title: HiChIP, CTCF, IMR90, MyoD WT vector, replicate 2

city: La jolla

first: Chiara

last: Nicoletti

address: 10901 North Torrey Pines Road

department: Development, Aging and Regeneration Program

institute: Sanford Burnham Prebys Medical Discovery Institute

description: Library name: HiChIP_CTCF_MYOD_wt_rep2

data_processing:
For RNA-seq: Quality control of the raw data has been performed with FASTQC (v0.11.9), reads were trimmed with Trimmomatic (v0.39) to eliminate low quality bases and adapters (parameters: PE -phred33 ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:2:true MAXINFO:40:0.1 MINLEN:45), and aligned to the hg19 Ensembl (November 2015) version of the human genome with STAR (v 2.7.3a), using a custom genome and index to simultaneously map and quantify ERCC92 spike-in-derived reads (parameters: --runMode alignReads --runThreadN 12 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts). Counts data (from STAR output in column 4, based on library preparation strandedness: second-strand) from all conditions were filtered based on their raw count, keeping genes where the sum of the counts for all samples was higher than 10. Size factors were calculated using the R environment (v4.1.3) package DESeq2 (v1.34.0) estimateSizeFactors function - using the counts related to the spike-in transcripts as control genes, then normalized and logged with the rlog function. DESeq2 was also used to perform Principal Component Analysis (PCA) and differential gene expression analysis (significance threshold: BH FDR<0.05). Differential expression analysis results were visualized with the heatplot function (parameters: method="complete", labRow= FALSE, dend="row", returnSampleTree=F, zlim=c(-5,5)) from the made4 (v1.68.0) package, after expression values from the DESeq2 object were turned into a matrix of Z-scores. Gene Ontology was performed on down- and up-regulated genes separately, using the gene symbols as input in EnrichR, and gene sets repositories GO Biological Processes 2023 and Descartes Cell Types and Tissue 2021. Top10 gene ontology terms shown in figure panels were ordered by pvalue. Gene Ontology bubble plots to summarize top50 gene ontology terms, were generated with the Python (v.3.8.1) GO-Figure script (parameters: -j standard -c log10-pval -e 100 -si 0.5 -s members -g single -n bpo --font_size small -q svg). For ATAC-seq: Quality control of the raw data has been performed with FASTQC (v0.11.9), reads were trimmed with Trimmomatic (v0.39) to eliminate low quality bases and adapters (parameters: PE -phred33 ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:2:true MAXINFO:40:0.1 MINLEN:45), aligned to the hg19 UCSC (January 2016) version of the human genome with Bowtie2 (v2.3.5.1) (parameters: --no-unal --local --very-sensitive-local --no-discordant --no-mixed --dovetail --phred33), sorted and converted into BAM format with the SAMtools sort function. Peak calling was performed with the Macs2 (v2.2.6) callpeak function (parameters: -f BAMPE -g hs -B -q 0.05 --nomodel --shift -100 --extsize 200) and filtered for black-list regions with the BEDtools suite (v2.29.2) intersect (parameters: -v), and sorted with the sort function (parameters: -k8,8nr). Irreproducible Discovery Rate (IDR) was calculated with the idr function (v2.0.3) (parameters: --input-file-type narrowPeak --plot --only-merge-peaks) to retain a single peaks list from each condition. Differential chromatin accessibility analysis was carried out in R, with the DESeq2 package. The R package ChIPQC (v1.30.0), (GetGRanges function was used to import peak lists from each biological replicate, a consensus peak list was calculated for all conditions using the IRanges (v2.28.0),function reduce, keeping peaks that were called in at least two samples. Counts for each peak in each biological replicate were quantified with the Rsubread (v2.8.2) featureCounts function (parameters: isPairedEnd= T, countMultiMappingReads= F, maxFragLength= 100). Counts were normalised and logged with the DESeq2 function rlog; DESeq2 was also used to perform Principal Component Analysis (PCA), and differential chromatin accessibility analysis (significance threshold: BH FDR<0.05). Differentially Accessible Regions (DARs) at gene promoter regions were retrieved with the IRanges function promoters (parameters: TxDb.Hsapiens.UCSC.hg19.knownGene, 1000, 200; mouse genome version was: TxDb.Mmusculus.UCSC.mm10.knownGene). Promoter DARs were visualized with the made4 function heatplot (parameters: method="complete", labRow= FALSE, dend="row", returnSampleTree=F, zlim=c(-5,5)), after expression values from the DESeq2 object were turned into a matrix of Z-scores. Due to R visualization limits, only promoters with |log2FC|>1.5 were plotted. Motif analysis was carried out with the HOMER (v4.11), findMotifsGenome function (parameters: hg19 -size given -nomotif). For ChIP-seq: Quality control of the raw data has been performed with FASTQC (v0.11.9) and aligned to the hg19 UCSC (January 2016) version of the human genome with Bowtie2 (parameters: --very-sensitive-local). Peak calling was performed with the Macs2 callpeak function (parameters: -g hs -B --nomodel --SPMR -q 0.05), using input chromatin as control. For CUT&RUN: Quality control of the raw data has been performed with FASTQC (v0.11.9), reads were trimmed with Trimmomatic (v0.39) to eliminate low quality bases and adapters (parameters: PE -phred33 ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:2:true MAXINFO:40:0.1 MINLEN:45), aligned either to the hg19 UCSC (January 2016) version of the human genome (for the CUT&RUN for histone marks in IMR90 and IMR90/MyoD), or to the mm10 Ensembl (November 2019) version of the mouse genome (for the CUT&RUN of AcMe and MyoD in muSC),  with Bowtie2 (parameters: --phred33 --end-to-end --no-unal --local --very-sensitive-local --no-mixed --no-discordant -I 10 -X 700 –dovetail) and converted to BAM format with the SAMtools (v1.10) function view (parameters: -bS). Peak calling was performed with the Macs2 callpeak function (parameters: -g hs --nomodel --SPMR --call-summits -p 0.05) using input chromatin as control, and filtered for black-list regions with BEDtools intersect (parameters: -v), and sorted with the Unix sort function (parameters: -k8,8nr). Irreproducible Discovery Rate (IDR) was calculated with the idr function (parameters: --input-file-type narrowPeak --plot --only-merge-peaks) to retain a single peaks list from each condition. ChromHMM (v1.24) BinarizeBed function (parameters: -b 200 -peaks) was used to bin the genome in 200bp windows according to each IDR peak list. The BinarizeBed output was used as input to ChromHMM LearnModel (parameters: -b 200 12 hg19), to build a 12 chromatin states model based on the histone marks IDR peaks. Chromatin state numbers were converted to chromatin states names in R, based on the combination of histone marks they were enriched for. For HiChIP: Quality control of the raw data has been performed with FASTQC (v0.11.9). Alignment, filtering, normalization, and loop calling were performed with the Arima version of MAPS (v2.0) bash script (parameters: -C 0 -F 1 -M 1 -H 1 -o hg19 -f 1 -s 5000 -r 2000000 -d 2 -Q 30 -l 1000). Irreproducible Discovery Rate (IDR) was calculated with IDR2D parameters: value transformation= log additive inverse (-log(x)), ambiguity resolution method= overlap, remove non-standard chromosome, max gap= 1000, max factor= 1.5, jitter factor= 0.0001, mu= 0.1, sigma=1, rho=0.2, p=0.5, epsilon=0.001). Differential HiChIP analysis was performed with the DiffAnalysisHiChIP.r script within FitHiChIP (v7.1), and significance threshold was set to p-value<0.05.
Assembly: hg19, mm10
Supplementary files format and content: TXT raw counts files (RNA-seq)
Supplementary files format and content: BEDGRAPH pileup signal tracks, with TBI index (RNA-seq)
Supplementary files format and content: BIGWIG signal tracks (ATAC-seq data, CUT&RUN), also biological replicates average signal tracks
Supplementary files format and content: ARCPLOTS of looping interactions, with TBI index (HiChIP)
Library strategy: HiChIP

growth_protocol: IMR90 cells were cultured in EMEM supplemented with 10% FBS

extract_protocol:
For RNA-seq: IMR90 or IMR90/MyoD cells total RNA was extracted using Quick-RNA Microprep KIT (Zymo Research, R1051) following the manufacturer’s recommendation. RNA concentration was measured on Qubit (Invitrogen). For ATAC-seq: IMR90 or IMR90/MyoD cells were freshly collected directly processed for the library preparation. For ChIP-seq: IMR90 or IMR90/MyoD cells were fixed with 1% FA for 10 minutes at RT followed by quenching with glycine (final concentration 200 mM) for 15 minutes on ice. Nuclei were then extracted in hypotonic buffer (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.05% NP-40, 1 mM PMSF and 1x protease inhibitor) and lysed in lysis buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 5 mM EDTA, pH 8.0, 0.5% SDS, 0.5% NP-40, 1 mM PMSF and 1x protease inhibitor and lysed in lysis buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 5 mM EDTA, pH 8.0, 0.5% SDS, 0.5% NP-40, 1 mM PMSF and 1x protease inhibitor). Chromatin was sheared with sonicator (S2 Covaris) to an average DNA fragment length of 200-500bp. 15µg of sonicated chromatin were diluted in 500µl RIPA Dilution Buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, pH 8.0, 0.1% Sodium Deoxycholate, 0.7% NP-40, 1 mM PMSF and 1x protease inhibitor), and precleared for 3 hours at 4°C with Protein A/G dinabeads. In parallel, 10µl of CTCF antibody (CST Cat#3418S), or 1µg of rabbit IgG (Santa Cruz #sc-2027) were prebound to Protein A/G dynabeads in 500µl of PBS containing 5 µg/ml BSA, for 3 hours at 4°C. Beads bound antibody were mixed with precleared chromatin and incubated overnight at 4°C on a rotator. Chromatin bound fraction was washed with RIPA washing buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, pH 8.0, 0.5% Sodium Deoxycholate, 1% NP-40) for 4 times, followed by LiCl washing buffer (10 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1 mM EDTA, pH 8.0, 1% Sodium Deoxycholate, 1% NP-40), and TE buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA), each wash for 10 minutes at 4°C. Chromatin was then eluted in elution buffer (1% SDS in TE buffer) at 65°C for 6 hours 600 RPM rotation. For CUT&RUN: IMR90 or IMR90/MyoD cells or Muscle Stem Cells (MuSCs) were used as input. CUT&RUN experiments were performed using the CUT&RUN Assay Kit (CST #86652) with the following modification: cells were briefly fixed with 0.1% FA for 2 minutes at RT followed by quenching with glycine; antibody binding was performed O/N at 4C. Antibodies used: anti-MYOD (BD Bioscience, #554130), anti-H4K5/K12AcMe, anti-panAcMe, anti-H3K27ac (Active Motif #91193), anti-H3K4me3 (CST #9751), anti-H3K4me1 (Active Motif #39635), anti-H3K27me3 (Active Motif #39155), anti-H3K9me3 (Active Motif #39161). For HiChIP: IMR90 or IMR90/MyoD cells were fixed with 2%FA for 10 minutes at RT followed by quenching with STOP solution1 according to ARIMA HiC+ protocol. Digestion was performed overnight at 37C. Biotinylated enriched fragments were pulled down with anti-H3K27ac (Active Motif #91193) or anti-CTCF (Active Motif #91285). Experiments were performed using the ARIMA HiC+ kit according to manufacturer’s protocol.
For RNA-seq: Equal inputs of total RNA (10-100 ng) were used to generate stranded total RNA libraries for sequencing using the Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus (Illumina #20040525). ERCC RNA Spike-in mix was added at the start of the protocol according to manufacturer’s instruction (Thermo Fisher Scientific #4456740). Libraries were sequenced at a depth of ~50M per library on NOVASeqS4 PE 2x100. For ATAC-seq: Freshly collected cells were subjected to ATAC-seq library preparation using the ATAC-seq Kit (Active Motif #53150) according to manufacturer’s protocol. For ChIP-seq: Precipitated chromatin and 10ng of input were used for library preparation using Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences #21096) according to manufacturer’s protocol. Obtained libraries were sequenced at a depth of ~100M per library on NOVASeqS4 PE 2x100. For CUT&RUN: Libraries have been generated using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB #E7645S) according to manufacturer’s protocol. Libraries were sequenced at a depth of ~20M per library on NOVASeqS4 PE 2x100. For HiChIP: H3K27ac or CTCF enriched material was then used as input for library preparation using Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences  #21096) according to ARIMA HiChIP library preparation protocol. Obtained libraries were sequenced at a depth of ~300M per library on NOVASeqS4 PE 2x100.

