromal cells maintained in DMEM/F12 without phenolic red (Gibco) at the present of 10%charcoal stripped fetal bovine serum (CS-FBS, Biological Industries), glucose (3.1 g/L), sodium pyruvate (1 mM, Sigma); sodium bicarbonate (1.5 g/L, Sigma), Penicillin-Streptomycin (50 mg/ml, Solarbio); insulin-transferrin-selenium (ITS, 1%, Thermo Fisher) and puromycin (500 ng/ml). The primary cultured cells were maintained only in DMEM/F12 (Gibco) without phenolic red and CS-FBS 10%. For decidualization, hESCs were cultured in medium at the present of estrogen (E2, 10nM, Sigma), medroxyprogesterone acetate (MPA, 1 mM, Sigma), and dibutyl cyclophospsinoside (db-cAMP, 0.5 mM, MCE) in 2% CS-FBS with different days. All the cells were cultured in 5% CO2, 95% air, 100% humidity at 37 C and culture medium was replaced every 48 h.

extract_protocol:
primary decidualized stromal cells were cross-linked with 1/15 volume of 16% formaldehyde (CST) at room temperature for 10 minutes and quenched with 1/10 volume of 1.25 M glycine for 15 minutes on ice. Cell lysate in lysis buffer III were sonicated using Bioruptor pico (Diagenode) and then incubated with 4 µg antibody overnight at 4℃ with rotation. Immunoprecipitated complexes were collected with 15 µl Protein A Dynabeads (Invitrogen, 10002D) for 1 hour at 4℃ with rotation. Subsequently, beads were washed sequentially once with low-salt buffer, twice with high-salt buffer, once with LiCl buffer, twice with TE, and then eluted in 400 µl of elution buffer for 30 min at 65℃. The eluates were incubation at 65℃ for 8 h to reverse the cross-linking. Next, eluates were treated with proteinase K for 1 h at 55℃ and then RNase A for 30 min at 37℃ before DNA was extracted and purified.
The ChIP libraries were prepared using KAPA HyperPrep Kits (Roche, 07962347001) and then run on the Illumina sequencer Hiseq-Xten PE150 using standard Illumina protocols

value: Human uterus

value: Endoemtrium primary stromal cells

tag: chip antibody

value: HA-Tag (C29F4) Rabbit mAb , vendor:Cell signaling Technology (CST); catalog number:#3724;  lot/batch number:4


title: H3K27me3_IFNg_Ezh2i_0uM_rep2

description:
processed data file: IFNg_0Ezh2i_H3K27me3_dupmark.bam_peaks.broadPeak
P15158_1035_S35

value: Sox10GFP+ oligodendrocyte precursor cells (OPCs)

value: IFNg

tag: antibody


title: Donor 1 B cells control

description: Total RNA was hybridized to Nanostring chips and analyzed for RNA counts

tag: cell

value: Purified B cell

tag: donor

tag: treatment

value: Control


title: HA-SOX4 in primary decidualized stromal cells repeat 1

tag: cell type


title: H3K27me3_Ctr_Ezh2i_0uM_rep2

description:
processed data file: Ctr_0Ezh2i_H3K27me3_dupmark.bam_peaks.broadPeak
P15158_1034_S34

tag: condition

value: Cell Signaling 9733S; rabbit; 1ug


title: TWCM-H3

description:
DCM_Cells.Robj
DCM_Integrated.Robj

value: Transmural LV Apex


title: H_ZC-11-292

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj

value: Non-diseased


title: H3K27ac_IFNg_Ezh2i_1.5uM_rep1

description:
processed data file: IFNg_15Ezh2i_H3K27ac_dupmark.bam_peaks.broadPeak
P15158_1033_S33

source_name: Sox10GFP+ OPCs_H3K27ac_IFNg_Ezh2i_1.5uM

value: Abcam ab177178; rabbit; 1ug


title: 4d_PE_8_hyp_fib

city: Philadelphia

first: Benjamin

last: Prosser

state: PA

address: 700 CRB, 415 Curie Blvd

department: Physiology

institute: University of Pennsylvania

description: total RNA from day 4 mouse heart tissue harvested after 10mg/kg phenylephrine injections on day 0 and day 2

hyb_protocol: NanoString probes were hybridized as per the manufacturer's protocol.

data_processing: The geometric means of the positive control values were used to threshold followed by data normalization using the geometric means of the three housekeeping genes (GAPDH, Rpl4, Tbp).

label: Nanostring Label

source_name: heart tissue

label_protocol: NanoString probes were labelled as per the manufacturer's protocol.

extract_protocol: total RNA was extracted from ~10mg of heart tissue using RNAzol as per the manufacturer's protocol

tag: time

value: Phenylephrine


title: rIL-17B2

city: Jining

first: Qingli

last: Bie

state: Sandong

address: 89 Guhuai Road

department: Department of Laboratory Medicine

institute: Affiliated Hospital of Jining Medical University

data_processing:
The reference genomes and the annotation file were downloaded from ENSEMBL database. Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0.
Genome_build: hg38
Supplementary_files_format_and_content: raw gene counts for every gene and every sample

source_name: HGC-27 cell line

extract_protocol:
The RNA-seq of monocytes were performed by the Smart-Seq2 method. Briefly samples were collected in tubes with lysis component and ribonuclease inhibitor. Then an Oligo-dT primer was introduced to the reverse transcription reaction for first-strand cDNA synthesis, followed by PCR amplification to enrich the cDNA and magbeads purification step to clean up the production.
cDNAs were amplificated according to Smart-seq2 procedures for construct Illumina RNA sequencing library.

tag: cell line

value: HGC-27 GC cells were treated with200ng/ml rIL-17B, replicate 2.

tag: treatment time


title: rIL-17B1

value: HGC-27 GC cells were treated with200ng/ml rIL-17B, replicate 1.


title: 4d_PE_6_hyp_fib


title: MDAMB436_2

city: Naples

first: Gennaro

last: Gambardella

address: Via Campi Flegrei 34,

country: Italy

institute: Telethon Institute of Genetics and Medicine (TIGEM)

description: single cell transcriptomic

data_processing:
Drop-seq Core Coputational Core (https://github.com/broadinstitute/Drop-seq)
Genome_build: GENCODE v28
Supplementary_files_format_and_content: UMI Counts txt file. This file includes data from 3 files: matrix.mtx with raw counts stored in the MatrixMarket format and two additional files genes and barcodes that contains the names of the rows (genes) and the coloumns (barcodes) of the matrix.

source_name: Immortalized Breast Cancer Cell-line

extract_protocol:
Cell Lysis
Drop-seq Protocol

tag: breast cancer subtype

value: TNA

tag: medium

value: RPMI 2mM L-Glutamine, 10 %FBS

tag: derivation

value: metastatic site:pleural effusion


title: PBS2

value: HGC-27 GC cells were treated with PBS, replicate 2.


