title: Pooled_PBEC_rep3

city: Belfast

first: Clifford

last: Taggart

state: Northern Ireland

address: 97 Lisburn Rd

department: Wellcome-Wolfson Institute for Experimental Medicine

country: United Kingdom

institute: Queen's University Belfast

description: 10x Genomics

data_processing:
bcl2fastq (2.20) was used to demultiplex the sequencing libraries and convert raw BaseCall files from Illumna sequencing data to FASTQ files.
FASTQ files were processed in Cellranger (3.0.2) Count, aligned against GRCh38 reference package with default parameters, generating BAM files and count matrices
BAM files from pooled libraries were demultiplexed into their constituent samples on basis of genetic variants using the Demuxlet package. Each cell was provided a corresponding sample ID associated with their biological sample origin.
Raw and filtered count matrices were processed in SoupX software to minimise ambient mRNA contamination, providing adjusted count matrices for downstream analysis.
SoupX-adjusted count matrices were processed in R using Seurat package, with corresponding sample ID imported to each cell. Basic cell- and gene-QC filtering was employed, followed by the standard Seurat integration and analysis workflow
Assembly: GRCh38
Supplementary files format and content: Comma-separated values count data

source_name: Primary bronchial epithelial cell

extract_protocol:
At 28 day of ALI, the apical compartment of the traswells were washes twice with 250ul of PBS. The cells were then trypsinised before centrifugation at 1600 x rpm for 5 min. Cells were collected into sterile 1 x PBS and viability of all six populations was confirmed by trypan blue staining (Sigma-Aldrich) and found to be at or above 92% viable. Cells from different individuals were pooled into multiplexed cell suspensions and subsequently demultiplexed after sequencing on the basis of genetic variants
Chromium Single Cell 3ʹ v3

value: Primary bronchial epithelial cell

value: COPD

value: 4 weeks


title: Pooled_PBEC_rep2

status: Public on Oct 01 2025

type: SRA

description: 10x Genomics

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: disease state

value: COPD and Healthy

tag: age


title: D0_Mll2-KO_rep1

city: Santander

first: Lucio

last: Di Filippo

state: Cantabria

address: PCTCAN - Cl. Albert Einstein, 22

country: Spain

institute: IBBTEC

description: Library name: Sample 7

library_source: transcriptomic

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools (v1.13)
Reads were trimmed Trim Galore 3.4
Reads were mapped to the mouse  reference assembly (mm10) using STAR 2.7.10a
Reads were quantiﬁed using RSEM 1.3.1
Read count means, fold-change (FC) and p-adj were calculated with DEseq2 v1.34.0
Assembly: mm10
Supplementary files format and content: Tab-delimited .tsv matrix: rows contain gene symbols, columns contain all samples. The values are DESeq2 size-factor normalized counts (no log transform). The header is included.

molecule: polyA RNA

organism: Mus musculus

source_name: Mll2-KO mESC

growth_protocol: mESC were grown on 0.1% gelatin-coated plates, using KnockOutTM DMEM (Thermo Fisher Scientific, 10829018) supplemented with 15% fetal bovine serum (FBS; Thermo Fisher Scientific, A5256801), 1x antibiotic and antimycotic solution (Sigma-Aldrich, A5955), 1x glutaMAX (Thermo Fisher Scientific, 35050038), 1x non-essential amino acids (NEAA; Thermo Fisher Scientific, 11140035), 0.1 mM β-mercaptoethanol (Thermo Fisher Scientific, 21985023) and leukemia inhibitory factor (LIF; made in-house). Cells were maintained at 37 °C with 5% CO2. For the multilineage differentiation, cells were grown on 0.1% gelatin-coated plates, using KnockOutTM DMEM supplemented with 10% FBS, 2 mM L-glutamine (Thermo Fisher Scientific, 25030024), 0.1 nM β-mercaptoethanol, 1x NEAA, 1x antibiotic and antimycotic solution and 1 µM retinoic acid (RA; Sigma-Aldrich, R2625) for 4 days.