treatment_protocol: IMR90 cells were transfected with vector containing TET-inducible MYOD (WT or domain-deleted mutant) or EMPTY vector control, cells were terated with 200ng/ml doxycycline for 24hrs in EMEM 10% FBS and collected for GM time point

value: Fetal lung fibroblasts

value: Myogenic transdifferentiation


title: apj1d sis1-4xcga, riboseq, 10min, bio rep1

status: Public on Aug 08 2025

type: SRA

city: Heidelberg

first: Lucia

last: Svoboda

address: Im Neuenheimer Feld 345

country: Germany

institute: ZMBH

description: Library name: apj1dsis14x_1_t10

library_source: transcriptomic

data_processing:
sequences were trimmed for adaptors and sequence/ low-quality sequence using cutadapt version 3.5
UMIs were extracted from trimmed sequence reads using a custom Julia script
reads were aligned to S. cerevisiae rRNA sequences with bowtie version 1.3.1 using  -n 2 alignment mode and --best reporting mode. Only reads that did not align were kept.
reads were mapped to S. cerevisiae S288C Genome (Assembly: GCA_000146045.2) using STAR version 2.7.10a. Following mapping parameters were used: --outSAMmultNmax 1; --outFilterType BySJout; --alignIntronMin 5; --quantMode GeneCounts; --twopassMode Basic; --outSAMattributes All XS
With a custom Julia script reads were processed as described here: Reads from PCR dupicates were detected using UMI and were collapsed to a single read. Ribosomal positions were assigned.
Assembly: GCA_000146045.2
Supplementary files format and content: cds_umi_psite.h5
Supplementary files format and content: Reads mapped to the CDS, filtered for UMIs, aligned to the p-site
Library strategy: Ribo-Seq

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Whole cell

growth_protocol: Yeast were inocculated from overnight culture at OD600 0.05 in homemade YPD, and grown shaking with 140 rpm at 25°C (steady state) or 30°C (heat-shock timecourse) until OD600 0.5-0.6, before harvest.

treatment_protocol: Cells were heat-shocked in a shaking waterbath at 140 rpm and 38°C for the indicated times (10 mins or 60 mins) after reaching OD600 0.3 (60 mins) or OD600 0.4 (10 mins), before harvest

tag: tissue

value: Whole cell

tag: genotype

value: BY4741 apj1d sis1-4xcga

tag: treatment

value: 10 min HS 38°C

tag: batch


title: 967895_D2-WT-LT-control

city: Tarrytown

first: Wei Keat

last: Lim

state: NY

address: 777 Old Saw Mill River Rd

country: USA

institute: Regeneron

description:
Library name: 967895_1_1_1-HGFW7BGX3
10x Chromium

library_source: transcriptomic single cell

data_processing:
CellRanger Single Cell Software Suite 1.3 was used to perform sample demultiplexing, barcode processing, and single cell gene counting (Alignment, Barcoding and UMI Count) at the University of Michigan Biomedical Core Facilities DNA Sequencing Core.
Replicates from time points were aligned to mm10 genome, while downstream analysis was performed with Seurat 3.0
Assembly: mm10
Supplementary files format and content: Tab-separated matrix files

organism: Mus musculus

source_name: gluteus medius

extract_protocol:
Induction of the FOP mouse model in Acvr1[R206H]FlEx/+; Gt(ROSA26)SorCreERT2/+ mice and Acvr1+/+; Gt(ROSA26)SorCreERT2/+ control mice were performed as described [S.J. Hatsell et al, "ACVR1R206H receptor mutation causes fibrodysplasia ossificans progressiva by imparting responsiveness to activin A", Sci. Transl. Med. 7 (303) (2015) 303ra137.].
Library was performed according to the manufacter's insturction - 10× Genomics Chromium Controller (v2 reagent kit)

value: gluteus medius


title: 967894_D2-WT-RT-Injured

description:
Library name: 967894_1_1_1-HGFW7BGX3
10x Chromium


title: apj1d sis1-4xcga, riboseq, 10min, bio rep2, tech rep 3

description: Library name: apj1dsis14x_2_t10_3


title: HiChIP, CTCF, IMR90, MyoD WT vector, replicate 1

state: CA

description: Library name: HiChIP_CTCF_MYOD_wt_rep1

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type


title: 967893_D2-FOP-RT-Injured

description:
Library name: 967893_1_1_1-HGFW7BGX3
10x Chromium


title: apj1d sis1-4xcga, riboseq, 0min, bio rep1

description: Library name: apj1dsis14x_1_t0


title: sis1-4xcga, riboseq, 60min, bio rep2

description: Library name: sis14xcga_2_t60

value: BY4741 sis1-4xcga

value: 60 min HS 38°C


title: HiChIP, CTCF, IMR90, Empty vector, replicate 1

description: Library name: HiChIP_CTCF_Empty_rep1

value: Empty


title: HiChIP, CTCF, IMR90, Empty vector, replicate 2

description: Library name: HiChIP_CTCF_Empty_rep2


title: Dendritic Cells

city: Detroit

first: Aditi

last: Singh

state: MI

address: 275 E Hancock St

department: CMMG

institute: Wayne State University

description: Library name: Dendritic Cells

data_processing:
Raw reads generated from the MARS-seq2.0 protocol were processed using HISAT (version 0.1.6) to align sequences to the human reference genome (hg38) with default parameters. Reads with multiple mapping positions were excluded to ensure data integrity. Gene association was performed by mapping reads to exonic regions using the Homo sapiens Ensembl90 reference annotation. Unique molecular identifiers (UMIs) were used to remove PCR duplicates, and the data was condensed to represent original transcript counts. Quality control was performed by assessing low cross single-cell contamination (<3%) through the detection of spurious UMIs in empty wells. Processed gene expression data were normalized and analyzed to assess cell-type-specific transcriptional profiles.
Assembly: The human genome reference build used for alignment and analysis was hg38, with annotations from Homo sapiens Ensembl90
Supplementary files format and content: DC_count.txt- This file containes the count matrix
Supplementary files format and content: DC_stage.txt- This file contains information specifying the menstrual cycle stage associated with each individual cell.

source_name: Endometrial

extract_protocol:
Endometrial biopsies were collected from healthy women with regular menstrual cycles across 10 stages of the menstrual cycle, classified through cycle-tracking and histological evaluation. Tissues were digested in RPMI-1640 medium containing 2 mg/mL collagenase IV and 0.0125 mg/mL DNase I at 37°C for 20 minutes. The digested material was passed through a 70 μM cell strainer to obtain single-cell suspensions. Red blood cells were lysed with RBC lysis buffer at room temperature for 10 minutes, followed by PBS washes. CD45+ cells were isolated using fluorescence-activated cell sorting (FACS) with a BD FACSAria Fusion sorter and deposited into 384-well plates for single-cell RNA sequencing (scRNAseq). RNA libraries were prepared using the MARS-seq2.0 protocol, and sequencing reads were mapped to the human genome (hg38) using HISAT with default parameters. Reads were assigned to genes based on exon mapping using Homo sapiens Ensembl90. Unique molecular identifiers (UMIs) were used to reduce noise and accurately quantify transcript counts, with batch cross-contamination rates confirmed to be under 3%.
Single-cell RNA sequencing libraries were prepared using the MARS-seq2.0 protocol. Fluorescence-activated cell sorting (FACS) was used to isolate CD45+ cells into 384-well plates, each containing lysis buffer. Reverse transcription and barcoding of transcripts were performed in each well to generate unique molecular identifiers (UMIs) for each cell. Following reverse transcription, cDNA libraries were pooled and subjected to in vitro transcription (IVT) to amplify RNA. Amplified RNA was fragmented and converted into sequencing-ready libraries through ligation of sequencing adapters and PCR amplification. Libraries were validated for quality and quantified before sequencing.

value: Endometrial

value: Dendritic Cells

value: No Treatment


title: 967892_D2-FOP-RT-Injured

description:
Library name: 967892_1_1_1-HGFW7BGX3
10x Chromium


title: HiChIP, H3K27ac, IMR90, MyoD WT vector, replicate 2

description: Library name: HiChIP_H3K27ac_MYOD_wt_rep2


title: RMS, replicate8, scRNA

city: Charlestown

first: David

last: Langenau

state: MA

department: Molecular Pathology

institute: Massachusetts General Hospital

data_processing:
Single cell sequencing data were demultiplexed and processed using the 10X cellranger 3.1.0 pipeline to generate the read count matrices.
Assembly: hg19
Supplementary files format and content: Filtered feature - barcode HDF5 file output from CellRanger pipeline

molecule: polyA RNA

source_name: tumor disscociated single cell

extract_protocol:
Freshly harvest tumor transplanted on NSG mice were dissociated using tumor dissociation kit (Miltenyi Biotec, cat log. 130-095-929) according to the manufacturer’s instruction to get single cell suspensions.
Single cells dissociated from harvest tumor were immediately processed for library preparation using 10X Genomics Chromium Chip A/B Single Cell kit and Single Cell GEM, Library & Gel Bead kit (cat. nos. 1000092/100075 and 1000073/1000074), according to manufacturer protocols.

treatment_protocol: Animals were orally gavaged with vehicle control (1% carboxymethylcellulose) or OT combination (olaparib (50 mg/kg) and temozolomide (25 mg/kg)). Olaparib was administered twice daily, 8 h apart while temozolomide was administered once a day 4 h after the first olaparib administration. In all experiments, animals were treated for five days, and allowed to rest for 16 days and the cycle repeated for up to three cycles.