title: MCF7_2

description: single cell transcriptomic

value: LA

value: MEM 2mM L-Glutamine, 10 %FBS, 1% NEAA


title: 4d_PE_5_hyp_fib


title: Patient 4 pretreatment biopsy [NS_CancerPath_C2535]

description:
100 ng of total RNA was hybridyzed with the NanoString nCounter panel of probes
07670151C

tag: timepoint

value: Baseline

tag: dose, bln cells

tag: cohort

tag: best overall response

value: Stable Disease


title: TWCM-10-68

description:
DCM_Nuclei.Robj
DCM_Integrated.Robj

tag: tissue

tag: storage condition

tag: technology

value: Single Nuclei

tag: disease state


title: ZR751

description: single cell transcriptomic

value: metastatic site:ascites


title: PBS1

tag: treatment

value: HGC-27 GC cells were treated with PBS, replicate 1.


title: H3K27ac_Ctr_Ezh2i_0uM_rep1

description:
processed data file: Ctr_0Ezh2i_H3K27ac_dupmark.bam_peaks.broadPeak
P15158_1030_S30

source_name: Sox10GFP+ OPCs_H3K27ac_Ctr_Ezh2i_0uM

tag: cell type

value: Sox10GFP+ oligodendrocyte precursor cells (OPCs)

value: Ctr

tag: antibody


title: 4d_PE_4_hyp_fib

tag: time


title: H3K27ac_Ctr_Ezh2i_1.5uM_rep1

description:
processed data file: Ctr_15Ezh2i_H3K27ac_dupmark.bam_peaks.broadPeak
P15158_1032_S32

source_name: Sox10GFP+ OPCs_H3K27ac_Ctr_Ezh2i_1.5uM

tag: condition

value: Abcam ab177178; rabbit; 1ug


title: IFNg_STAT1 B (14994S) rep3

description: IFNg_STAT1 B (14994S)

data_processing:
CUT&TAG data processing was following https://yezhengstat.github.io/CUTTag_tutorial/ combined with parameters from bulk ATAC-seq processing. Aligment was performed with Bowtie2, reads were aligned to mouse genome (GRCm38/mm10) with parameters --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700 -p 3 –x . Peaks were called with MACS2 with parameters,_-q 0.1 --keep-dup all
Genome_build: mm10
Supplementary_files_format_and_content: Cut&Tag peaks signal in wig files for Ctrl and IFNg samples, per individual replicate. Merged replicates peaks signal in wig format for Ctrl and IFNg STAT1 CUT&Tag, replicates combined signal and normalized to efformalized to effec (mm10)nome size, binsize 10 and RPGC from Deeptoo bamCoerage

extract_protocol:
CUT&Tag was performed as previously described (Kaya-Okur et al., 2019) with minor adaptations. Primary OPCs were washed from the plate with PBS at room temperature. Cells were centrifuged for 5 minutes at 300xg and room temperature and then resuspended in wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x Roche Complete Protease Inhibitor tablet). 100 000 cells per condition were centrifuged for 5 minutes at 300xg and room temperature and resuspended in wash buffer. Activated Concanavalin-A beads (Bangs Laboratories BP531) in binding buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2) was added to each condition and incubated for 10 minutes on a rotator at room temperature. Beads with nuclei were now kept on a magnetic stand and washed twice with Antibody buffer (2mM EDTA, 0.1% BSA and 0.05% digitonin in wash buffer). After discarding the liquid, beads were resuspended with primary antibody (STAT1, Cell Signaling 14994S; rabbit, monoclonal, 1:100) in antibody buffer and incubated overnight at 4°C on a rotator. Then beads were washed with freshly prepared Dig-wash buffer (0.05% digitonin in wash buffer) and incubated with secondary antibody (guinea pig anti-rabbit, NBP1-72763, Novus biologicals, 1:100) in Dig-wash buffer on a rotator for 30-60 minutes. After three washes with Dig-wash buffer, the beads were incubated with pA-Tn5  (Kaya-Okur et al., 2019) adapter complex (1:250) in Dig-300-wash buffer (300mM NaCl and 0.05% digitonin in wash buffer) and incubated for 1 hour at room temperature on a rotator. After two washes with Dig-300-wash buffer, the beads were resuspended in tagmentation buffer (10 mM MgCl2, 300mM NaCl and 0.05% digitonin in wash buffer) and incubated at 37° for 1 hr in a PCR cycler with heated lid. To stop the tagmentation reaction and to solubilize DNA fragments, 2.5 µL of 0.5M EDTA, 5 µL 10% SDS and 2 µL of 20 mg/ml Proteinase K was added to the beads and an incubation of 1 hour at 55°C.
DNA from the samples was purified using the Zymo DNA Clean & Concentrator kit (D4014, Zymo) according to manufacturer’s instructions, then amplified according to the number of cycles analyzed with qRT-PCR. SPRI bead (B23317, Beckman Coulter) purification was performed on the post-amplification libraries to remove remaining adapter dimers. Three replicates per condition were performed with primary OPCs obtained from different litters. Libraries were sequenced on the Illumina Nextseq 500/550 with 37-8-8-37 bp set-up.
CUT&Tag (Kaya-Okur et al., 2019) . Libraries were sequenced on the Illumina Nextseq 500/550 with 37-8-8-37 bp set-up.

treatment_protocol: Cells were treated with IFN-gamma (100ng/ml, 485-MI-100, R&D) for 48 hours.

value: IFNg

tag: replicate


title: T47D

description: single cell transcriptomic

tag: cell line

tag: breast cancer subtype

value: RPMI 2mM L-Glutamine, 10 %FBS, 1 mM sodium pyruvate, 10 mM HEPES


title: H3K27me3_IFNg_Ezh2i_1.5uM

description:
processed data file: IFNg_15Ezh2i_H3K27me3_dupmark.bam_peaks.broadPeak
P15158_1029_S29

value: Cell Signaling 9733S; rabbit; 1ug


title: 4d_PE_3_hyp_fib

value: Phenylephrine


title: Control_STAT1 B (14994S) rep3

description: Control_STAT1 B (14994S)


title: H3K27me3_Ctr_Ezh2i_1.5uM_rep2

description:
processed data file: Ctr_15Ezh2i_H3K27me3_dupmark.bam_peaks.broadPeak
P15158_1036_S36

source_name: Sox10GFP+ OPCs_H3K27me3_Ctr_Ezh2i_1.5uM


title: 4d_PE_2_hyp_fib


title: H3K27me3_Ctr_Ezh2i_1.5uM_rep1

description:
processed data file: Ctr_15Ezh2i_H3K27me3_dupmark.bam_peaks.broadPeak
P15158_1028_S28