extract_protocol:
Total RNA was extracted using the NZY Total RNA Isolation Kit (NZYTech, MB13402), according to the protocol provided by the manufacturer. Libraries were prepared with the RNA sample preparation kit (Truseq stranded mRNA Library).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Starting from a previously described Cre-inducible Mll2-KO mESC line, Mll1-KO mESC were generated via CRISPR editing. Two sg-RNAs were designed flanking the region to-be deleted for each line, using Benchling’s CRISPR tool (https://www.benchling.com/crispr). For each sgRNA, two oligonucleotides were synthesized , annealed and cloned into a CRISPR-Cas9 expression vector (pX330-hCas9-long-chimeric-grna-g2p, provided by Leo Kurian’s lab). mESC were transfected with CRISPR-Cas9 constructs using LipofectamineTM 3000 (Thermo Fisher Scientific, L3000001).  For the generation of Mll2-KO and double-KO mESC lines, cells were treated with (Z)-4-Hydroxytamoxifen (4-OHT; Sigma-Aldrich, H7904) at a final concentration of 800 nM for 48 hours.

value: Mll2-KO mESC

tag: cell type

value: mESC

tag: genotype

tag: treatment

value: 4-OHT treated


title: hSI26,seqRun0

city: Clayton

first: Stuart

middle: Kenneth

last: Archer

state: VIC

address: 15 Innovation Walk, Monash University

department: Monash Bioinformatics Platform

country: Australia

institute: Monash University

description:
Library name: hSI26
gene_counts_IBD_orgs.txt.gz

data_processing:
Reads were de-multiplexed using SABRE version 663365f.
Reads were mapped to the human genome reference, GRCh38.p12, using STAR v2.7.2b, and aliments sorted using SAMtools v1.9.
Positional puplicate alignments were marked using Picard MarkDuplicates v2.18.9. UMIs of positional duplicates were analysed with Je markdupes version 2.0RC and true duplicates were flagged.
Non-duplicate alignments within gene features were counted using FeatureCounts in Rsubread version 1.6.1 resulting in a gene-count matrix.
Assembly: GRCh38.p12
Supplementary files format and content: tab-separated values. Table of unique read counts per gene, columns as samples, genes as rows.

source_name: Duodenum

growth_protocol: Biopsy samples were collected for organoid and bacterial culturing from control patients and patients newly diagnosed with IBD. Organoids were grown as described in: Engel RM, Jardé T, Oliva K, Kerr G, Chan WH, Hlavca S, et al. Modeling colorectal cancer: A bio-resource of 50 patient-derived organoid lines. J Gastroenterol Hepatol. 2022;37(5):898-907.

extract_protocol:
Total RNA was isolated using the RNeasy Micro Kit (Qiagen, #74004) and assessed for quality using the Bioanalyzer (Agilent) and Qubit (Invitrogen).
Novel MHTP pooled RNA-Seq pipeline (Version 03/04/2018) for generating Illumina-compatible libraries. All samples were processed starting with 20 ng of total RNA respectively, quantitated by Qubit. Libraries were made by individual first strand synthesis with an indexed pA primer to add the index sequence, then cDNA of all samples in a sequencing run were pooled for subsequent processing. Pooled samples were amplified using a template switching oligo. P5 is added by PCR and P7 by Nextera transposase. I7 indexes were added to the final libraries to enable parsing of sample sets. Library is designed so custom R1 primer reads directly into index followed by 10bp UMI. R2 primer reads into RNA in the sense direction.

treatment_protocol: For microinjections, glass capillaries were pulled to a fine point with a 5 - 10 μm opening and loaded with 4 kDa fluorescein isothiocyanate (FITC)- dextran, with or without bacterial sample, or 40 kda FITC-dextran in 1X PBS for microinjection into cystic organoids. All microinjections were carried out under a Zeiss SteREO Discovery V8 microscope using the Injectman 4 Micromanipulator coupled with FemtoJet 4i system (Eppendorf). Injection parameters were set at 120 hPa (injection pressure), 0.25 seconds (injection time) and 0 hPa (compensation pressure). Microinjected bacterial strains included the two closely related Bacteroidaceae isolates E4 (CC01454; from a healthy patient) and E2 (CC01453; from a Crohn's patient with inflammation). They also included the two closely related Enterobacteriaceae isolates B2 (CC00517; from healthy patient) and G11 (CC00518; from an ulcerative colitis patient with inflammation).