value: tumor disscociated single cell

value: RMS

value: olaparib+temozolomide


title: RMS, replicate7, scRNA

value: Vehicle control


title: 967891_D2-WT-RT-Injured

description:
Library name: 967891_1_1_1-HGFW7BGX3
10x Chromium


title: sis1-4xcga, riboseq, 10min, bio rep2, tech rep 2

description: Library name: sis14xcga_2_t10_2


title: sis1-4xcga, riboseq, 10min, bio rep2, tech rep 1

description: Library name: sis14xcga_2_t10_1


title: RMS, replicate6, scRNA


title: HiChIP, H3K27ac, IMR90, Empty vector, replicate 2

description: Library name: HiChIP_H3K27ac_Empty_rep2


title: 963266_FOP-LT-control

description:
Library name: 963266_1_1_1-H3L25BGX3
10x Chromium

value: FOP-LT-control


title: sis1-4xcga, riboseq, 60min, bio rep1

description: Library name: sis14xcga_1_t60


title: RMS, replicate5, scRNA


title: 963265_WT-RT-Injured

description:
Library name: 963265_1_1_1-H3L25BGX3
10x Chromium

value: WT-RT-Injured


title: 963264_WT-LT-control

description:
Library name: 963264_1_1_1-H3L25BGX3
10x Chromium

value: WT-LT-control


title: HiChIP, H3K27ac, IMR90, Empty vector, replicate 1

description: Library name: HiChIP_H3K27ac_Empty_rep1

value: Fetal lung fibroblasts


title: RMS, replicate4, scRNA


title: ChIPseq, CTCF Input, IMR90, MyoD WT vector

description: Library name: ChIPseq_CTCF_Input_MYOD_wt

data_processing:
For RNA-seq: Quality control of the raw data has been performed with FASTQC (v0.11.9), reads were trimmed with Trimmomatic (v0.39) to eliminate low quality bases and adapters (parameters: PE -phred33 ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:2:true MAXINFO:40:0.1 MINLEN:45), and aligned to the hg19 Ensembl (November 2015) version of the human genome with STAR (v 2.7.3a), using a custom genome and index to simultaneously map and quantify ERCC92 spike-in-derived reads (parameters: --runMode alignReads --runThreadN 12 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts). Counts data (from STAR output in column 4, based on library preparation strandedness: second-strand) from all conditions were filtered based on their raw count, keeping genes where the sum of the counts for all samples was higher than 10. Size factors were calculated using the R environment (v4.1.3) package DESeq2 (v1.34.0) estimateSizeFactors function - using the counts related to the spike-in transcripts as control genes, then normalized and logged with the rlog function. DESeq2 was also used to perform Principal Component Analysis (PCA) and differential gene expression analysis (significance threshold: BH FDR<0.05). Differential expression analysis results were visualized with the heatplot function (parameters: method="complete", labRow= FALSE, dend="row", returnSampleTree=F, zlim=c(-5,5)) from the made4 (v1.68.0) package, after expression values from the DESeq2 object were turned into a matrix of Z-scores. Gene Ontology was performed on down- and up-regulated genes separately, using the gene symbols as input in EnrichR, and gene sets repositories GO Biological Processes 2023 and Descartes Cell Types and Tissue 2021. Top10 gene ontology terms shown in figure panels were ordered by pvalue. Gene Ontology bubble plots to summarize top50 gene ontology terms, were generated with the Python (v.3.8.1) GO-Figure script (parameters: -j standard -c log10-pval -e 100 -si 0.5 -s members -g single -n bpo --font_size small -q svg). For ATAC-seq: Quality control of the raw data has been performed with FASTQC (v0.11.9), reads were trimmed with Trimmomatic (v0.39) to eliminate low quality bases and adapters (parameters: PE -phred33 ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:2:true MAXINFO:40:0.1 MINLEN:45), aligned to the hg19 UCSC (January 2016) version of the human genome with Bowtie2 (v2.3.5.1) (parameters: --no-unal --local --very-sensitive-local --no-discordant --no-mixed --dovetail --phred33), sorted and converted into BAM format with the SAMtools sort function. Peak calling was performed with the Macs2 (v2.2.6) callpeak function (parameters: -f BAMPE -g hs -B -q 0.05 --nomodel --shift -100 --extsize 200) and filtered for black-list regions with the BEDtools suite (v2.29.2) intersect (parameters: -v), and sorted with the sort function (parameters: -k8,8nr). Irreproducible Discovery Rate (IDR) was calculated with the idr function (v2.0.3) (parameters: --input-file-type narrowPeak --plot --only-merge-peaks) to retain a single peaks list from each condition. Differential chromatin accessibility analysis was carried out in R, with the DESeq2 package. The R package ChIPQC (v1.30.0), (GetGRanges function was used to import peak lists from each biological replicate, a consensus peak list was calculated for all conditions using the IRanges (v2.28.0),function reduce, keeping peaks that were called in at least two samples. Counts for each peak in each biological replicate were quantified with the Rsubread (v2.8.2) featureCounts function (parameters: isPairedEnd= T, countMultiMappingReads= F, maxFragLength= 100). Counts were normalised and logged with the DESeq2 function rlog; DESeq2 was also used to perform Principal Component Analysis (PCA), and differential chromatin accessibility analysis (significance threshold: BH FDR<0.05). Differentially Accessible Regions (DARs) at gene promoter regions were retrieved with the IRanges function promoters (parameters: TxDb.Hsapiens.UCSC.hg19.knownGene, 1000, 200; mouse genome version was: TxDb.Mmusculus.UCSC.mm10.knownGene). Promoter DARs were visualized with the made4 function heatplot (parameters: method="complete", labRow= FALSE, dend="row", returnSampleTree=F, zlim=c(-5,5)), after expression values from the DESeq2 object were turned into a matrix of Z-scores. Due to R visualization limits, only promoters with |log2FC|>1.5 were plotted. Motif analysis was carried out with the HOMER (v4.11), findMotifsGenome function (parameters: hg19 -size given -nomotif). For ChIP-seq: Quality control of the raw data has been performed with FASTQC (v0.11.9) and aligned to the hg19 UCSC (January 2016) version of the human genome with Bowtie2 (parameters: --very-sensitive-local). Peak calling was performed with the Macs2 callpeak function (parameters: -g hs -B --nomodel --SPMR -q 0.05), using input chromatin as control. For CUT&RUN: Quality control of the raw data has been performed with FASTQC (v0.11.9), reads were trimmed with Trimmomatic (v0.39) to eliminate low quality bases and adapters (parameters: PE -phred33 ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:2:true MAXINFO:40:0.1 MINLEN:45), aligned either to the hg19 UCSC (January 2016) version of the human genome (for the CUT&RUN for histone marks in IMR90 and IMR90/MyoD), or to the mm10 Ensembl (November 2019) version of the mouse genome (for the CUT&RUN of AcMe and MyoD in muSC),  with Bowtie2 (parameters: --phred33 --end-to-end --no-unal --local --very-sensitive-local --no-mixed --no-discordant -I 10 -X 700 –dovetail) and converted to BAM format with the SAMtools (v1.10) function view (parameters: -bS). Peak calling was performed with the Macs2 callpeak function (parameters: -g hs --nomodel --SPMR --call-summits -p 0.05) using input chromatin as control, and filtered for black-list regions with BEDtools intersect (parameters: -v), and sorted with the Unix sort function (parameters: -k8,8nr). Irreproducible Discovery Rate (IDR) was calculated with the idr function (parameters: --input-file-type narrowPeak --plot --only-merge-peaks) to retain a single peaks list from each condition. ChromHMM (v1.24) BinarizeBed function (parameters: -b 200 -peaks) was used to bin the genome in 200bp windows according to each IDR peak list. The BinarizeBed output was used as input to ChromHMM LearnModel (parameters: -b 200 12 hg19), to build a 12 chromatin states model based on the histone marks IDR peaks. Chromatin state numbers were converted to chromatin states names in R, based on the combination of histone marks they were enriched for. For HiChIP: Quality control of the raw data has been performed with FASTQC (v0.11.9). Alignment, filtering, normalization, and loop calling were performed with the Arima version of MAPS (v2.0) bash script (parameters: -C 0 -F 1 -M 1 -H 1 -o hg19 -f 1 -s 5000 -r 2000000 -d 2 -Q 30 -l 1000). Irreproducible Discovery Rate (IDR) was calculated with IDR2D parameters: value transformation= log additive inverse (-log(x)), ambiguity resolution method= overlap, remove non-standard chromosome, max gap= 1000, max factor= 1.5, jitter factor= 0.0001, mu= 0.1, sigma=1, rho=0.2, p=0.5, epsilon=0.001). Differential HiChIP analysis was performed with the DiffAnalysisHiChIP.r script within FitHiChIP (v7.1), and significance threshold was set to p-value<0.05.
Assembly: hg19, mm10
Supplementary files format and content: TXT raw counts files (RNA-seq)
Supplementary files format and content: BEDGRAPH pileup signal tracks, with TBI index (RNA-seq)
Supplementary files format and content: BIGWIG signal tracks (ATAC-seq data, CUT&RUN), also biological replicates average signal tracks
Supplementary files format and content: ARCPLOTS of looping interactions, with TBI index (HiChIP)

value: Myogenic transdifferentiation


title: sis1-4xcga, riboseq, 0min, bio rep1

description: Library name: sis14xcga_1_t0

value: Whole cell


title: 963263_FOP-LT-control

description:
Library name: 963263_1_1_1-H3L25BGX3
10x Chromium

value: gluteus medius


title: RMS, replicate3, scRNA


title: 963262_FOP-RT-Injured

description:
Library name: 963262_1_1_1-H3L25BGX3
10x Chromium

value: FOP-RT-Injured


title: apj1d, riboseq, 60min, bio rep2, tech rep 3

description: Library name: apj1d_2_t60_3

value: BY4741 apj1d

value: 60 min HS 38°C


title: sis1-4xcga, riboseq, 0min, bio rep2

description: Library name: sis14xcga_2_t0

value: BY4741 sis1-4xcga


title: ChIPseq, CTCF, IMR90, MyoD WT vector

description: Library name: ChIPseq_CTCF_MYOD_wt


title: HiChIP, H3K27ac, IMR90, MyoD WT vector, replicate 1

description: Library name: HiChIP_H3K27ac_MYOD_wt_rep1


title: RMS, replicate2, scRNA

description: RD-R

value: RD


title: RMS, replicate1, scRNA

description: RD-S


title: apj1d, riboseq, 60min, bio rep2, tech rep 2

description: Library name: apj1d_2_t60_2


title: 963261_WT-RT-Injured

description:
Library name: 963261_1_1_1-H3L25BGX3
10x Chromium


title: ASO-NC#2

city: Xi'an

first: Xiaodi

last: Zhao

address: No.127 Changle West Road

department: Xijing Hospital of Digestive Diseases

country: China

institute: Xijing Hospital of Fourth Military Medical University

data_processing:
Aligned to the human genome hg19 using TopHat2.
The number of reads mapped to each gene was calculated by HTseq.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

extract_protocol:
Total RNA from cells was isolated by TRIzol Reagent (Invitrogen) and then purified using the RNeasyMini Kit (Qiagen).The concentration and integrity of total RNA were estimated using a Qubit 2.0 Fluorometer (Invitrogen) and an Agilent 2100 Bioanalyzer (Agilent Technologies), respectively.
For RNA-seq, the NEBNext DNA Library Prep Master Mix Set for Illumina (New England BioLabs) was used to prepare a next-generation sequencing expression library following the manufacturer’s protocol.

tag: group

value: control


title: apj1d, riboseq, 60min, bio rep2, tech rep 1

description: Library name: apj1d_2_t60_1


title: apj1d, riboseq, 10min, bio rep2, tech rep 2

description: Library name: apj1d_2_t10_2

value: 10 min HS 38°C


title: 963260_WT-RT-Injured

description:
Library name: 963260_1_1_1-H3L25BGX3
10x Chromium


title: ChIPseq, CTCF, IMR90, Empty vector

description: Library name: ChIPseq_CTCF_Empty

value: Empty


title: 963259_FOP-RT-Injured

description:
Library name: 963259_1_1_1-H3L25BGX3
10x Chromium


title: ASO-NC#1


title: ChIPseq, H3K27ac Input, IMR90, MyoD WT vector

description: Library name: ChIPseq_H3K27ac_Input_MYOD_wt


title: Kras-G12D;Setd2-/- neoplastic cells, replicate 4

city: Xiamen

first: Hongchen

last: Cai

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang'an Campus

institute: Xiamen University

description: Library name: Kras;Setd2_rep4

data_processing:
The raw sequencing reads were trimmed to remove low-quality nucleotides.
Paired-end reads were aligned to the mm10 mouse genome using STAR (ENCODE RNA-seq pipeline).
The read counts were calculated by RSEM (ENCODE RNA-seq pipeline).
Since principal component analysis determined that the two technical replicates of Kras_rep2 exhibited little variation, these two technical replicates were merged as one biological replicate.
DESeq2, DEX-seq and GSEA analyses were performed successively.
Assembly: GRCm38 (mm10)
Supplementary files format and content: RSEM output tab-delimited files that include expected count, TPM, FPKM and related information of individual samples.

source_name: Lung

growth_protocol: Tumors were initiated in Kras-LSL-G12D;Rosa26-LSL-tdTomato;H11-LSL-Cas9 mice following protocols described in DuPage et al., 2009 (DOI: 10.1038/nprot.2009.95) and Rogers et al., 2017 (DOI: 10.1038/nmeth.4297).

extract_protocol:
RNA was purified using RNA/DNA All Prep kit (Qiagen, 80284).
RNA-seq library was generated with Trio RNA-Seq library preparation kit with Mouse rRNA depletion probes (Tecan, 0507-32).

treatment_protocol: Lung neoplastic cells were FACS purified for RNA extraction, library preparation and sequencing.