title: H3K27me3_IFNg_Ezh2i_0uM_rep1

description:
processed data file: IFNg_0Ezh2i_H3K27me3_dupmark.bam_peaks.broadPeak
P15158_1027_S27

source_name: Sox10GFP+ OPCs_H3K27me3_IFNg_Ezh2i_0uM


title: IFNg_STAT1 B (14994S) rep2

description: IFNg_STAT1 B (14994S)


title: MX1

description: single cell transcriptomic

value: TNB

tag: medium

value: DMEM/F12 - 1:1 mixture of Dulbecco's Modified Eagle Medium and Nutrient Mixture F-12, 2 mM L-Glutamine, 10% FBS

tag: derivation

value: originated from primary breast cancer. Primary xenotransplant from an infiltrating duct carcinoma


title: MDAMB468

description: single cell transcriptomic

value: TNA

value: RPMI 2mM L-Glutamine, 10 %FBS

value: metastatic site:pleural effusion


title: MDAMB453

description: single cell transcriptomic

value: H

value: metastatic site:pericardial effusion


title: Control_STAT1 B (14994S) rep2

description: Control_STAT1 B (14994S)


title: 4d_PE_1_hyp_fib


title: 4d_Iso_8_hyp_fib

description: total RNA from day 4 mouse heart tissue harvested after 5mg/kg isoproterenol injections on day 0 and day 2

value: Isoproterenol


title: TWCM-H1

description:
DCM_Cells.Robj
DCM_Integrated.Robj

data_processing:
Alignment: Cell Ranger V3, aligned to GRCh38 transcriptome, or custom pre-mrna reference.
QC and Filtering: Seurat V3/V4
Unsupervised Clustering: Seurat V3/V4
Genome_build: GRCh38 V3.0.0
Supplementary_files_format_and_content: Seurat V4 R Objects
Supplementary_files_format_and_content: I*Counts.csv: Comma-separated expression matrices.

extract_protocol:
Transmural tissue samples were removed from the left ventricle apex during LVAD implantation or after whole heart explantation. Samples for single cell were processed fresh by enzymatic digestion while samples for single nuclei were frozen in liquid nitrogen and stored at -80C until use and processed by mechanical homogenization. All single cell/nuclei suspensions were sorted by FACS to remove debris and dead cells.
10X Genomics Chromium Single Cell 5’ Reagent V1.1.

value: Transmural LV Apex

value: Used fresh/not stored

value: Single Cell

value: Dilated cardiomyopathy


title: IFNg_STAT1 B (14994S) rep1

description: IFNg_STAT1 B (14994S)

value: IFNg


title: H3K27me3_Ctr_Ezh2i_0uM_rep1

description:
processed data file: Ctr_0Ezh2i_H3K27me3_dupmark.bam_peaks.broadPeak
P15158_1026_S26

source_name: Sox10GFP+ OPCs_H3K27me3_Ctr_Ezh2i_0uM

value: Sox10GFP+ oligodendrocyte precursor cells (OPCs)

value: Ctr


title: 4d_Iso_7_hyp_fib


title: MDAMB436_1

description: single cell transcriptomic


title: H3K4me3_IFNg_Ezh2i_1.5uM_rep1

description:
processed data file: IFNg_15Ezh2i_H3K4me3_dupmark.bam_peaks.broadPeak
P15158_1025_S25

source_name: Sox10GFP+ OPCs_H3K4me3_IFNg_Ezh2i_1.5uM

value: Diagenode C15410003-50; rabbit; 1ug


title: MDAMB415

description: single cell transcriptomic

value: LA

value: RPMI 2mM L-Glutamine, 10 %FBS, 10 µg/mL insulin,  10 µg/mL glutathione, 15% FBS


title: H3K4me3_Ctr_Ezh2i_1.5uM_rep1

description:
processed data file: Ctr_15Ezh2i_H3K4me3_dupmark.bam_peaks.broadPeak
P15158_1024_S24

source_name: Sox10GFP+ OPCs_H3K4me3_Ctr_Ezh2i_1.5uM


title: H3K27ac_IFNg_Ezh2i_0uM_rep1

description:
processed data file: IFNg_0Ezh2i_H3K27ac_dupmark.bam_peaks.broadPeak
P15158_1031_S31

source_name: Sox10GFP+ OPCs_H3K27ac_IFNg_Ezh2i_0uM

value: Abcam ab177178; rabbit; 1ug


title: H3K4me3_IFNg_Ezh2i_0uM_rep1

description:
processed data file: IFNg_0Ezh2i_H3K4me3_dupmark.bam_peaks.broadPeak
P15158_1023_S23

source_name: Sox10GFP+ OPCs_H3K4me3_IFNg_Ezh2i_0uM


title: 4d_Iso_6_hyp_fib


title: 4d_Iso_5_hyp_fib


title: MDAMB361

description: single cell transcriptomic

value: LB

value: RPMI 2mM L-Glutamine, 20 %FBS

value: metastatic site:brain


title: H3K4me3_Ctr_Ezh2i_0uM_rep1

description:
processed data file: Ctr_0Ezh2i_H3K4me3_dupmark.bam_peaks.broadPeak
P15158_1022_S22