tag: tissue

value: Duodenum

value: organoids

tag: patient id

value: none,Non Inflammed

tag: batch


title: D0_WT_rep3

description: Library name: Sample 3

source_name: WT mESC

value: WT mESC

value: WT

value: Untreated


title: hSI25,seqRun0

description:
Library name: hSI25
gene_counts_IBD_orgs.txt.gz

value: Crohns,Inflammed


title: hESC cells, TUBBP2 KO, Hi-C rep2

city: Beijing

first: Liu

last: He

address: No. 5, Dongdan Sanjo, Dongcheng District

country: China

institute: Peking Union Medical College

library_source: genomic

data_processing:
Clean reads from different libraries of the same sample were first merged by Linux command cat. Then the merged reads were mapped to human genome hg19 using bwa mem with parameters ‘-A 1 -B 4 -E 50 -L 0’
The HiCExplorer(v3.4.3) was used for the processing of valid mapped Hi-C reads. Mapped reads were used to generate raw Hi-C matrices using hicBuildMatrix with parameter ‘--binSize 5000’ , then the matrices were corrected using hicCorrectMatrix with parameter ‘--filterThreshold -3 3’ . We also converted matrices into .hic format files with hicConvertFormat subcommand and used these .hic files for heat map visualization.
For TAD analysis, hicFindTADs subcommand was used to calculate the TAD separation scores at 40 kb resolution using parameters ’--minDepth 300000 --maxDepth 3000000 --step 300000 --minBoundaryDistance 400000 --correctForMultipleTesting fdr --delta 0.01’. Insulation scores and TAD boundary strengths were calculated by FanC(v0.9.24) with parameter -w 1mb
For compartment and loop analysis, HOMER software was used for the processing of valid mapped Hi-C reads. We first removed PCR duplicates from aligned reads with ‘-tbp 1’ of makeTagDirectory subcommand. Then analyzeHiC subcommand was used to make interaction matrices and normalize interaction counts with parameters ‘-res 10000 -window 15000 -balance’ .We also transformed the matrices to .bedpe file format for loop analysis. Compartment analysis was performed by runHiCpca.pl script with parameters ‘-res 100000 -superRes 200000’ .
We used cLoops2(v0.0.3) to achieve loop analysis. Calling loops was performed using callLoops command with parameters ‘-eps 2000,5000,10000 -minPts 20,50’. Then callDiffLoops subcommand was used to Call differentially enriched intra-chromosomal loops(absolute scaled fold change of PETs > 1 and poissonPvalue<0.05).
Assembly: h19
Supplementary files format and content: .h5 files for corrected Hi-C matrics in 10kb resolution.

molecule: genomic DNA

source_name: hESC

extract_protocol:
1) Lyse cells by grinding and lysing in an ice bath of lysate to obtain nuclei samples; 2) Restriction enzyme (DpnII) digestion was followed to break the original genomic DNA structure to form a molecular group in units of "protein-DNA cross-linking complex"; 3) Cleave the cleavage site using dNTP-labeled repair enzymes with biotin labeling; 4) Using DNA ligase treatment, the flat ends of DNA molecules on the same "protein-DNA crosslinking complex" were connected to each other, so that the DNA fragment reconstructs the structure based on spatial location to form Hi-C molecules. The junction of the reconstituted molecule would be marked with biotin; 5) Protease 65°C high temperature treatment, unlink protein cross-linking and release DNA, and then use phenolic chloroform extraction to obtain Hi-C characteristic DNA molecules;
6) Remove unsuccessfully ligated DNA fragment ends using T4 DNA polymerase exonuclease activity to eliminate residual biotin labeling. 7) Fragmented DNA molecules were interrupted using ultrasound, followed by terminal repair, A-tail ligation, streptavidin-activated magnetic beads to retrieve biotin marker molecules, sequencing linker ligation, PCR enrichment for library preparation, and finally recovered the fragments of interest using AMPure XP beads or agarose gel electrophoresis to obtain the final Hi-C library.

value: hESC

value: TUBBP2 KO


title: Normal_1_3_1_1

city: Guangzhou

first: Lin

last: Li

address: Shatai South Road

department: Pathophysiology

institute: Southern Medical University

description: Sample 321

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
For bisulfite-seq data, Trim Galore (v0.3.3) was used to remove the first 6 bases of random primer, adaptor sequences and low quality bases; for RNA-seq data, each single cell was separated by unique cell barcode, then template switch oligo (TSO), ployA tails, adaptors and low quality bases were removed.
For bisulfite-seq data, clean reads were first mapped to human reference genome hg19 with Bismark (v0.7.6) in paired-end and non-directional module, and then the unmapped reads were realigned to the same reference genome in single-end and non-directional module; for RNA-seq data, clean reads were mapped to human genome hg19 with Tophat (v2.0.14), and then unique UMI counts were calculated by HTSeq.
WCG and GCH methylation level of cytosines was estimated using comstomized scripts.
Genome_build: hg19
Supplementary_files_format_and_content: UMI_count.txt files include UMI counts of RefSeq genes. While WCG.txt and GCH.txt files include the read counts of cytosines in WCG and GCH context respectively. The columns in WCG.txt or GCH.txt files represent "chr" "position" "unmethylated read counts" "methylated read counts".