value: Lung

value: adenoma or adenocarcinoma


title: ChIPseq, H3K27ac, IMR90, MyoD WT vector

description: Library name: ChIPseq_H3K27ac_MYOD_wt


title: siSMARCA1#3

value: case


title: sis1-4xcga, riboseq, 10min, bio rep1

description: Library name: sis14xcga_1_t10


title: apj1d, riboseq, 10min, bio rep2, tech rep 1

description: Library name: apj1d_2_t10_1


title: ChIPseq, CTCF Input, IMR90, Empty vector

description: Library name: ChIPseq_CTCF_Input_Empty


title: Kras-G12D;Setd2-/- neoplastic cells, replicate 3

description: Library name: Kras;Setd2_rep3


title: siSMARCA1#2


title: apj1d, riboseq, 0min, bio rep2, tech rep 2

description: Library name: apj1d_2_t0_2


title: ChIPseq, PanAcMe Input, IMR90, MyoD WT vector

description: Library name: ChIPseq_PanAcMe_Input_MYOD_wt


title: apj1d, riboseq, 0min, bio rep2, tech rep 1

description: Library name: apj1d_2_t0_1


title: ChIPseq, PanAcMe Input, IMR90, Empty vector

description: Library name: ChIPseq_PanAcMe_Input_Empty


title: siSMARCA1#1


title: ChIPseq, PanAcMe, IMR90, MyoD WT vector, replicate 3

description: Library name: ChIPseq_PanAcMe_MYOD_wt_rep3


title: Kras-G12D;Setd2-/- neoplastic cells, replicate 1

description: Library name: Kras;Setd2_rep1


title: apj1d, riboseq, 60min, bio rep1

description: Library name: apj1d_1_t60


title: Kras-G12D neoplastic cells, replicate 7

description: Library name: Kras_rep7


title: Kras-G12D;Setd2-/- neoplastic cells, replicate 2

description: Library name: Kras;Setd2_rep2


title: ChIPseq, PanAcMe, IMR90, MyoD WT vector, replicate 2

description: Library name: ChIPseq_PanAcMe_MYOD_wt_rep2


title: apj1d, riboseq, 10min, bio rep1, tech rep 2

description: Library name: apj1d_1_t10_2


title: Kras-G12D neoplastic cells, replicate 6

description: Library name: Kras_rep6


title: siNC#3


title: siNC#2


title: ChIPseq, PanAcMe, IMR90, MyoD WT vector, replicate 1

description: Library name: ChIPseq_PanAcMe_MYOD_wt_rep1


title: ChIPseq, PanAcMe, IMR90, Empty vector, replicate 3

description: Library name: ChIPseq_PanAcMe_Empty_rep3


title: siNC#1


title: Kras-G12D neoplastic cells, replicate 5

description: Library name: Kras_rep5


title: ChIPseq, PanAcMe, IMR90, Empty vector, replicate 2

description: Library name: ChIPseq_PanAcMe_Empty_rep2


title: siPTBP1#1


title: apj1d, riboseq, 0min, bio rep1

description: Library name: apj1d_1_t0


title: siPTBP1#2


title: ChIPseq, PanAcMe, IMR90, Empty vector, replicate 1

description: Library name: ChIPseq_PanAcMe_Empty_rep1


title: Kras-G12D neoplastic cells, replicate 3

description: Library name: Kras_rep3


title: WT, riboseq, 60min, bio rep2

description: Library name: WT_2_t60

value: BY4741 WT


title: ASO-MIR99AHG#2


title: CUTnRUN, IgG, IMR90, MyoD WT vector, replicate 2

description: Library name: CUTnRUN_IgG_MYOD_wt_rep2

data_processing:
For RNA-seq: Quality control of the raw data has been performed with FASTQC (v0.11.9), reads were trimmed with Trimmomatic (v0.39) to eliminate low quality bases and adapters (parameters: PE -phred33 ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:2:true MAXINFO:40:0.1 MINLEN:45), and aligned to the hg19 Ensembl (November 2015) version of the human genome with STAR (v 2.7.3a), using a custom genome and index to simultaneously map and quantify ERCC92 spike-in-derived reads (parameters: --runMode alignReads --runThreadN 12 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts). Counts data (from STAR output in column 4, based on library preparation strandedness: second-strand) from all conditions were filtered based on their raw count, keeping genes where the sum of the counts for all samples was higher than 10. Size factors were calculated using the R environment (v4.1.3) package DESeq2 (v1.34.0) estimateSizeFactors function - using the counts related to the spike-in transcripts as control genes, then normalized and logged with the rlog function. DESeq2 was also used to perform Principal Component Analysis (PCA) and differential gene expression analysis (significance threshold: BH FDR<0.05). Differential expression analysis results were visualized with the heatplot function (parameters: method="complete", labRow= FALSE, dend="row", returnSampleTree=F, zlim=c(-5,5)) from the made4 (v1.68.0) package, after expression values from the DESeq2 object were turned into a matrix of Z-scores. Gene Ontology was performed on down- and up-regulated genes separately, using the gene symbols as input in EnrichR, and gene sets repositories GO Biological Processes 2023 and Descartes Cell Types and Tissue 2021. Top10 gene ontology terms shown in figure panels were ordered by pvalue. Gene Ontology bubble plots to summarize top50 gene ontology terms, were generated with the Python (v.3.8.1) GO-Figure script (parameters: -j standard -c log10-pval -e 100 -si 0.5 -s members -g single -n bpo --font_size small -q svg). For ATAC-seq: Quality control of the raw data has been performed with FASTQC (v0.11.9), reads were trimmed with Trimmomatic (v0.39) to eliminate low quality bases and adapters (parameters: PE -phred33 ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:2:true MAXINFO:40:0.1 MINLEN:45), aligned to the hg19 UCSC (January 2016) version of the human genome with Bowtie2 (v2.3.5.1) (parameters: --no-unal --local --very-sensitive-local --no-discordant --no-mixed --dovetail --phred33), sorted and converted into BAM format with the SAMtools sort function. Peak calling was performed with the Macs2 (v2.2.6) callpeak function (parameters: -f BAMPE -g hs -B -q 0.05 --nomodel --shift -100 --extsize 200) and filtered for black-list regions with the BEDtools suite (v2.29.2) intersect (parameters: -v), and sorted with the sort function (parameters: -k8,8nr). Irreproducible Discovery Rate (IDR) was calculated with the idr function (v2.0.3) (parameters: --input-file-type narrowPeak --plot --only-merge-peaks) to retain a single peaks list from each condition. Differential chromatin accessibility analysis was carried out in R, with the DESeq2 package. The R package ChIPQC (v1.30.0), (GetGRanges function was used to import peak lists from each biological replicate, a consensus peak list was calculated for all conditions using the IRanges (v2.28.0),function reduce, keeping peaks that were called in at least two samples. Counts for each peak in each biological replicate were quantified with the Rsubread (v2.8.2) featureCounts function (parameters: isPairedEnd= T, countMultiMappingReads= F, maxFragLength= 100). Counts were normalised and logged with the DESeq2 function rlog; DESeq2 was also used to perform Principal Component Analysis (PCA), and differential chromatin accessibility analysis (significance threshold: BH FDR<0.05). Differentially Accessible Regions (DARs) at gene promoter regions were retrieved with the IRanges function promoters (parameters: TxDb.Hsapiens.UCSC.hg19.knownGene, 1000, 200; mouse genome version was: TxDb.Mmusculus.UCSC.mm10.knownGene). Promoter DARs were visualized with the made4 function heatplot (parameters: method="complete", labRow= FALSE, dend="row", returnSampleTree=F, zlim=c(-5,5)), after expression values from the DESeq2 object were turned into a matrix of Z-scores. Due to R visualization limits, only promoters with |log2FC|>1.5 were plotted. Motif analysis was carried out with the HOMER (v4.11), findMotifsGenome function (parameters: hg19 -size given -nomotif). For ChIP-seq: Quality control of the raw data has been performed with FASTQC (v0.11.9) and aligned to the hg19 UCSC (January 2016) version of the human genome with Bowtie2 (parameters: --very-sensitive-local). Peak calling was performed with the Macs2 callpeak function (parameters: -g hs -B --nomodel --SPMR -q 0.05), using input chromatin as control. For CUT&RUN: Quality control of the raw data has been performed with FASTQC (v0.11.9), reads were trimmed with Trimmomatic (v0.39) to eliminate low quality bases and adapters (parameters: PE -phred33 ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:2:true MAXINFO:40:0.1 MINLEN:45), aligned either to the hg19 UCSC (January 2016) version of the human genome (for the CUT&RUN for histone marks in IMR90 and IMR90/MyoD), or to the mm10 Ensembl (November 2019) version of the mouse genome (for the CUT&RUN of AcMe and MyoD in muSC),  with Bowtie2 (parameters: --phred33 --end-to-end --no-unal --local --very-sensitive-local --no-mixed --no-discordant -I 10 -X 700 –dovetail) and converted to BAM format with the SAMtools (v1.10) function view (parameters: -bS). Peak calling was performed with the Macs2 callpeak function (parameters: -g hs --nomodel --SPMR --call-summits -p 0.05) using input chromatin as control, and filtered for black-list regions with BEDtools intersect (parameters: -v), and sorted with the Unix sort function (parameters: -k8,8nr). Irreproducible Discovery Rate (IDR) was calculated with the idr function (parameters: --input-file-type narrowPeak --plot --only-merge-peaks) to retain a single peaks list from each condition. ChromHMM (v1.24) BinarizeBed function (parameters: -b 200 -peaks) was used to bin the genome in 200bp windows according to each IDR peak list. The BinarizeBed output was used as input to ChromHMM LearnModel (parameters: -b 200 12 hg19), to build a 12 chromatin states model based on the histone marks IDR peaks. Chromatin state numbers were converted to chromatin states names in R, based on the combination of histone marks they were enriched for. For HiChIP: Quality control of the raw data has been performed with FASTQC (v0.11.9). Alignment, filtering, normalization, and loop calling were performed with the Arima version of MAPS (v2.0) bash script (parameters: -C 0 -F 1 -M 1 -H 1 -o hg19 -f 1 -s 5000 -r 2000000 -d 2 -Q 30 -l 1000). Irreproducible Discovery Rate (IDR) was calculated with IDR2D parameters: value transformation= log additive inverse (-log(x)), ambiguity resolution method= overlap, remove non-standard chromosome, max gap= 1000, max factor= 1.5, jitter factor= 0.0001, mu= 0.1, sigma=1, rho=0.2, p=0.5, epsilon=0.001). Differential HiChIP analysis was performed with the DiffAnalysisHiChIP.r script within FitHiChIP (v7.1), and significance threshold was set to p-value<0.05.
Assembly: hg19, mm10
Supplementary files format and content: TXT raw counts files (RNA-seq)
Supplementary files format and content: BEDGRAPH pileup signal tracks, with TBI index (RNA-seq)
Supplementary files format and content: BIGWIG signal tracks (ATAC-seq data, CUT&RUN), also biological replicates average signal tracks
Supplementary files format and content: ARCPLOTS of looping interactions, with TBI index (HiChIP)
Library strategy: CUT&Run


title: Kras-G12D neoplastic cells, replicate 2

description: Library name: Kras_rep2


title: ASO-MIR99AHG#1


title: WT, riboseq, 10min, bio rep2

description: Library name: WT_2_t10


title: Kras-G12D neoplastic cells, replicate 1

description: Library name: Kras_rep1


title: apj1d, riboseq, 10min, bio rep1, tech rep 3

description: Library name: apj1d_1_t10_3


title: CUTnRUN, IgG, IMR90, MyoD WT vector, replicate 1

description: Library name: CUTnRUN_IgG_MYOD_wt_rep1


title: WT, riboseq, 0min, bio rep2

description: Library name: WT_2_t0


title: apj1d, riboseq, 10min, bio rep1, tech rep 1

description: Library name: apj1d_1_t10_1


title: Tfap2a_Control2

city: Hannover

first: Karen

middle: I.

last: Lopez-Cayuqueo

address: Carl-Neuberg-Str.1,30625 Hannover

department: Department of Nephrology and Hypertension

institute: Hannover Medical School (MHH)

description:
Library name: Sample4
10x Genomics

data_processing:
Obtained libraries were sequenced on Illumina HiSeq 4000 sequencers (paired-end). Digital expression matrices were generated using the 10x Genomics Cell Ranger version 3.0.2 with –force-cells 10000 against a genome composed of the mouse mm10. Sequencing data generated from Hoxb7Cre+;Tfap2afl/fl  and control mice were analyzed with Seurat version 3.2.1.35 Initial filtering was performed by excluding nuclei with genes/cell < 500 or > 4000, and mitochondrial reads > 5 %. Genes expressed in less than three nuclei were not included in the analysis. Nuclei passing the initial quality control were analyzed following Seurat’s workflow for data integration (https://satijalab.org/seurat/articles/integration_introduction.html) with default parameters for NormalizeData(x), and FindVariableFeatures(x), followed by RunUMAP (dims = 1:30), FindNeighbors (dims = 1:30), and FindClusters (resolution = 0.5). Clusters were assigned to renal cell types based on their marker gene expression. Identified clusters representing the same cell type were summarized to one cluster (broad cell type). Nuclei from clusters showing marker gene expression for more than one cell type or high percentage of mitochondrial reads were assigned as damaged and excluded (2 clusters with 1,236 nuclei). The final Seurat object contained 26,105 nuclei. Relative abundances were calculated for broad cell types. Replicates from one group were averaged.
Assembly: mm10
Supplementary files format and content: CellRanger output files: feature.tsv, barcodes.tsv, matrix.tsv

source_name: Kidney

extract_protocol:
Mouse kidneys of 12-week-old male Hoxb7Cre+;Tfap2afl/fl or control mice (n = 2 per group) were dissected and washed in ice-cold PBS. A middle slice of 1–2 mm was taken, and the cortex was trimmed to enrich for medullary cell types. Mouse kidney specimens were stored in pre-cooled RNAlater (Invitrogen # AM7020) at 4°C for 24 hours and then stored at -80°C until nuclei isolation as reported in Leiz, Hinze et al (J Vis Exp, 2021).
All samples were subjected to single-nuc sequencing following the 10x Genomics protocol (Document #CG000204 Rev D) for Chromium Next GEM Single Cell 3’ v3.1 chemistry targeting 9,000–10,000 nuclei.

value: Kidney


title: CUTnRUN, IgG, IMR90, Empty vector, replicate 2

description: Library name: CUTnRUN_IgG_Empty_rep2

value: Fetal lung fibroblasts


title: CUTnRUN, H3K9me3, IMR90, MyoD WT vector, replicate 2

description: Library name: CUTnRUN_H3K9me3_MYOD_wt_rep2

value: Myogenic transdifferentiation


title: M2 BMDM, SA@BATMAN5, rep3

city: Beijing

first: Qing

last: Guangchao

address: No. 11, First North Road, Zhongguancun, Beijing, 100190, P.R. China

institute: National Center for Nanoscience and Technology

description: Library name: Sample 6

data_processing:
Hisat2 v2.2.0
StringTie v2.1.2
ASprofile 1.0.4
DESeq2 1.26.0
BLAST 2.2.31+
Assembly: GRCm39.108
Supplementary files format and content: xlsx file include FPKM values for each Sample

source_name: Primary bone marrow cells

growth_protocol: Bone marrow cells were isolated from mouse femurs, and were suspended in complete RPMI-1640 (supplemented with 10% (vol/vol) inactivated foetal bovine serum (FBS, WISENT), 1% penicillin and streptomycin (100 U/ml, WISENT)) with 10 ng/ml MCSF, and seeded on 12-well plate (1 × 10^6 cells/ml, 2 ml) or 8-well culture slide (25,000 cells/ml, 100 μl) at 37°C in 5% CO2 atmosphere. On day 3, non-adherent cells were discarded and adherent cells were further cultured for four more days with fresh medium supplemented with 10 ng/ml MCSF. Adherent cells confirmed to be F4/80+ were considered to be mature BMDMs (M0). For M2 activation, M0 cells were incubated with 20 ng/ml IL-4 for 24 hours.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used forthe construction of sequencing libraries.
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg Library Prep Kitfollowing manufacturer's protocols.