source_name: Sox10GFP+ OPCs_H3K4me3_Ctr_Ezh2i_0uM


title: MCF7_1

description: single cell transcriptomic

value: MEM 2mM L-Glutamine, 10 %FBS, 1% NEAA

value: metastatic site:pleural effusion


title: H3K4me3_IFNg_rep2

source_name: Sox10GFP+ OPCs

extract_protocol:
Cut&Run was performed as previously described (Skene&Henikoff, 2017) with minor adaptations. Primary OPCs were incubated with TrypLE (Gibco #12605010) at 37°C for 5 minutes and collected in cell culture media. Cells were centrifuged for 5 minutes at 300xg and room temperature and then resuspended in wash buffer (20mM HEPES pH 7.5, 150 mM NaCl, 0.5mM Spermidine, 0.01%BSA, 1x Roche Complete Protease Inhibitor tablet). 250 000 cells per condition were centrifuged for 3 minutes at 600xg and room temperature and resuspended in wash buffer. Activated Concanavalin-A beads (Bangs Laboratories BP531) in binding buffer (20mM HEPES pH 7.5, 10mM KCl, 1mM CaCl2, 1mM MnCl2) was added to each condition and incubated for 10 minutes on a rotator at room temperature. Beads with nuclei were now kept on a magnetic stand and washed with Dig-wash buffer (0.05% digitonin in wash buffer). After discarding the liquid, beads were resuspended with primary antibody in antibody buffer (2mM EDTA in Dig-wash buffer) and incubated overnight at 4°C on a nutator. Then beads were washed with freshly prepared Dig-wash buffer and incubated with 2ug/mL Protein A-MNase (Schmid et al., 2004) in Dig-wash buffer for 1 hour at 4°C on a nutator. After two washes with Dig-wash buffer and one wash with low-salt rinse buffer (20mM HEPES pH 7.5, 0.5mM spermidine, 0.05% digitonin) ice-cold incubation buffer (3.5mM HEPES pH 7.5, 10mM CaCl2, 0.05% digitonin) was added to the beads which were subsequently placed in a metal block in an ice-water bath maintained at 0°C for 5 minutes. The beads were then placed on a magnet stand and liquid discarded. Stop buffer (170mM NaCl, 20mM EGTA, 0.05% digitonin, 50ug/mL RNase A, 25ug/mL glycogen, 2pg/mL Yeast spike-in DNA) was added to the beads and incubated for 30 minutes at 37°C. Beads were placed on a magnet stand and supernatant was collected. 2uL of 10% SDS and 2.5uL of 20mg/mL Proteinase K was added to the supernatant and incubated for 1 hour at 50°C. DNA from the samples was purified using the MinElute PCR purification kit (Qiagen) according to manufacturer’s instructions. Antibodies were used against H3K27me3 (Cell Signaling 9733S; rabbit; 1ug), H3K4me3 (Diagenode C15410003-50; rabbit; 1ug), H3K27ac (Abcam ab177178; rabbit; 1ug), CTCF (Cell Signaling 3418S; rabbit; 1:100).
Sequencing libraries were prepared using KAPA HyperPrep kit (Roche #07962363001) and KAPA Unique Dual-Indexed Adapters (Roche #08861919702) according to manufacturer’s instructions, but with the following adjustments. Two post-adapter ligation clean-ups were performed using 0.7x and 1.1x AMPure XP beads respectively. PAGE purification was performed on the post-amplification libraries to remove remaining adapter dimers. Two or three replicates per condition were performed with primary OPCs obtained from different litters. Libraries were sequenced on the Illumina Novaseq 6000 with a 50-8-8-50 read setup.


title: MCF12A

description: single cell transcriptomic

source_name: Immortalized Breast Cell-line

value: Basal-like

value: DMEM/F12 - 1:1 mixture of Dulbecco's Modified Eagle Medium and Nutrient Mixture F-12, 20 ng/mL EGF, 0.03 µM ITS, 10% FBS

value: mammary gland; non-tumorigenic, fibrocystic breast disease


title: 4d_Iso_2_hyp_fib

value: Isoproterenol


title: 4d_Iso_3_hyp_fib


title: ChIP_PU1_ERHoxB8_CRISPR-region6

extract_protocol:
Culture media was removed, and plates were washed once with PBS and then fixed for 10 minutes with 1% formaldehyde (Thermo Fisher Scientific) in PBS at room temperature. Reaction was then quenched by adding glycine (Thermo Fisher Scientific) to 0.125M. After fixation, cells were washed once with cold PBS and then scraped into supernatant using a rubber policeman, pelleted for 5 minutes at 400xg at 4°C. Cells were transferred to Eppendorf DNA LoBind tubes and pelleted at 700xg for 5 minutes at 4°C, snap-frozen in liquid nitrogen and stored at -80°C until ready for ChIP-seq protocol preparation. Chromatin immunoprecipitation (ChIP) was performed in biological replicates as described previously (Hoeksema et al., 2020). Samples were sonicated using a probe sonicator in 500 µl lysis buffer (10 mM Tris/HCl pH 7.5, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% deoxycholate, 0.5% sarkozyl, 1x protease inhibitor cocktail). After sonication, 10% Triton X-100 was added to 1% final concentration and lysates were spun at full speed for 10 minutes. 1% was taken as input DNA, and immunoprecipitation was carried out overnight with 20 µl Protein A Dynabeads (Invitrogen) and 2 µg specific antibodies for C/EBPβ (Santa Cruz, sc-150), PU.1 (Cell Signaling, #2258), and H3K27ac (Active Motif, 39135). Beads were washed three times each with wash buffer I (20 mM Tris/HCl, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA), wash buffer II (10 mM Tris/HCl, 250 mM LiCl, 1% IGEPAL CA-630, 0.7% Na-deoxycholate, 1 mM EDTA), TE 0.2% Triton X-100 and TE 50 mM NaCl and subsequently resuspended 25 µl 10 mM Tris/HCl pH 8.0 and 0.05% Tween-20. ChIP-seq libraries were prepared on the Dynabeads as described below. For locus specific enrichment ChIP-seq, bead complex was resuspended in 50 µl 1% SDS-TE. 4 µl ProtK, 4 µl RNase A, 3 µl 5 M NaCl was added to these and the input samples and incubated at 50℃ for 1 hour, reverse crosslinked at 65℃ overnight and then eluted from the beads.
For wild-type cells, ChIP libraries were prepared while bound to Dynabeads using NEBNext Ultra II Library preparation kit (NEB) using half reactions. DNA was polished, polyA-tailed and ligated after which dual UDI (IDT) or single (Bioo Scientific) barcodes were ligated to it. Libraries were eluted and crosslinks reversed by adding to the 46.5 µl NEB reaction 16 µl water, 4 µl 10% SDS, 4.5 µl 5 M NaCl, 3 µl 0.5 M EDTA, 4 µl 0.2 M EGTA, 1 µl RNAse (10 mg/ml) and 1 µl 20 mg/ml proteinase K, followed by incubation at 55℃ for 1 hour and 75℃ for 30 minutes in a thermal cycler. Dynabeads were removed from the library using a magnet and libraries were cleaned up by adding 2 µl SpeedBeads 3 EDAC (Thermo) in 124 µl 20% PEG 8000/1.5 M NaCl, mixing well, then incubating at room temperature for 10 minutes. SpeedBeads were collected on a magnet and washed two times with 150 µl 80% ethanol for 30 seconds. Beads were collected and ethanol removed following each wash. After the second ethanol wash, beads were air dried and DNA eluted in 12.25 µl 10 mM Tris/HCl pH 8.0 and 0.05% Tween-20. DNA was amplified by PCR for 14 cycles in a 25 µl reaction volume using NEBNext Ultra II PCR master mix and 0.5 µM each Solexa 1GA and Solexa 1GB primers. Libraries were size selected using TBE gels for 200 – 500 bp and DNA eluted using gel diffusion buffer (500 mM ammonium acetate, pH 8.0, 0.1% SDS, 1 mM EDTA, 10 mM magnesium acetate) and purified using ChIP DNA Clean & Concentrator (Zymo Research).
For CRISPR/Cas9-mutated cells, after performing the target-specific ChIPs, we performed an initial PCR for locus-specific amplicon enrichment using NEBNext 2X High Fidelity PCR MM (NEB) and 5’-biotinylated stub adapter primers specific to appropriate genomic regions to be interrogated (Figure 5-table supplement 1). Initial hotstart/denaturation at 98℃ for 30 sec was followed by 10 cycles of amplification (98℃ for 15 sec, 65-67℃ for 15 sec, 72oC for 30 sec) and then a final elongation at 72℃ for 5 min. After this, we performed a 0.7X AmpureXP clean-up and eluted in 20 µl 0.5x TT (5 mM Tris pH 8.0 + 0.025% Tween20). Dynabeads MyOne Streptavidin T1 beads were then washed in 1x Wash Binding Buffer (WBB, 2X WBB: 10 mM Tris-HCl (pH 7.5), 1 mM EDTA, 2 M NaCl, 0.1% Tween) and resuspended beads at 20 µl per sample in 2x WBB. 20 µl prepared Dynabeads MyOne Streptavidin T1 beads (in 2x WBB) were then added to cleaned up 20 µl 0.5x TT PCR fragments, mixed and incubated for 60min at RT with mild shaking. After this, beads were collected on a magnet and washed twice with 150 µl 1x WBB and once with 180 µl TET (TE + 0.05% Tween-20). Finally, beads were resuspended in 25 µl 0.5x TT and on bead PCR for addition of Illumina-specific adapters and 10-bp Unique Dual Indexes (UDIs) using NEBNext 2X High Fidelity PCR MM (NEB) and 25 PCR cycles was performed (Figure 5-table supplement 2). Libraries were size selected using TBE gels for 300-500 bp and DNA eluted using gel diffusion buffer and purified using ChIP DNA Clean & Concentrator (Zymo Research).