source_name: testis

extract_protocol:
An individual cell was picked into the cell lysis buffer with vitro methylation (IVM) mixture containing 4 U RNase inhibitor (TAKARA, Cat. 2313B), 0.25% IGEPAL CA-630 (SIGMA, Cat. I3021), 1X GC reaction buffer and 2 U M. CviPI (NEB, Cat. M0227L). After gently vortexed for 10 sec, the cell lysate was incubated at 37 °C for 20 min and then at 65 °C for 25 min. Then, the cell lysate could be directly processed for RNA/DNA separation or stored at -80 °C.
For RNA part, a modified Smart-seq2 protocol was applied for single-cell RNA-seq. For DNA part, Bisulfite-converted DNA was amplified with biotinylated random primer and klenow exo– polymerase (NEB, M0212L) for 7 rounds and excess primer was removed by exonuclease I (NEB, M0293L). After second strands synthesis, the library was amplified by KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602) for 14 cycles.

tag: gender

value: male

tag: condition

value: Normal

tag: testis

value: testis


title: Pooled_PBEC_rep1

description: 10x Genomics

value: Primary bronchial epithelial cell

value: 4 weeks


title: D0_Mll1-KO_rep1

description: Library name: Sample 4

source_name: Mll1-KO mESC

value: Mll1-KO mESC


title: hSI27,seqRun0

description:
Library name: hSI27
gene_counts_IBD_orgs.txt.gz


title: hSI24,seqRun0

description:
Library name: hSI24
gene_counts_IBD_orgs.txt.gz

value: Crohns,Non Inflammed


title: Normal_1_2_9_4

description: Sample 318


title: Normal_1_2_9_3

description: Sample 317


title: hSI23,seqRun0

description:
Library name: hSI23
gene_counts_IBD_orgs.txt.gz


title: Normal_1_2_9_2

description: Sample 316


title: Normal_1_2_9_6

description: Sample 320


title: Normal_1_3_1_3

description: Sample 323


title: Pooled_PBEC_rep4

description: 10x Genomics

value: Healthy


title: hESC cells, TUBBP2 KO, Hi-C rep1


title: D0_WT_rep1

description: Library name: Sample 1

value: mESC


title: hSI22,seqRun0

description:
Library name: hSI22
gene_counts_IBD_orgs.txt.gz

value: Duodenum

value: organoids


title: D0_WT_rep2

description: Library name: Sample 2

value: WT mESC


title: hESC cells, WT, Hi-C, rep2

value: WT


title: Normal_1_2_8_8

description: Sample 315


title: Normal_1_2_8_7

description: Sample 314


title: hESC cells, WT, Hi-C, rep1


title: D4_double-KO_H3K27me3_repA

description: Library name: Sample 84

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and MultiQC. The removal of read adapters and low-quality filtering was done with trimgalore(v0.6.7).
Reads were mapped to the mm10 reference genome with STAR v2.6.1d (--outSAMtype BAM Unsorted --runMode alignReads --outFilterMultimapNmax 5000 --outSAMmultNmax 1 --outFilterMismatchNmax 3 --outMultimapperOrder Random --winAnchorMultimapNmax 5000 --alignEndsType EndToEnd --alignIntronMax 1 --alignMatesGapMax 350 --seedSearchStartLmax 30 --alignTranscriptsPerReadNmax 30000 --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000 --readFilesCommand zcat).
Duplicate reads were marked with picard tool (3.1.1)
Bigwig files were generated with deepTools v3.5.1 using bamCoverage (--normalizeUsing 'RPGC').
Assembly: mm10