treatment_protocol: M2 BMDMs were seeded in 12-well plates (1 × 10^6 cells per well) and allowed to grow for 24 hours. Then, cells were incubated with SA@BATMAN5 for 24 hours.

value: Primary bone marrow cells

value: bone marrow-derived macrophages

value: WT


title: CUTnRUN, IgG, IMR90, Empty vector, replicate 1

description: Library name: CUTnRUN_IgG_Empty_rep1


title: M2 BMDM, SA@BATMAN5, rep1

description: Library name: Sample 4


title: M2 BMDM, SA@BATMAN5, rep2

description: Library name: Sample 5


title: Kras-G12D neoplastic cells, replicate 4

description: Library name: Kras_rep4


title: WT, riboseq, 10min, bio rep1

description: Library name: WT_1_t10

value: Whole cell


title: Tfap2a_cKO2

description:
Library name: Sample2
10x Genomics


title: Tfap2a_Control1

description:
Library name: Sample3
10x Genomics


title: WT, riboseq, 0min, bio rep1

description: Library name: WT_1_t0


title: WT, riboseq, 60min, bio rep1

description: Library name: WT_1_t60

value: 60 min HS 38°C


title: M2 BMDM, Control, rep3

description: Library name: Sample 3

value: PBS


title: Tfap2a_cKO1

description:
Library name: Sample1
10x Genomics


title: apj1d ydj1-4xcga, RNAseq, steadystate, rep2

description: Library name: RNAseq_apj1dydj14x_2_25

data_processing:
sequences were trimmed for adaptors and sequence/ low-quality sequence using cutadapt version 3.5
UMIs were extracted from trimmed sequence reads using a custom Julia script
reads were aligned to S. cerevisiae rRNA sequences with bowtie version 1.3.1 using  -n 2 alignment mode and --best reporting mode. Only reads that did not align were kept.
reads were mapped to S. cerevisiae S288C Genome (Assembly: GCA_000146045.2) using STAR version 2.7.10a. Following mapping parameters were used: --outSAMmultNmax 1; --outFilterType BySJout; --alignIntronMin 5; --quantMode GeneCounts; --twopassMode Basic; --outSAMattributes All XS
With a custom Julia script reads were processed as described here: Reads from PCR dupicates were detected using UMI and were collapsed to a single read. Ribosomal positions were assigned.
Assembly: GCA_000146045.2
Supplementary files format and content: cds_umi_psite.h5
Supplementary files format and content: Reads mapped to the CDS, filtered for UMIs, aligned to the p-site

value: BY4741 apj1d ydj1-4xcga


title: CUTnRUN, H3K9me3, IMR90, MyoD WT vector, replicate 1

description: Library name: CUTnRUN_H3K9me3_MYOD_wt_rep1


title: CUTnRUN, H3K9me3, IMR90, Empty vector, replicate 2

description: Library name: CUTnRUN_H3K9me3_Empty_rep2


title: M2 BMDM, Control, rep1

description: Library name: Sample 1


title: apj1d ydj1-4xcga, RNAseq, steadystate, rep1

description: Library name: RNAseq_apj1dydj14x_1_25


title: pLN cKO_3

city: Palo Alto

first: Xiangyue

last: Zhang

address: 3373 Hillview ave

department: Pathology

institute: Stanford University

description: Library name: Sample12

data_processing:
The sequencing reads in fastq files were mapped to the reference genome using hisat2 v2.1.0.
The mapped bam files were converted to gene count files using featureCounts 2.0.8.
Assembly: mm10
Supplementary files format and content: text files including raw counts for each sample

source_name: Peripheral lymph node

extract_protocol:
Total RNA was isolated using NucleoSpin RNA (Takara Ref: 740955.50) and the quality and quantity were measured using Tapestation 4200 (Agilent Technologies) and Qubit (Invitrogen) respectively.
Takara SMART-Seq mRNA Kit was used to generate full-length cDNA from 10ng total RNA samples by following the manufacturer's instructions. The process started with first-strand cDNA synthesis, where the 3’ SMART-Seq CDS Primer II A and the SMART-Seq v4 Oligonucleotide were used to prime and template switch at the 5’ end of the transcript. This step was followed by LD PCR amplification using the PCR Primer II A to amplify the cDNA. The amplified cDNA was then purified using the Agencourt AMPure XP Kit to remove any contaminants. Finally, the quality and quantity of the cDNA were validated using Tapestation 4200 (Agilent Technologies) and Qubit (Invitrogen) respectively. The full length cDNA fragments were converted into libraries using Nextera XT DNA library kit (Catalog No.: FC-131-1096). 150pg was used for tagmentation using Nextera transposon, in which the full length cDNA were fragmented and tagged with the adapter sequences. These fragments were further amplified using indexed primers resulting in Illumina compatible libraries. The quality and quantity were measured using Tapestation 4200 (Agilent Technologies) and Qubit (Invitrogen) respectively. Prior to sequencing, libraries were diluted to 4nmoles and pooled.

value: Peripheral lymph node

value: CCR7+ XCR1+SIPRa-cDC1s migratory cDC1s

value: Epor-Xcr1-Cre cKO


title: M2 BMDM, Control, rep2

description: Library name: Sample 2


title: pLN cKO_2

description: Library name: Sample11


title: CreERT2_Ly_rep3

city: New Haven

first: Mark

last: Robinson

state: CT

address: 300 George St

department: Center of Molecular and Cellular Oncology

institute: Yale University

data_processing:
Quality control of RNA-Seq reads was performed using FastQC v0.11.9, samtools v1.7 and Picard v2.23.8.
Transcipts were quantified with Salmon v1.4.062 against Gencode vM24 mm10/GRCm38
Differential expression was perfomed in R using DESeq2 v1.30.1
Assembly: mm10
Supplementary files format and content: rlog_norm_expr.csv - rlog normalized expression values per sample, using standard DESeq2 model, row names are ensembl IDs

source_name: bone marrow

growth_protocol: pre-B cells are grown ex vivo in IMDM + 20% FBS + 10 ng/ml IL7 for 2 weeks, retrovirally transformed with BCR-ABL1 oncogene and IL7 removed.

extract_protocol:
RNA was isolated using Macherey-Nagel RNA extraction kit according to manufacturer’s instructions. RNA concentration was measured by NanoDrop 1000 (Thermo Fisher Scientific) and RNA integrity was determined using Bioanalyzer (Agilent).
). Library construction of 280 ng total RNA for each sample was made using KAPAStrandedmRNA-Seq Kit (Illumina Platforms; Kapa Biosystems) using 10cycles of PCR amplification. Libraries were purified using AxyPrep Mag PCR Clean-up kit (AxygenTM). Each library was quantified using a Qubit fluorometer (Life Technologies) and the size distribution assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA). Sequencing was performed on an Illumina®Hiseq 2500 (Illumina, San Diego, CA, USA) instrument using the TruSeq PE Cluster Kit V4-cBot-HS (Illumina®) to generate 101 bp Paired-end reads sequencing with v4 chemistry.

value: bone marrow

value: pre-B

value: Ctnnb1 fl/fl + BCR-ABL1

value: 2 days 4-OHT+ 1day LY2090314


title: apj1d sis1-4xcga, RNAseq, steadystate, rep2

description: Library name: RNAseq_apj1dsis14x_2_25

value: BY4741 apj1d sis1-4xcga


title: CUTnRUN, H3K4me3, IMR90, MyoD WT vector, replicate 2

description: Library name: CUTnRUN_H3K4me3_MYOD_wt_rep2

value: Fetal lung fibroblasts


title: pLN cKO_1

description: Library name: Sample10


title: apj1d sis1-4xcga, riboseq, 60min, bio rep1, tech rep 1

description: Library name: apj1dsis14x_1_t60_1


title: CreERT2_Ly_rep2


title: pLN Ctrl_3

description: Library name: Sample9

value: Eporflox/flox


title: CUTnRUN, H3K4me3, IMR90, Empty vector, replicate 2

description: Library name: CUTnRUN_H3K4me3_Empty_rep2

value: Empty


title: apj1d sis1-4xcga, RNAseq, steadystate, rep1

description: Library name: RNAseq_apj1dsis14x_1_25


title: CUTnRUN, H3K4me3, IMR90, MyoD WT vector, replicate 1

description: Library name: CUTnRUN_H3K4me3_MYOD_wt_rep1

value: Myogenic transdifferentiation


title: pLN Ctrl_2

description: Library name: Sample8


title: CreERT2_Ly_rep1


title: sis1-4xcga, RNAseq, steadystate, rep2

description: Library name: RNAseq_sis14xcga_2_25

value: BY4741 sis1-4xcga


title: CUTnRUN, H3K4me3, IMR90, Empty vector, replicate 1

description: Library name: CUTnRUN_H3K4me3_Empty_rep1


title: pLN Ctrl_1

description: Library name: Sample7


title: ydj1-4xcga, RNAseq, steadystate, rep1

description: Library name: RNAseq_ydj14xcga_1_25

value: Whole cell

value: BY4741 ydj1-4xcga


title: ERT2_Ly_rep2


title: sis1-4xcga, RNAseq, steadystate, rep1

description: Library name: RNAseq_sis14xcga_1_25


title: ERT2_Ly_rep1


title: CUTnRUN, H3K4me1, IMR90, MyoD WT vector, replicate 1

description: Library name: CUTnRUN_H3K4me1_MYOD_wt_rep1


title: ydj1-4xcga, RNAseq, steadystate, rep2

description: Library name: RNAseq_ydj14xcga_2_25


title: ERT2_Ly_rep3


title: Spleen cKO_3

description: Library name: Sample6

source_name: Spleen

value: Spleen

value: CCR7+ XCR1+SIPRa-cDC1s


title: CUTnRUN, H3K9me3, IMR90, Empty vector, replicate 1

description: Library name: CUTnRUN_H3K9me3_Empty_rep1


title: apj1d, RNAseq, steadystate, rep2

description: Library name: RNAseq_apj1d_2_25

value: BY4741 apj1d


title: Spleen cKO_2

description: Library name: Sample5


title: CUTnRUN, H3K4me1, IMR90, Empty vector, replicate 2

description: Library name: CUTnRUN_H3K4me1_Empty_rep2


title: apj1d, RNAseq, steadystate, rep1

description: Library name: RNAseq_apj1d_1_25


title: CreERT2_rep3

value: 2 days 4-OHT


title: WT, RNAseq, steadystate, rep2

description: Library name: RNAseq_WT_2_25

value: BY4741 WT


title: Spleen Ctrl_3

description: Library name: Sample3


title: WT, RNAseq, steadystate, rep1

description: Library name: RNAseq_WT_1_25


title: Spleen Ctrl_2

description: Library name: Sample2


title: ERT2_rep1

value: bone marrow


title: CUTnRUN, H3K4me1, IMR90, Empty vector, replicate 1

description: Library name: CUTnRUN_H3K4me1_Empty_rep1


title: ERT2_rep2

value: pre-B


title: ERT2_rep3

value: Ctnnb1 fl/fl + BCR-ABL1


title: CUTnRUN, H3K27me3, IMR90, Empty vector, replicate 1

description: Library name: CUTnRUN_H3K27me3_Empty_rep1


title: Dysf_D19_r2

city: Columbus

first: Hazem

middle: E

last: Ghoneim

state: Ohio

address: 460 W 12th Ave

department: Microbial Infection and Immunity

institute: The Ohio State University

description: Library name: MC08

data_processing:
The generated FASTQ files were used for pre-alignment QA/QC, then aligned to the mouse mm10 genome by STAR.
The resultant aligned reads were quantified to the mm10 RefSeq Transcripts using Quantify to annotation model, followed by filtering to exclude features where maximum < 50.0.
DESeq2 analysis was performed first by normalization of the filtered gene counts for median ratio to compare among the conditions.
Assembly: mm10
Supplementary files format and content: raw counts for each Sample

extract_protocol:
RNA was isolated for RNA-seq using PicoPure RNA isolation Kit (Applied Biosystems) following manufacturer's protocols.
Libraries were prepared for Illumina NovaSeq by Genewiz (Azenta), with PolyA selection.

treatment_protocol: Naïve P14 CD8+ T cells were activated using anti-CD3 and anti-CD28-coated plates for 2 days. Then, activated P14 cells were either cultured without GP33 peptide and maintained in peptide-free T Cell Media until day 19 (Acute-2d_D19), or repeatedly stimulated with GP33 peptide until day 7 followed by culture in peptide-free T Cell Media until day 19 (Acute-7d_D19). Chronically stimulated P14 cells were continuously treated with TGFβ1 beginning on day 7 and repeatedly stimulated using GP33 peptide-containing medium until day 19 (Dysf_D19).