tag: strain

tag: genotype/variation

tag: chip antibody

value: PU1 (Cell Signaling, #2258)


title: ChIP_PU1_ERHoxB8_CRISPR-region5


title: ChIP_PU1_ERHoxB8_CRISPR-region1


title: KPL1

description: single cell transcriptomic

value: DMEM 2mM L-Glutamine, 10 %FBS

value: metastatic site:pleural fluid


title: Soxertini568_maxilar

data_processing:
The 10x Genomics Cell Ranger Suite (version 2.0.2) was used to perform sample demultiplexing, barcode processing, alignment (mm10) and generation of digital gene expression matrix. Default parameters were used.
Processed data files are gene expression matrices with genes by rows, cells by colums. Gene expression is measured in UMI counts. Processed data files still have to undergo quality filtering and normalization, as specified below.
Each gene expression matrix was loaded in R separately, retaining genes expressed in at least 3 cells, and cells expressing at least 50 genes. Moreover, we excluded cells expressing less than 200 genes or having a percentage of mitochondrial genes greater than 25%.
After quality filtering, UMI counts were log-normalized.
Genome_build: mm10
Supplementary_files_format_and_content: Digital gene expression matrix (UMI counts) for each sample and each gene. Files provided in tab-delimited format.

source_name: MYC extracranial rhabdoid tumor

extract_protocol:
Fresh tumor tissues were isolated macroscopically and minced using scalpels prior to enzymatic dissociation for 20 minutes at 37°C using PBS-diluted Accutase, accompanied by mechanical dissociation and followed by the lysis of red blood cells using ACK lysis buffer. Cells were stained with the dye 7-AAD for cell sorting to exclude dead cells. Vital cells were loaded as input on the 10x Genomics Chromium controller.
Indexed-single cell RNA libraries were prepared for sequencing using the 10X Chromium Single Cell 3' Gel Bead Kit and Chromium i7 Multiplex Kit (10x Genomics, PN-120262). Each sample was sequenced across 4 lanes with Illumina NextSeq 500 System (2 x 75bp).

tag: tissue

value: MYC extracranial rhabdoid tumor

tag: age (weeks)

tag: tumor localization

value: Extracranial, jaw


title: H3K27me3_IFNg_rep2

value: Sox10GFP+ oligodendrocyte precursor cells (OPCs)

value: IFNg

value: Cell Signaling 9733S; rabbit; 1ug


title: H3K4me3_Ctr_rep2

description:
P16151_1005_S5
processed data file: Ctr_Ctcf_dupmark.bam_peaks.narrowPeak

value: Ctr

value: Diagenode C15410003-50; rabbit; 1ug


title: 4d_Ctrl_7_hyp_fib

description: total RNA from day 4 mouse heart tissue harvested after ascorbic acid injections on day 0 and day 2

value: Ascorbic acid


title: JIMT1

description: single cell transcriptomic

value: H


title: 4d_Ctrl_8_hyp_fib


title: H3K27me3_Ctr_rep2


title: Rosini1148

value: Extracranial, gland


title: 4d_Ctrl_6_hyp_fib


title: HS578T

description: single cell transcriptomic

value: TNB

value: RPMI 2mM L-Glutamine, 10 %FBS

value: mammary gland/breast


title: Ctcf_Ctr_rep3

value: Cell Signaling 3418S; rabbit; 1:100


title: HCC70

description: single cell transcriptomic

value: TNA

value: mammary gland; breast/duct


title: Control_STAT1 B (14994S) rep1

description: Control_STAT1 B (14994S)


title: 4d_Ctrl_5_hyp_fib


title: HDQP1

description: single cell transcriptomic

value: DMEM 2mM L-Glutamine, 10 %FBS

value: primary ductal infiltrating breast carcinoma


title: 4d_Ctrl_4_hyp_fib


title: 4d_Ctrl_2_hyp_fib


title: HCC38

description: single cell transcriptomic


title: H3K4me3_Ctr_rep1

source_name: Sox10GFP+ OPCs_H3K4me3_Ctr


title: Ctcf_IFNg_rep2

source_name: Sox10GFP+ OPCs_Ctcf_IFNg


title: Ctcf_IFNg_rep3

value: Cell Signaling 3418s; rabbit; 1:100


title: Rosini1232

source_name: MYC spinal rhabdoid tumor

value: MYC spinal rhabdoid tumor

value: Spinal


title: 4d_Ctrl_1_hyp_fib

source_name: heart tissue


title: Rosini1177


title: Rosini1172


title: H3K4me3_IFNg_rep1

source_name: Sox10GFP+ OPCs_H3K4me3_IFNg

value: Sox10GFP+ oligodendrocyte precursor cells (OPCs)