value: Primary CD8 T cells

value: Dysfunctional

tag: time

value: Day 19


title: CRE_IKZF-KO_r3

data_processing:
Transcipts were quantified with Salmon v1.4.0, and reads aligned using STAR v2.7.6 to the mouse genome (mm10/GRCm38, gencode vM24).
Normalised rlog gene counts calculated with DESeq2 v1.30.1
Genome_build: mm10
Supplementary_files_format_and_content: Normalised rlog gene counts calculated with DESeq2 v1.30.1

source_name: mouse pre-B cells transformed with BCR-ABL1

growth_protocol: Bone marrow cells were harvested from 6-12 weeks old mice by flushing cavities of femur and tibia with ice-cold PBS supplemented with 2% FBS and cells were filtered through 70 μm mesh to generate single cell suspensions. Cells from spleen and thymus were extracted by forcing tissues through a 40 μm strainer into ice-cold PBS with 2% FBS. Erythrocyte lysis was performed for bone marrow and spleen cells (RBC Lysis Buffer, BioLegend). After making single cell suspensions, bone marrow cells were cultured in Iscove’s modified Dulbecco’s medium (IMDM; Gibco) with GlutaMAX containing 20% FBS, 50 μmol ml-1 2-mercaptoethanol, 100 IU ml-1 P/S. Bone marrow cells were cultured in 10 ng ml-1 recombinant mouse IL-7 (Peprotech) to generate IL-7 dependent pre-B cells. Pre-B cells were retrovirally transduced by BCR-ABL1 and IL-7 was removed to promote the outgrowth of the transformed cells.

extract_protocol:
RNA was isolated using Macherey-Nagel RNA extraction kit according to manufacturer’s instructions. RNA concentration was measured by NanoDrop 1000 (Thermo Fisher Scientific) and RNA integrity was determined using Bioanalyzer (Agilent).
Library construction of 280 ng total RNA for each sample was made using KAPA Stranded mRNA-Seq Kit (Illumina Platforms; Kapa Biosystems) using 10 cycles of PCR amplification. Libraries were purified using AxyPrep Mag PCR Clean-up kit (AxygenTM). Each library was quantified using a Qubit fluorometer (Life Technologies) and the size distribution assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).

treatment_protocol: CRISPR/Cas9-RNP electroporation was performed by using NeonTM Transfection system (Invitrogen) with either non-targeting or IKZF1/IKZF3-targeting guides. Single cell derived colonies were generated to obtain fully knock-out cell lines. These cells were transduced with ERT2 and Cre-ERT2 vectors expressing GFP and sorted for GFP+ cells. Chip-seq analysis was performed 1 day after 4-OHT mediated b-catenin activation.

tag: celltype

value: preB-ALL

value: BCR-ABL1 Ctnnb1Ex3fl/+ Cre-ERT2 sgIkzf1 Ikzf3


title: Spleen Ctrl_1

description: Library name: Sample1

value: Eporflox/flox


title: Dysf_D19_r1

description: Library name: MC07


title: CUTnRUN, H3K4me1, IMR90, MyoD WT vector, replicate 2

description: Library name: CUTnRUN_H3K4me1_MYOD_wt_rep2

value: Fetal lung fibroblasts

value: Myogenic transdifferentiation


title: Spleen cKO_1

description: Library name: Sample4

value: Epor-Xcr1-Cre cKO


title: CUTnRUN, H3K27ac, IMR90, MyoD WT vector, replicate 2

description: Library name: CUTnRUN_H3K27ac_MYOD_wt_rep2


title: Acute-7d_D19_r2

description: Library name: MC04

value: Spleen


title: rAAV transfection at 72h, biological rep3

type: RNA

city: Biberach an der Riß

first: Madina

last: Burkhart

address: Hubertus-Liebrecht-Straße 35

department: Institute for Applied Biotechnology

institute: Hochschule Biberach

description: Microarray expression data for triple rAAV plasmid transfection

hyb_protocol: Hybridization was performed according to the instructions in the FlashTagTM Biotin HSR RNA Labeling Kit.

scan_protocol: Scan was performed according to Affymetrix protocols using a GeneChip 3000 Scanner.

data_processing: Affymetrix Expression Console 1.4.1.46 for normalization (RMA+DBAG; human only); BRB Array (https://brb.nci.nih.gov/BRB-ArrayTools/) tools for statistical analysis

label: Biotin

source_name: HEK293F cells

label_protocol: FlashTagTM Biotin HSR RNA Labeling Kit (Genisphere, LLC, Hatfield, PA, USA) according to the instructions of the manufacturer.

growth_protocol: HEK293F cells were seeded at a viable cell density of 2E+06 vc/ml in a total volume of 10 ml in TubeSpin® bioreactor tubes.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: For rAAV production, pAAV-SEAP transgene plasmid, rep/cap plasmid pAAV2/2 (Addgene plasmid #104963) and pAdDeltaF6 helper plasmid (Addgene plasmid #112867) were mixed in a molar ratio of 1:1:1 and transfected using PEIpro (Polyplus, Illkirch, France). In addition, untransfected cells (0 h) and a mock transfection using same amounts of transfection reagents but lacking plasmid DNA were included.

value: Commercially available human embryonic kidney-293 cells adapted to grow in suspension (ThermoFisher)


title: CreERT2_rep2


title: CRE_IKZF-KO_r2


title: Acute-7d_D19_r1

description: Library name: RESUB-MC03


title: CUTnRUN, H3K27ac, IMR90, MyoD WT vector, replicate 1

description: Library name: CUTnRUN_H3K27ac_MYOD_wt_rep1


title: CUTnRUN, H3K27me3, IMR90, MyoD WT vector, replicate 2

description: Library name: CUTnRUN_H3K27me3_MYOD_wt_rep2


title: CreERT2_rep1


title: rAAV transfection at 72h, biological rep2


title: CUTnRUN, H3K27me3, IMR90, Empty vector, replicate 2

description: Library name: CUTnRUN_H3K27me3_Empty_rep2

value: Empty


title: CRE_IKZF-KO_r1


title: CUTnRUN, H3K27me3, IMR90, MyoD WT vector, replicate 1

description: Library name: CUTnRUN_H3K27me3_MYOD_wt_rep1


title: rAAV transfection at 48h, biological rep3


title: rAAV transfection at 72h, biological rep1


title: ERT2_IKZF-KO_r3

value: BCR-ABL1 Ctnnb1Ex3fl/+  ERT2 sgIkzf1 Ikzf3


title: Effector-D7_r2

description: Library name: RESUB-MC17

value: Effector

value: Day 7


title: CUTnRUN, H3K27ac, IMR90, Empty vector, replicate 1

description: Library name: CUTnRUN_H3K27ac_Empty_rep1


title: CUTnRUN, H3K27ac, IMR90, Empty vector, replicate 2

description: Library name: CUTnRUN_H3K27ac_Empty_rep2


title: ATACseq, IMR90, MyoD DRem vector, replicate 2

description: Library name: ATACseq_MYOD_DRem_rep2


title: Acute-2d_D19_r2

description: Library name: MC02


title: ERT2_IKZF-KO_r2


title: CRE_IKZF-WT_r3

value: BCR-ABL1 Ctnnb1Ex3fl/+ Cre-ERT2 sgNTC


title: Spl3_Dysf_PD1hi Tim3+_D23_PD1hi Tim3+

description: Library name: RDP02

data_processing:
The data was analyzed using cutadapt 1.18, Bowtie2, Picard 2.18.17, samtools, and deepTools 3.3.0.  First, the fastq files were trimmed using cutadapt, and then aligned to mouse mm10 genome assembly using Bowtie2.
Duplicate reads were removed using Picard 2.18.17 and bigWig files were generated with deepTools.
Assembly: mm10
Supplementary files format and content: bigWig files

extract_protocol:
Following FACS sorting, nuclei were isolated from cells using ATAC lysis buffer (10 mM Tris-HCL pH 7.5, 10 mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin) and then transposed for 30 minutes at 37oC using Tagment DNA TDE1 Enzyme (Illumina, 20034197).
ATAC libraries were prepared using Omni-ATAC protocol. Transposed DNA was purified, and libraries were generated using Nextera XT DNA Library Preparation Kit (Illumina, FC-131-2001).

treatment_protocol: P14 CD8 T cells sorted from day 19 of chronic stimulation were cultured in complete RPMI medium containing IL-15 until day 23. P14 cells were isolated for ATAC-sequencing using the Sony MA900 Cell Sorter on both day 19 and day 23, including Acute-7d or TDysf PD-1+ Tim3+ on day 19, and resting TDysf cells isolated as PD-1+ Tim3- (Rest-SP) or PD-1+ Tim3+ (Rest-DP) on day 23.

value: Dysf_PD1hi Tim3+_D23_PD1hi Tim3+

value: Day 23


title: Effector-D7_r1

description: Library name: RESUB-MC16

value: Primary CD8 T cells


title: CRE_IKZF-WT_r1


title: ERT2_IKZF-KO_r1


title: rAAV transfection at 48h, biological rep2


title: CRE_IKZF-WT_r2


title: Acute-2d_D19_r1

description: Library name: MC01

value: Day 19


title: ATACseq, IMR90, MyoD WT vector, replicate 2

description: Library name: ATACseq_MYOD_wt_rep2


title: ATACseq, IMR90, MyoD DRem vector, replicate 1

description: Library name: ATACseq_MYOD_DRem_rep1


title: rAAV transfection at 24h, biological rep1


title: rAAV transfection at 48h, biological rep1


title: ATACseq, IMR90, MyoD WT vector, replicate 3

description: Library name: ATACseq_MYOD_wt_rep3


title: rAAV transfection at 12h, biological rep2


title: ERT2_IKZF-WT_r3

value: preB-ALL

value: BCR-ABL1 Ctnnb1Ex3fl/+  ERT2 sgNTC


title: rAAV transfection at 24h, biological rep2


title: ATACseq, IMR90, MyoD DAct vector, replicate 2

description: Library name: ATACseq_MYOD_Dact_rep2


title: rAAV transfection at 24h, biological rep3


title: Spl1_Dysf_PD1hi Tim3+_D23_PD1hi Tim3+

description: Library name: RDP01


title: Spl1_Dysf_PD1hi Tim3+_D23_PD1int Tim3-

description: Library name: RSP01

value: Dysf_PD1hi Tim3+_D23_PD1int Tim3-


title: rAAV transfection at 12h, biological rep3


title: ATACseq, IMR90, MyoD DAct vector, replicate 1

description: Library name: ATACseq_MYOD_Dact_rep1

value: Fetal lung fibroblasts


title: ATACseq, IMR90, MyoD WT vector, replicate 1

description: Library name: ATACseq_MYOD_wt_rep1

value: Myogenic transdifferentiation


title: ERT2_IKZF-WT_r2


title: rAAV transfection at 12h, biological rep1


title: Spl2_Dysf_D19_PD1hi Tim3+

description: Library name: DP02

value: Dysf_PD1hi Tim3+


title: ERT2_IKZF-WT_r1


title: ATACseq, IMR90, Empty vector, replicate 3

description: Library name: ATACseq_Empty_rep3


title: Spl2_Dysf_D19_PD1int Tim3-

description: Library name: SP02

value: Spleen

value: Dysf_PD1int Tim3-


title: rAAV transfection at 6h, biological rep3

value: Commercially available human embryonic kidney-293 cells adapted to grow in suspension (ThermoFisher)


title: ATACseq, IMR90, Empty vector, replicate 2

description: Library name: ATACseq_Empty_rep2

value: Empty


title: Spl2_Acute7d-stim_D19_PD1low Tim3-

description: Library name: AC02

value: Acute7d_PD1low Tim3-


title: CRE_IKZF-KO_H3K27ac_rep2

data_processing:
Reads were aligned with BWA v0.7.17 against the mouse genome (mm10/GRCm38, gencode vM24).
Peak calling was performed with MACS2 v2.2.7.1
BigWig were generated using DeepTools, in the case of histone modifications signal was normalized to total library size (RPM) whereas for TFs, signal was normalized to total signal within peak regions.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig tracks of normalised signal within 50bp windows with 100bp smoothing

extract_protocol:
B-ALL cells were counted and fixed with 1% formaldehyde for 10 min at room temperature and quenched by 125 mmol l-1 glycine. B-ALL cells were spiked with fixed Drosophila S2 cells, and subjected to nuclear extraction. Nuclei were lysed with SDS lysis buffer and sonicated by Bioruptor (Diagenode). After sonication, cell debris was removed by centrifugation (13,000 rpm, 10 min), while supernatant was diluted and pre-cleared by incubation with a blend of isotype control IgG, Dynabeads Protein A and Dynabeads Protein G (Invitrogen). ChIP was performed using antibodies specifically recognizing either H3K27ac (Active motif, #39133) or H3K4me3 (Millipore, MC315). ChIPed DNA was reverse-crosslinked overnight at 65℃, and purified by QIAquick PCR purification kit (Qiagen). For ChIP-seq of IKZF1 and IKZF3, B-ALL cells were crosslinked by 2 mmol l-1 disuccinimidyl glutarate for 45 min and 1% formaldehyde for 10 min at room temperature before chromatin enrichment and library construction. These antibodies were used for ChIP-seq of  IKZF1 (GeneTex, GTX129438) and IKZF3 (CST, D1C1E). β-catenin ChIP was performed by Active Motif, Inc. (Carlsbad, CA, USA) using the monoclonal antibody CAT-15 (Thermo).
ChIP-seq libraries were constructed by a SMARTer ThruPLEX DNA-seq Kit (Takara).