value: IFNg


title: HCC1954

description: single cell transcriptomic

source_name: Immortalized Breast Cancer Cell-line


title: ChIP_CEBPb_ERHoxB8_CRISPR_region6

description: processing data file: ChIP_ERHoxB8_CRISPR_tagCounts.tsv

data_processing:
FASTQ files from sequencing experiments were mapped to the mm10 genome using Bowtie2 (Langmead and Salzberg, 2012). Wild-type data were mapped using default parameters whereas CRISPR data were mapped using "--local --rdg 10,1 --rfg 10,1" to allow different sizes of gaps/InDels. HOMER was used to convert aligned reads into “tag directories” for downstream analysis (Heinz et al., 2010).
The enriched regions (i.e. peaks) were identified using HOMER (Heinz et al., 2010) to call 200-bp peaks (command “findPeaks -style factor -size 200”).
H3K27ac tag counts were computated within +/- 500 bp around ATAC peaks using HOMER annotatePeaks.pl script with parameter "-norm 1e7 -size -500,500".
The CRISPR mapped reads were grouped based on the InDel size and whether the InDel overlaps with any of the PU.1 and C/EBP motifs. In processed file "ChIP_ERHoxB8_CRISPR_tagCounts.tsv", each column represents an InDel group.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file containing called peaks in the HOMER peak file format

extract_protocol:
Culture media was removed, and plates were washed once with PBS and then fixed for 10 minutes with 1% formaldehyde (Thermo Fisher Scientific) in PBS at room temperature. Reaction was then quenched by adding glycine (Thermo Fisher Scientific) to 0.125M. After fixation, cells were washed once with cold PBS and then scraped into supernatant using a rubber policeman, pelleted for 5 minutes at 400xg at 4°C. Cells were transferred to Eppendorf DNA LoBind tubes and pelleted at 700xg for 5 minutes at 4°C, snap-frozen in liquid nitrogen and stored at -80°C until ready for ChIP-seq protocol preparation. Chromatin immunoprecipitation (ChIP) was performed in biological replicates as described previously (Hoeksema et al., 2020). Samples were sonicated using a probe sonicator in 500 µl lysis buffer (10 mM Tris/HCl pH 7.5, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% deoxycholate, 0.5% sarkozyl, 1x protease inhibitor cocktail). After sonication, 10% Triton X-100 was added to 1% final concentration and lysates were spun at full speed for 10 minutes. 1% was taken as input DNA, and immunoprecipitation was carried out overnight with 20 µl Protein A Dynabeads (Invitrogen) and 2 µg specific antibodies for C/EBPβ (Santa Cruz, sc-150), PU.1 (Cell Signaling, #2258), and H3K27ac (Active Motif, 39135). Beads were washed three times each with wash buffer I (20 mM Tris/HCl, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA), wash buffer II (10 mM Tris/HCl, 250 mM LiCl, 1% IGEPAL CA-630, 0.7% Na-deoxycholate, 1 mM EDTA), TE 0.2% Triton X-100 and TE 50 mM NaCl and subsequently resuspended 25 µl 10 mM Tris/HCl pH 8.0 and 0.05% Tween-20. ChIP-seq libraries were prepared on the Dynabeads as described below. For locus specific enrichment ChIP-seq, bead complex was resuspended in 50 µl 1% SDS-TE. 4 µl ProtK, 4 µl RNase A, 3 µl 5 M NaCl was added to these and the input samples and incubated at 50℃ for 1 hour, reverse crosslinked at 65℃ overnight and then eluted from the beads.
For wild-type cells, ChIP libraries were prepared while bound to Dynabeads using NEBNext Ultra II Library preparation kit (NEB) using half reactions. DNA was polished, polyA-tailed and ligated after which dual UDI (IDT) or single (Bioo Scientific) barcodes were ligated to it. Libraries were eluted and crosslinks reversed by adding to the 46.5 µl NEB reaction 16 µl water, 4 µl 10% SDS, 4.5 µl 5 M NaCl, 3 µl 0.5 M EDTA, 4 µl 0.2 M EGTA, 1 µl RNAse (10 mg/ml) and 1 µl 20 mg/ml proteinase K, followed by incubation at 55℃ for 1 hour and 75℃ for 30 minutes in a thermal cycler. Dynabeads were removed from the library using a magnet and libraries were cleaned up by adding 2 µl SpeedBeads 3 EDAC (Thermo) in 124 µl 20% PEG 8000/1.5 M NaCl, mixing well, then incubating at room temperature for 10 minutes. SpeedBeads were collected on a magnet and washed two times with 150 µl 80% ethanol for 30 seconds. Beads were collected and ethanol removed following each wash. After the second ethanol wash, beads were air dried and DNA eluted in 12.25 µl 10 mM Tris/HCl pH 8.0 and 0.05% Tween-20. DNA was amplified by PCR for 14 cycles in a 25 µl reaction volume using NEBNext Ultra II PCR master mix and 0.5 µM each Solexa 1GA and Solexa 1GB primers. Libraries were size selected using TBE gels for 200 – 500 bp and DNA eluted using gel diffusion buffer (500 mM ammonium acetate, pH 8.0, 0.1% SDS, 1 mM EDTA, 10 mM magnesium acetate) and purified using ChIP DNA Clean & Concentrator (Zymo Research).    For CRISPR/Cas9-mutated cells, after performing the target-specific ChIPs, we performed an initial PCR for locus-specific amplicon enrichment using NEBNext 2X High Fidelity PCR MM (NEB) and 5’-biotinylated stub adapter primers specific to appropriate genomic regions to be interrogated (Figure 5-table supplement 1). Initial hotstart/denaturation at 98℃ for 30 sec was followed by 10 cycles of amplification (98℃ for 15 sec, 65-67℃ for 15 sec, 72oC for 30 sec) and then a final elongation at 72℃ for 5 min. After this, we performed a 0.7X AmpureXP clean-up and eluted in 20 µl 0.5x TT (5 mM Tris pH 8.0 + 0.025% Tween20). Dynabeads MyOne Streptavidin T1 beads were then washed in 1x Wash Binding Buffer (WBB, 2X WBB: 10 mM Tris-HCl (pH 7.5), 1 mM EDTA, 2 M NaCl, 0.1% Tween) and resuspended beads at 20 µl per sample in 2x WBB. 20 µl prepared Dynabeads MyOne Streptavidin T1 beads (in 2x WBB) were then added to cleaned up 20 µl 0.5x TT PCR fragments, mixed and incubated for 60min at RT with mild shaking. After this, beads were collected on a magnet and washed twice with 150 µl 1x WBB and once with 180 µl TET (TE + 0.05% Tween-20). Finally, beads were resuspended in 25 µl 0.5x TT and on bead PCR for addition of Illumina-specific adapters and 10-bp Unique Dual Indexes (UDIs) using NEBNext 2X High Fidelity PCR MM (NEB) and 25 PCR cycles was performed (Figure 5-table supplement 2). Libraries were size selected using TBE gels for 300-500 bp and DNA eluted using gel diffusion buffer and purified using ChIP DNA Clean & Concentrator (Zymo Research).

value: CEBPb (Santa Cruz, sc-150, lot G1814)


title: HCC1500

description: single cell transcriptomic

value: LA


title: HCC1937

description: single cell transcriptomic


title: ChIP_input_ERHoxB8_CRISPR_region6

value: input


title: 4h_PE_4_hyp_fib

description: total RNA from mouse heart tissue harvested after 4 hours of 10mg/kg phenylephrine injection

value: Phenylephrine


title: Soxertini593

value: MYC extracranial rhabdoid tumor

value: Extracranial, shoulder


title: 4h_PE_6_hyp_fib


title: ChIP_CEBPb_ERHoxB8_CRISPR_region5


title: 4h_PE_5_hyp_fib


title: ChIP_input_ERHoxB8_CRISPR_region5


title: HCC1187

description: single cell transcriptomic

value: RPMI 2mM L-Glutamine, 10 %FBS

value: mammary gland; breast


title: H3K27ac_IFNg_rep3

source_name: Sox10GFP+ OPCs_H3K27ac_IFNg

value: Abcam ab177178; rabbit; 1ug


title: H3K27ac_Ctr_rep3

source_name: Sox10GFP+ OPCs_H3K27ac_Ctr

value: Ctr


title: ChIP_CEBPb_ERHoxB8_CRISPR_region4


title: 4h_PE_3_hyp_fib


title: HCC1143

description: single cell transcriptomic

value: TNA

value: RPMI 2mM L-Glutamine, 20 %FBS

value: mammary gland; breast/duct


title: H3K27me3_Ctr_rep3

source_name: Sox10GFP+ OPCs_H3K27me3_Ctr

value: Cell Signaling 9733S; rabbit; 1ug


title: 4h_PE_2_hyp_fib


title: EVSAT

description: single cell transcriptomic

value: EVSAT

value: H

value: MEM 2mM L-Glutamine, 10 %FBS, 25 mM HEPES

value: metastatic site:malignant ascitic effusion


title: ChIP_CEBPb_ERHoxB8_CRISPR_region3

value: CEBPb (Santa Cruz, sc-150, lot G1814)


title: EFM19

description: single cell transcriptomic

value: LA

value: metastatic site:pleural effusion


title: H3K27ac_Ctr_rep2

value: Sox10GFP+ oligodendrocyte precursor cells (OPCs)


title: 4h_PE_1_hyp_fib

value: Phenylephrine


title: DU4475

description: single cell transcriptomic

value: metastatic site:skin carcinoma


title: 4h_Iso_6_hyp_fib

description: total RNA from mouse heart tissue harvested after 4 hours of 5mg/kg isoproterenol injection

value: Isoproterenol


title: ChIP_CEBPb_ERHoxB8_CRISPR_region2


title: H3K27me3_IFNg_rep1

source_name: Sox10GFP+ OPCs_H3K27me3_IFNg

value: IFNg


title: CAMA1

description: single cell transcriptomic

value: MEM 2mM L-Glutamine, 10 %FBS, 1% NEAA


title: Ctcf_Ctr_rep2

description:
P15158_1018_S18
processed data file: Ctr_Ctcf_dupmark.bam_peaks.narrowPeak

source_name: Sox10GFP+ OPCs_Ctcf_Ctr

value: Ctr

value: Cell Signaling 3418S; rabbit; 1:100


title: H3K27me3_Ctr_rep1


title: 4h_Iso_4_hyp_fib


title: CAL851

description: single cell transcriptomic

value: TNB

value: DMEM 2mM L-Glutamine, 10 %FBS, 1mM sodium pyruvate

value: relapsing invasive galactophoric breast adenocarcinoma


title: 4h_Iso_5_hyp_fib


title: ChIP_input_ERHoxB8_CRISPR_region2

value: input


title: Ctcf_IFNg_rep1


title: CAL51

description: single cell transcriptomic

value: DMEM 2mM L-Glutamine, 10 %FBS


title: ChIP_CEBPb_ERHoxB8_CRISPR_region1


title: Ctcf_Ctr_rep1

description:
P15158_1005_S5
processed data file: Ctr_Ctcf_dupmark.bam_peaks.narrowPeak


title: BT549

description: single cell transcriptomic

value: RPMI 2mM L-Glutamine, 10 %FBS

value: mammary gland; breast


title: H3K27ac_IFNg_rep1

value: Abcam ab177178; rabbit; 1ug


title: 4h_Iso_3_hyp_fib


title: ChIP_input_ERHoxB8_CRISPR_region1


title: 4h_Iso_2_hyp_fib


title: BT483

description: single cell transcriptomic

value: LA

value: RPMI 2mM L-Glutamine,  0.01 mg/mL bovine insulin, 20 %FBS


title: 4h_Iso_1_hyp_fib


title: TEPP-46

city: Birmingham

first: Anna

last: Thalacker-Mercer

state: Alabama

address: 1900 University Blvd

institute: University of Alabama at Birmingham

data_processing:
The resulting reads were processed using TrimGalore v0.6.0 with cutadapt [33] and fastQC. Reads were mapped to the reference genome (Ensembl GRCm38), then normalized read counts were generated using SARTools [34] and DESEq2 v1.26.0 [35].
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: Reported value are FPKM values

source_name: C2C12 cells

growth_protocol: Cells were cultured in high glucose DMEM with 10% fetal bovine serum

extract_protocol:
E.Z.N.A Total RNA kit (Omega Biotek) with an on-column DNA digest (Qiagen)
Libraries were prepped with a A NEBNext Poly(A) mRNA magnetic isolation Module and NEBNext Ultra II RNA Library Prep Kit, quantified with a Qubit 2.0 then sequenced using a NextSeq500.