tag: chip target

tag: spike-in

value: Drosophila chromatin spike-in

value: BCR-ABL1 Ctnnb1Ex3fl/+ Cre-ERT2 sgIkzf1 Ikzf3 clone 3E


title: Spl1_Dysf_D19_PD1hi Tim3+

description: Library name: DP01


title: rAAV transfection at 6h, biological rep2


title: ATACseq, IMR90, MyoD D102-135 vector, replicate 3

description: Library name: ATACseq_MYOD_D135_rep3


title: Spl1_Dysf_D19_PD1int Tim3-

description: Library name: SP01


title: Spl1_Acute7d-stim_D19_PD1low Tim3-

description: Library name: AC01


title: ATACseq, IMR90, MyoD D102-135 vector, replicate 2

description: Library name: ATACseq_MYOD_D135_rep2


title: ERT2_IKZF-KO_H3K4me3_rep2

value: BCR-ABL1 Ctnnb1Ex3fl/+  ERT2 sgIkzf1 Ikzf3 clone 3E


title: rAAV transfection at 6h, biological rep1


title: mock transfection at 72h, biological rep2

description: Microarray expression data for mock transfection (only transfection reagent)


title: mock transfection at 72h, biological rep3


title: mock transfection at 48h, biological rep3


title: mock transfection at 72h, biological rep1


title: CRE_IKZF-WT_IKZF3_rep2

value: BCR-ABL1 Ctnnb1Ex3fl/+ Cre-ERT2 sgNTC clone 6H


title: CUTnRUN, IgG, 60h post muscle injury, replicate 2

description: Library name: CUTnRUN_IgG_60hpi_rep2

source_name: Skeletal muscle

value: Skeletal muscle

value: Muscle Stem Cells

value: Skeletal muscle injury


title: ATACseq, IMR90, MyoD D102-135 vector, replicate 1

description: Library name: ATACseq_MYOD_D135_rep1


title: CRE_IKZF-WT_IKZF1_rep2

value: preB-ALL


title: ATACseq, IMR90, MyoD D102-114 vector, replicate 3

description: Library name: ATACseq_MYOD_D114_rep3


title: CUTnRUN, IgG, 60h post muscle injury, replicate 1

description: Library name: CUTnRUN_IgG_60hpi_rep1


title: CRE_IKZF-KO_H3K4me3_rep2


title: ATACseq, IMR90, MyoD D102-114 vector, replicate 2

description: Library name: ATACseq_MYOD_D114_rep2


title: mock transfection at 48h, biological rep2


title: CRE_IKZF-WT_H3K4me3_rep2


title: ATACseq, IMR90, Empty vector, replicate 1

description: Library name: ATACseq_Empty_rep1


title: CRE_IKZF-WT_H3K27ac_rep2


title: mock transfection at 48h, biological rep1


title: ERT2_IKZF-KO_H3K27ac_rep2


title: CUTnRUN, IgG, 4h post muscle injury, replicate 1

description: Library name: CUTnRUN_IgG_4hpi_rep1


title: ATACseq, IMR90, MyoD D102-114 vector, replicate 1

description: Library name: ATACseq_MYOD_D114_rep1


title: ERT2_IKZF-WT_IKZF3_rep2

value: BCR-ABL1 Ctnnb1Ex3fl/+  ERT2 sgNTC clone 6H


title: CUTnRUN, MYOD, 60h post muscle injury, replicate 2

description: Library name: CUTnRUN_MYOD_60hpi_rep2


title: RNAseq, IMR90, MyoD DRem vector, replicate 2

description: Library name: RNAseq_MYOD_DRem_rep2

value: Fetal lung fibroblasts


title: mock transfection at 24h, biological rep3


title: RNAseq, IMR90, MyoD DRem vector, replicate 1

description: Library name: RNAseq_MYOD_DRem_rep1

value: Myogenic transdifferentiation


title: ERT2_IKZF-WT_IKZF1_rep2


title: mock transfection at 24h, biological rep2


title: mock transfection at 24h, biological rep1


title: RNAseq, IMR90, MyoD DAct vector, replicate 2

description: Library name: RNAseq_MYOD_DAct_rep2


title: CUTnRUN, MYOD, 4 h post muscle injury, replicate 2

description: Library name: CUTnRUN_MYOD_4hpi_rep2


title: Spl3_Dysf_PD1hi Tim3+_D23_PD1int Tim3-

description: Library name: RSP02

value: Primary CD8 T cells

value: Dysf_PD1hi Tim3+_D23_PD1int Tim3-

value: Day 23


title: RNAseq, IMR90, MyoD DAct vector, replicate 1

description: Library name: RNAseq_MYOD_DAct_rep1


title: CUTnRUN, IgG, 4h post muscle injury, replicate 2

description: Library name: CUTnRUN_IgG_4hpi_rep2


title: mock transfection at 12h, biological rep3

value: Commercially available human embryonic kidney-293 cells adapted to grow in suspension (ThermoFisher)


title: CUTnRUN, MYOD, 4h post muscle injury, replicate 1

description: Library name: CUTnRUN_MYOD_4hpi_rep1


title: CRE_IKZF-KO_H3K4me3_rep1


title: CUTnRUN, H4AcMe, 60h post muscle injury, replicate 2

description: Library name: CUTnRUN_H4AcMe_60hpi_rep2


title: RNAseq, IMR90, MyoD D102-135 vector, replicate 3

description: Library name: RNAseq_MYOD_D135_rep3


title: mock transfection at 12h, biological rep2


title: CUTnRUN, MYOD, 60h post muscle injury, replicate 1

description: Library name: CUTnRUN_MYOD_60hpi_rep1


title: ERT2_IKZF-WT_H3K4me3_rep2


title: RNAseq, IMR90, MyoD D102-135 vector, replicate 2

description: Library name: RNAseq_MYOD_D135_rep2


title: CUTnRUN, H4AcMe, 60h post muscle injury, replicate 1

description: Library name: CUTnRUN_H4AcMe_60hpi_rep1


title: CRE_IKZF-KO_H3K27ac_rep1


title: ERT2_IKZF-WT_H3K27ac_rep2


title: CUTnRUN, H4AcMe, 4h post muscle injury, replicate 1

description: Library name: CUTnRUN_H4AcMe_4hpi_rep1


title: ERT2_IKZF-KO_H3K27ac_rep1


title: RNAseq, IMR90, MyoD D102-114 vector, replicate 3

description: Library name: RNAseq_MYOD_D114_rep3


title: CUTnRUN, H4AcMe, 4h post muscle injury, replicate 2

description: Library name: CUTnRUN_H4AcMe_4hpi_rep2


title: CUTnRUN, PanAcMe, 60h post muscle injury, replicate 2

description: Library name: CUTnRUN_PanAcMe_60hpi_rep2


title: ERT2_IKZF-KO_H3K4me3_rep1


title: RNAseq, IMR90, MyoD D102-114 vector, replicate 1

description: Library name: RNAseq_MYOD_D114_rep1


title: CUTnRUN, PanAcMe, 60h post muscle injury, replicate 1

description: Library name: CUTnRUN_PanAcMe_60hpi_rep1


title: CRE_IKZF-WT_IKZF1_rep1


title: RNAseq, IMR90, MyoD WT vector, replicate 3

description: Library name: RNAseq_MYOD_wt_rep3


title: CRE_IKZF-WT_IKZF3_rep1


title: CRE_IKZF-WT_H3K4me3_rep1


title: CRE_IKZF-WT_H3K27ac_rep1


title: RNAseq, IMR90, MyoD D102-114 vector, replicate 2

description: Library name: RNAseq_MYOD_D114_rep2


title: OE_HA3

city: hengyang

first: shishi

last: luo

state: hunan

address: 28 West Changsheng Road

department: Hengyang Medical College

institute: University of South China

description: Library name: Sample 6

data_processing:
Adapter and low-quality reads were first trimmed using Trim Galore (version 0.4.4) in paired-end mode with default parameters. Trimmed reads were then mapped to the hg38 reference genome to count mapped reads for all human transcripts.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes log2normalized count values for each Sample

extract_protocol:
Extraction of total RNA following the manufacturer’s instruction of the AllPrep DNA/ RNA/miRNA Universal Kit (80224, Qiagen, USA).
For library preparation, 1 mg of total RNA from each sample was depleted for rRNA using the Ribo−Zero rRNA Removal Kit (RZH1046, EPICENTRE, USA), followed by construction of sequencing library using the TruSeq RNA Sample Prep Kit v2 (RS−122, Illumina, USA).

value: the kidney of a human embryo

value: SFXN2 overexpression


title: CUTnRUN, PanAcMe, 4h post muscle injury, replicate 1

description: Library name: CUTnRUN_PanAcMe_4hpi_rep1


title: pre-transfection at 0h, biological rep1

description: Microarray expression data pre-transfection (basal expression)


title: mock transfection at 12h, biological rep1


title: mock transfection at 6h, biological rep3


title: OE_HA2

description: Library name: Sample 5


title: mock transfection at 6h, biological rep2


title: ERT2_IKZF-WT_IKZF3_rep1


title: RNAseq, IMR90, MyoD WT vector, replicate 2

description: Library name: RNAseq_MYOD_wt_rep2


title: Zbtb16_KO

city: Shanghai

first: Wuchan

last: Wang

address: Tongji University

institute: Tongji University

data_processing:
For the scRNA-seq, raw sequencing data was processed with Cell Ranger for FASTQ generation and GRCm39 mouse reference genome was used for alignments. For filtering and unsupervised clustering, the gene expression matrixs from Cell Ranger results were used for downstream analysis, using R 4.1.1.
Assembly: GRCm39/mm39
Supplementary files format and content: outputs of cellranger software, which include barcodes, gene features and expression matrix for each sample

extract_protocol:
Cells were washed with 1× PBS detached with 0.25% Trypsin incubated for 3 minutes. Then cells were washed twice with 1× PBS with 1% FBS and resuspended in cold 1× PBS with 1% FBS. Cells were filtered through a 40 µm cell strainer and centrifuged at 500 g for 5 min at 4°C. Pellets were resuspended in cell resuspension buffer at 1000 cells per μl for library preparation.
The DNBelab C Series Single-Cell Library Prep Set (MGI) was used as previously described for single-cell RNA sequencing library preparation. In brief, single-cell suspensions were converted to barcoded scRNA-seq libraries through steps including droplet generation, emulsion breakage, mRNA captured bead collection, reverse transcription, cDNA amplification and purification. Indexed sequencing libraries were constructed according to the manufacturer’s protocol. The sequencing libraries were quantified by Qubit ssDNA Assay Kit (Thermo Fisher Scientific). Libraries were sequenced on the DNBSEQ platform at the China National GeneBank (Shenzhen, China) according to the manufacturer’s protocol.