treatment_protocol: shPKM2/shControl were given for 72 hours; Vehicle Control, shikonin, and TEPP-46 were given for 8 hours

value: Cultured, proliferating C2C12 cells


title: ChIP_input_ERHoxB8_CRISPR_region4


title: BT474

description: single cell transcriptomic

value: LB

value: mammary gland; breast/duct


title: Shikonin


title: Vehicle Control


title: BT20

description: single cell transcriptomic

value: TNA

value: MEM 2mM L-Glutamine, 10 %FBS

value: mammary gland/breast


title: H3K27ac_IFNg_rep2

value: Sox10GFP+ oligodendrocyte precursor cells (OPCs)

value: IFNg


title: 4h_Ctrl_6_hyp_fib

description: total RNA from mouse heart tissue harvested after 4 hours of ascorbic acid injection

value: Ascorbic acid


title: H3K27M Replicate 3

city: Pittsburgh

first: Sameer

last: Agnihotri

state: PENNSYLVANIA

address: 530 45TH ST, 7TH FL BAY 20 RANGOS RESEARCH

department: Neurosurgery

institute: University of Pittsburgh

data_processing:
Qiagen
Short  read sequences (150 bp, mate paired) obtained from sequencing were trimmed and further mapped to the reference human genome (hg19), and gene sequences were aligned using the Bowtie algorithm employed in the CLC genomics Software suite ((Ensemble version 54), Qiagen, CLC workbench 2020)
Genes with Transcript per million (TPM) values < 1 were considered to be not expressed at a sufficient level to permit reliable quantification and were removed
Sample counts were then normalized to counts per million (CPM) and transformed (log2CPM+2) using the edgeR package in the R computing environment
DeSeq and DESeq2 statistical packages in R were used to identify significant changes in gene expression between experimental conditions
Genome_build: mm9, hg19
Supplementary_files_format_and_content: matrix file containing normalized data, output from Deseq 2, with Edge

source_name: H3K27M Replicate 3

extract_protocol:
RNA was extracted from samples using the Qiagen RNeasy mini kit (Cat#74104) as per manufactures instructions
Strand-specific RNA-Seq library preparation and sequencing were performed at Novogene Biotech (Beijing, China) using standard Illumina protocols

value: H3K27M diffuse midline glioma (DMG) mouse model


title: ChIP_input_ERHoxB8_CRISPR_region3

value: input


title: 4h_Ctrl_5_hyp_fib


title: AU565

description: single cell transcriptomic

value: H

value: metastatic site:malignant pleural effusion


title: H3K27M Replicate 2

source_name: H3K27M Replicate 2


title: H3K27M Replicate 1

source_name: H3K27M Replicate 1


title: shControl


title: 4h_Ctrl_4_hyp_fib


title: H3KWT Replicate 3

source_name: H3KWT Replicate 3


title: 4h_Ctrl_3_hyp_fib


title: shPKM2


title: DIPG04-MAT2A_shRNA 4+ DOX Replicate 2

source_name: DIPG04-MAT2A_shRNA 4+ DOX Replicate 2


title: 4h_Ctrl_2_hyp_fib


title: DIPG04-MAT2A_shRNA 4+ DOX Replicate 1

source_name: DIPG04-MAT2A_shRNA 4 + DOX Replicate 1


title: H3KWT Replicate 2

source_name: H3KWT Replicate 2


title: 4h_Ctrl_1_hyp_fib


title: H3KWT Replicate 1

source_name: H3KWT Replicate 1


title: RNA_OE_rep2

city: Chongqing

first: Chuan

last: Liu

address: Chongwen Road

institute: Chongqing University of Posts and Telecommunications

data_processing:
Bisulfite-seq Data Processing: Quality control of WGBS data was performed using FastQC (version 0.11.9, Babraham Bioinformatics, UK). Sequencing adapters and low-quality reads were removed using Trimmomatic (Bolger et al., 2014). The trimmed reads were then aligned and mapped to the rice reference genome of Nipponbare (MSU_v7.0) using Bismark (Krueger and Andrews, 2011). The percentage methylation level was calculated by mC/(mC + umC), where mC and umC represent the number of methylated and unmethylated reads, respectively.
RNA-seq Data Processing: Sequencing adapters and low-quality reads were removed with fastp (version 0.20.1) (Chen et al., 2018), and the quality of raw reads was evaluated with FastQC (version 0.11.9, Babraham Bioinformatics, UK). The remaining clean reads were mapped to the rice reference genome of Nipponbare (MSU_v7.0) using Hisat2 (version 2.1.0) (Kim et al., 2019). TPMCalculator was used to count the reads mapped to individual genes as well as to measure gene expression levels by calculating transcripts per million (TPM) read values (Vera Alvarez et al., 2019).
Genome_build: Nipponbare (MSU_v7.0)
Supplementary_files_format_and_content: bigWig and expression matrix

organism: Oryza sativa Indica Group

source_name: OsPRR37 overexpression line (Guangluai 4 was used as recipient parent)

growth_protocol: Rice was planted in a growth chamber (PRX-380B, Shanghai Guning Instrument Co., Ltd) for 15 days after germination

extract_protocol:
Cetyltrimethylammonium bromide method was used for genomic DNA extraction. Total RNA from rice leaves was extracted using TRIzol Reagent (Invitrogen, CA, USA) for RNA sequencing
Genomic DNA (2-µg) spiked with 5-ng unmethylated Lambda DNA (Promega, Madison, WI, USA) was fragmented by sonication to generate fragments measuring 300–500 bp. These fragments were then ligated with 5-methylcytosine-modiﬁed adapters and subjected to bisulfide conversion using the ZYMO EZ DNA Methylation-Gold Kit (Zymo Research, Irvine, CA, USA). The bisulfide-converted DNA was purified, recycled, and then amplified by PCR with 10 cycles using KAPA HiFi HotStart Uracil + ReadyMix (Kapa Biosystems, Wilmington, MA, USA) and Illumina 8-bp index primers. RNA sequencing libraries were generated from the purified mRNA using the VAHTS Universal V6 RNA-seq Library Kit for MGI (Vazyme, Nanjing, China) following the manufacturer's recommendations with unique index codes.

treatment_protocol: The growth chamber was set at 28°C under a 14-h light/10-h dark cycle with the light period of 6:00–20:00

tag: cultivar

value: Guangluai 4

tag: genotype

value: OsPRR37 overexpression

value: leaves

tag: age

value: 15 days


title: DIPG04-MAT2A_shRNA 4 Replicate 3

source_name: DIPG04-MAT2A_shRNA 4 Replicate 3


title: RNA_OE_rep1


title: Control neural stem cells Replicate 3

source_name: Control neural stem cells Replicate 3

tag: cell type

value: Control neural stem cells


title: DIPG04-MAT2A_shRNA 4 Replicate 2

source_name: DIPG04-MAT2A_shRNA 4 Replicate 2


title: Control neural stem cells Replicate 2

source_name: Control neural stem cells Replicate 2


title: H3K27ac_Ctr_rep1

source_name: Sox10GFP+ OPCs_H3K27ac_Ctr

tag: treatment

value: Ctr

tag: antibody

value: Abcam ab177178; rabbit; 1ug


title: DIPG04-MAT2A_shRNA 4 Replicate 1

source_name: DIPG04-MAT2A_shRNA 4 Replicate 1


title: Control neural stem cells Replicate 1

source_name: Control neural stem cells Replicate 1


title: RNA_GL_rep2

source_name: Guangluai 4

value: WT


title: RNA_GL_rep1


title: DIPG04-MAT2A_shRNA 4+ DOX Replicate 3

source_name: DIPG04-MAT2A_shRNA 4+ DOX Replicate 3