value: mouse embryonic stem cell line

value: Zbtb16 knockout

value: cardiomyocyte differentiation


title: RNAseq, IMR90, MyoD WT vector, replicate 1

description: Library name: RNAseq_MYOD_wt_rep1

extract_protocol:
For RNA-seq: IMR90 or IMR90/MyoD cells total RNA was extracted using Quick-RNA Microprep KIT (Zymo Research, R1051) following the manufacturer’s recommendation. RNA concentration was measured on Qubit (Invitrogen). For ATAC-seq: IMR90 or IMR90/MyoD cells were freshly collected directly processed for the library preparation. For ChIP-seq: IMR90 or IMR90/MyoD cells were fixed with 1% FA for 10 minutes at RT followed by quenching with glycine (final concentration 200 mM) for 15 minutes on ice. Nuclei were then extracted in hypotonic buffer (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.05% NP-40, 1 mM PMSF and 1x protease inhibitor) and lysed in lysis buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 5 mM EDTA, pH 8.0, 0.5% SDS, 0.5% NP-40, 1 mM PMSF and 1x protease inhibitor and lysed in lysis buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 5 mM EDTA, pH 8.0, 0.5% SDS, 0.5% NP-40, 1 mM PMSF and 1x protease inhibitor). Chromatin was sheared with sonicator (S2 Covaris) to an average DNA fragment length of 200-500bp. 15µg of sonicated chromatin were diluted in 500µl RIPA Dilution Buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, pH 8.0, 0.1% Sodium Deoxycholate, 0.7% NP-40, 1 mM PMSF and 1x protease inhibitor), and precleared for 3 hours at 4°C with Protein A/G dinabeads. In parallel, 10µl of CTCF antibody (CST Cat#3418S), or 1µg of rabbit IgG (Santa Cruz #sc-2027) were prebound to Protein A/G dynabeads in 500µl of PBS containing 5 µg/ml BSA, for 3 hours at 4°C. Beads bound antibody were mixed with precleared chromatin and incubated overnight at 4°C on a rotator. Chromatin bound fraction was washed with RIPA washing buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, pH 8.0, 0.5% Sodium Deoxycholate, 1% NP-40) for 4 times, followed by LiCl washing buffer (10 mM Tris-HCl, pH 8.0, 250 mM LiCl, 1 mM EDTA, pH 8.0, 1% Sodium Deoxycholate, 1% NP-40), and TE buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA), each wash for 10 minutes at 4°C. Chromatin was then eluted in elution buffer (1% SDS in TE buffer) at 65°C for 6 hours 600 RPM rotation. For CUT&RUN: IMR90 or IMR90/MyoD cells or Muscle Stem Cells (MuSCs) were used as input. CUT&RUN experiments were performed using the CUT&RUN Assay Kit (CST #86652) with the following modification: cells were briefly fixed with 0.1% FA for 2 minutes at RT followed by quenching with glycine; antibody binding was performed O/N at 4C. Antibodies used: anti-MYOD (BD Bioscience, #554130), anti-H4K5/K12AcMe, anti-panAcMe, anti-H3K27ac (Active Motif #91193), anti-H3K4me3 (CST #9751), anti-H3K4me1 (Active Motif #39635), anti-H3K27me3 (Active Motif #39155), anti-H3K9me3 (Active Motif #39161). For HiChIP: IMR90 or IMR90/MyoD cells were fixed with 2%FA for 10 minutes at RT followed by quenching with STOP solution1 according to ARIMA HiC+ protocol. Digestion was performed overnight at 37C. Biotinylated enriched fragments were pulled down with anti-H3K27ac (Active Motif #91193) or anti-CTCF (Active Motif #91285). Experiments were performed using the ARIMA HiC+ kit according to manufacturer’s protocol.
For RNA-seq: Equal inputs of total RNA (10-100 ng) were used to generate stranded total RNA libraries for sequencing using the Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus (Illumina #20040525). ERCC RNA Spike-in mix was added at the start of the protocol according to manufacturer’s instruction (Thermo Fisher Scientific #4456740). Libraries were sequenced at a depth of ~50M per library on NOVASeqS4 PE 2x100. For ATAC-seq: Freshly collected cells were subjected to ATAC-seq library preparation using the ATAC-seq Kit (Active Motif #53150) according to manufacturer’s protocol. For ChIP-seq: Precipitated chromatin and 10ng of input were used for library preparation using Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences #21096) according to manufacturer’s protocol. Obtained libraries were sequenced at a depth of ~100M per library on NOVASeqS4 PE 2x100. For CUT&RUN: Libraries have been generated using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB #E7645S) according to manufacturer’s protocol. Libraries were sequenced at a depth of ~20M per library on NOVASeqS4 PE 2x100. For HiChIP: H3K27ac or CTCF enriched material was then used as input for library preparation using Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences  #21096) according to ARIMA HiChIP library preparation protocol. Obtained libraries were sequenced at a depth of ~300M per library on NOVASeqS4 PE 2x100.


title: pre-transfection at 0h, biological rep2


title: OE_HA1

description: Library name: Sample 4


title: pre-transfection at 0h, biological rep3


title: mock transfection at 6h, biological rep1


title: Ctrl

value: WT


title: ERT2_IKZF-WT_IKZF1_rep1


title: ERT2_IKZF-WT_H3K4me3_rep1

value: Drosophila chromatin spike-in


title: RNAseq, IMR90, Empty vector, replicate 2

description: Library name: RNAseq_Empty_rep2

value: Empty


title: ERT2_IKZF-WT_H3K27ac_rep1


title: Bone marrow-derived macrophages, IgG (Ctrl), 24h

city: Wuhan

first: Shi

last: Chen

state: Hubei

address: 1095 Jiefang Avenue, Qiaokou District, Wuhan

institute: Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using HISAT2 v2.1.0 genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to StringTie（V2.1.5） using HISAT2 v2.1.0 genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using HISAT2 v2.1.0 genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Bone marrow-derived macrophages

growth_protocol: Bone marrow was flushed from the tibias and femurs and passed through a 70um cell filter to remove fibrous tissue. Then, red blood cells were lysed with red blood cell lysis buffer. After centrifugation, washing, and resuspension, the bone marrow cells were cultured in Dulbecco's Modified Eagle Medium containing 10% heat-inactivated fetal bovine serum, 100 U/mL penicillin and 100 μg/mL streptomycin, supplemented with 20 ng/mL murine macrophage-colony stimulating factor at 37°C, 5% CO2.

extract_protocol:
According to the manufacturer's recommendations, all libraries were prepared using the TruSeq RNA Sample Preparation Kit (Illumina).
Total RNAs were isolated using the TRIzol reagent, 1.3 ug of total RNA was used for the construction of sequencing libraries.

treatment_protocol: Cells were treated with anti-mouse CD40 mAb (FGK4.5/FGK45) for 24h to activate, and the control groups were treated with IgG (Ctrl).

value: Bone marrow-derived macrophages

tag: strain

value: IgG


title: Bone marrow-derived macrophages, anti-CD40 mAb (FGK45) ,24h

value: anti-CD40 mAb (FGK45)


title: NC_HA2

description: Library name: Sample 2


title: RNAseq, IMR90, Empty vector, replicate 1

description: Library name: RNAseq_Empty_rep1

data_processing:
For RNA-seq: Quality control of the raw data has been performed with FASTQC (v0.11.9), reads were trimmed with Trimmomatic (v0.39) to eliminate low quality bases and adapters (parameters: PE -phred33 ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:2:true MAXINFO:40:0.1 MINLEN:45), and aligned to the hg19 Ensembl (November 2015) version of the human genome with STAR (v 2.7.3a), using a custom genome and index to simultaneously map and quantify ERCC92 spike-in-derived reads (parameters: --runMode alignReads --runThreadN 12 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts). Counts data (from STAR output in column 4, based on library preparation strandedness: second-strand) from all conditions were filtered based on their raw count, keeping genes where the sum of the counts for all samples was higher than 10. Size factors were calculated using the R environment (v4.1.3) package DESeq2 (v1.34.0) estimateSizeFactors function - using the counts related to the spike-in transcripts as control genes, then normalized and logged with the rlog function. DESeq2 was also used to perform Principal Component Analysis (PCA) and differential gene expression analysis (significance threshold: BH FDR<0.05). Differential expression analysis results were visualized with the heatplot function (parameters: method="complete", labRow= FALSE, dend="row", returnSampleTree=F, zlim=c(-5,5)) from the made4 (v1.68.0) package, after expression values from the DESeq2 object were turned into a matrix of Z-scores. Gene Ontology was performed on down- and up-regulated genes separately, using the gene symbols as input in EnrichR, and gene sets repositories GO Biological Processes 2023 and Descartes Cell Types and Tissue 2021. Top10 gene ontology terms shown in figure panels were ordered by pvalue. Gene Ontology bubble plots to summarize top50 gene ontology terms, were generated with the Python (v.3.8.1) GO-Figure script (parameters: -j standard -c log10-pval -e 100 -si 0.5 -s members -g single -n bpo --font_size small -q svg). For ATAC-seq: Quality control of the raw data has been performed with FASTQC (v0.11.9), reads were trimmed with Trimmomatic (v0.39) to eliminate low quality bases and adapters (parameters: PE -phred33 ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:2:true MAXINFO:40:0.1 MINLEN:45), aligned to the hg19 UCSC (January 2016) version of the human genome with Bowtie2 (v2.3.5.1) (parameters: --no-unal --local --very-sensitive-local --no-discordant --no-mixed --dovetail --phred33), sorted and converted into BAM format with the SAMtools sort function. Peak calling was performed with the Macs2 (v2.2.6) callpeak function (parameters: -f BAMPE -g hs -B -q 0.05 --nomodel --shift -100 --extsize 200) and filtered for black-list regions with the BEDtools suite (v2.29.2) intersect (parameters: -v), and sorted with the sort function (parameters: -k8,8nr). Irreproducible Discovery Rate (IDR) was calculated with the idr function (v2.0.3) (parameters: --input-file-type narrowPeak --plot --only-merge-peaks) to retain a single peaks list from each condition. Differential chromatin accessibility analysis was carried out in R, with the DESeq2 package. The R package ChIPQC (v1.30.0), (GetGRanges function was used to import peak lists from each biological replicate, a consensus peak list was calculated for all conditions using the IRanges (v2.28.0),function reduce, keeping peaks that were called in at least two samples. Counts for each peak in each biological replicate were quantified with the Rsubread (v2.8.2) featureCounts function (parameters: isPairedEnd= T, countMultiMappingReads= F, maxFragLength= 100). Counts were normalised and logged with the DESeq2 function rlog; DESeq2 was also used to perform Principal Component Analysis (PCA), and differential chromatin accessibility analysis (significance threshold: BH FDR<0.05). Differentially Accessible Regions (DARs) at gene promoter regions were retrieved with the IRanges function promoters (parameters: TxDb.Hsapiens.UCSC.hg19.knownGene, 1000, 200; mouse genome version was: TxDb.Mmusculus.UCSC.mm10.knownGene). Promoter DARs were visualized with the made4 function heatplot (parameters: method="complete", labRow= FALSE, dend="row", returnSampleTree=F, zlim=c(-5,5)), after expression values from the DESeq2 object were turned into a matrix of Z-scores. Due to R visualization limits, only promoters with |log2FC|>1.5 were plotted. Motif analysis was carried out with the HOMER (v4.11), findMotifsGenome function (parameters: hg19 -size given -nomotif). For ChIP-seq: Quality control of the raw data has been performed with FASTQC (v0.11.9) and aligned to the hg19 UCSC (January 2016) version of the human genome with Bowtie2 (parameters: --very-sensitive-local). Peak calling was performed with the Macs2 callpeak function (parameters: -g hs -B --nomodel --SPMR -q 0.05), using input chromatin as control. For CUT&RUN: Quality control of the raw data has been performed with FASTQC (v0.11.9), reads were trimmed with Trimmomatic (v0.39) to eliminate low quality bases and adapters (parameters: PE -phred33 ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:2:true MAXINFO:40:0.1 MINLEN:45), aligned either to the hg19 UCSC (January 2016) version of the human genome (for the CUT&RUN for histone marks in IMR90 and IMR90/MyoD), or to the mm10 Ensembl (November 2019) version of the mouse genome (for the CUT&RUN of AcMe and MyoD in muSC),  with Bowtie2 (parameters: --phred33 --end-to-end --no-unal --local --very-sensitive-local --no-mixed --no-discordant -I 10 -X 700 –dovetail) and converted to BAM format with the SAMtools (v1.10) function view (parameters: -bS). Peak calling was performed with the Macs2 callpeak function (parameters: -g hs --nomodel --SPMR --call-summits -p 0.05) using input chromatin as control, and filtered for black-list regions with BEDtools intersect (parameters: -v), and sorted with the Unix sort function (parameters: -k8,8nr). Irreproducible Discovery Rate (IDR) was calculated with the idr function (parameters: --input-file-type narrowPeak --plot --only-merge-peaks) to retain a single peaks list from each condition. ChromHMM (v1.24) BinarizeBed function (parameters: -b 200 -peaks) was used to bin the genome in 200bp windows according to each IDR peak list. The BinarizeBed output was used as input to ChromHMM LearnModel (parameters: -b 200 12 hg19), to build a 12 chromatin states model based on the histone marks IDR peaks. Chromatin state numbers were converted to chromatin states names in R, based on the combination of histone marks they were enriched for. For HiChIP: Quality control of the raw data has been performed with FASTQC (v0.11.9). Alignment, filtering, normalization, and loop calling were performed with the Arima version of MAPS (v2.0) bash script (parameters: -C 0 -F 1 -M 1 -H 1 -o hg19 -f 1 -s 5000 -r 2000000 -d 2 -Q 30 -l 1000). Irreproducible Discovery Rate (IDR) was calculated with IDR2D parameters: value transformation= log additive inverse (-log(x)), ambiguity resolution method= overlap, remove non-standard chromosome, max gap= 1000, max factor= 1.5, jitter factor= 0.0001, mu= 0.1, sigma=1, rho=0.2, p=0.5, epsilon=0.001). Differential HiChIP analysis was performed with the DiffAnalysisHiChIP.r script within FitHiChIP (v7.1), and significance threshold was set to p-value<0.05.
Assembly: hg19, mm10
Supplementary files format and content: TXT raw counts files (RNA-seq)
Supplementary files format and content: BEDGRAPH pileup signal tracks, with TBI index (RNA-seq)
Supplementary files format and content: BIGWIG signal tracks (ATAC-seq data, CUT&RUN), also biological replicates average signal tracks
Supplementary files format and content: ARCPLOTS of looping interactions, with TBI index (HiChIP)

value: Fetal lung fibroblasts


title: pooled_input_rep1

value: input

value: preB-ALL


title: NC_HA1

description: Library name: Sample 1