source_name: Double-KO differentiated cells

extract_protocol:
Approximately 10 million and 40 million cells were used for histone PTMs and COMPASS subunits ChIPs, respectively.  For histone modification ChIP assays, cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature (RT) before being quenched with 0.125 M glycine for another 10 minutes, while for COMPASS subunits ChIP assays cells were double crosslinked with ChIP cross-link Gold (Diagenode, C01019027) and 1% formaldehyde according to the manufactor’s instructions. Chromatin was isolated through sequential incubation with three distinct lysis buffers: LB1 (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100), LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), and LB3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine). Chromatin sonication was carried out in LB3 using an EpiShearTM sonicator (Active Motif; 4-5 minutes, 20 seconds ON and 30 seconds OFF at 25% amplitude). The sheared chromatin was then incubated O/N at 4 °C with either 5 or 10 μg of antibody for histone PTMs or COMPASS subunits respectively.
DNA libraries were prepared using the TruSeq ChIP-seq sample preparation kit. 10 ng of ChIP DNA was used as starting material.

value: Double-KO differentiated cells

value: Differentiated cells

value: Double-KO

value: H3K27me3 antibody (Active Motif, 39155)


title: hESC cells, KRT18P37 KO rep2

data_processing:
Reads were mapped to human genome version hg19 by STAR(v2.4.0j) with default settings
Uniquely aligned reads were then quantified using featureCounts(v1.6.3) with parameter ‘-s 2’
Normalization and differential expression analysis were performed using DESeq2(v1.26.0)
Differential expression genes were defined as those with large expression changes (absolute log2 fold change>1) and statistically significant (adjusted p value<0.05)
Assembly: hg19
Supplementary files format and content: .txt files of raw counts for RNA-seq

extract_protocol:
hESC was digested into single-cell using accutase and centrifuged at 1000 r.p.m. for 5 min. 1mL Trizol was added to mix the cell pellets, and 200μL chloroform was added for shaking violently. After centrifuging at 12000 r.p.m., 4 ° C for 15min, the upper water phase was absorbed, and added with equal volume isopropyl alcohol. RNA was precipitated by centrifugation at 12000 r.p.m., 4 ° C for 15min and cleaned with 75% ethanol then dissolved in RNase-free water. RNA concentration was measured using nanodrop.
Stranded sequencing library preparation by VAHTS Universal V6 RNA-seq Library Prep Kit for  Illumina(NR604-01/02) according to manufacturer's instructions.

value: hESC

value: KRT18P37  knockout


title: Normal_1_2_8_6

description: Sample 313

value: male

value: Normal

value: testis


title: hSI07,seqRun0

description:
Library name: hSI07
gene_counts_IBD_orgs.txt.gz

value: Crohns,Inflammed


title: hSI08,seqRun0

description:
Library name: hSI08
gene_counts_IBD_orgs.txt.gz

value: Crohns,Non Inflammed


title: hESC cells, KRT18P37 KO rep1

value: KRT18P37 knockout


title: hSI60, E2_Exposed, rep3, seqRun2

description:
Library name: hSI60_E2_Exposed_k1_R2
unfilt_gene_counts_210125.tsv

source_name: Terminal Ileum

treatment_protocol: For microinjections, glass capillaries were pulled to a fine point with a 5 - 10 μm opening and loaded with 4 kDa fluorescein isothiocyanate (FITC)- dextran, with or without bacterial sample, or 40 kda FITC-dextran in 1X PBS for microinjection into cystic organoids. All microinjections were carried out under a Zeiss SteREO Discovery V8 microscope using the Injectman 4 Micromanipulator coupled with FemtoJet 4i system (Eppendorf). Injection parameters were set at 120 hPa (injection pressure), 0.25 seconds (injection time) and 0 hPa (compensation pressure).

value: Terminal Ileum

value: none,Non Inflammed


title: D4_double-KO_H3K27ac_repB

description: Library name: Sample 83

value: H3K27ac antibody (Active Motif, 39133)


title: Normal_1_2_8_4

description: Sample 311


title: D4_double-KO_H3K27ac_repA

description: Library name: Sample 82


title: hSI60, mock_injected, rep6, seqRun2

description:
Library name: hSI60_none_Mock_k1_R2
unfilt_gene_counts_210125.tsv

value: organoids


title: hESC cells,WT-KRT18P37 rep2

value: WT


title: hSI60, E2_Injected, rep3, seqRun2

description:
Library name: hSI60_E2_Injected_k1_R2
unfilt_gene_counts_210125.tsv


title: D4_double-KO_H3K4me3_repB

description: Library name: Sample 81

value: Double-KO differentiated cells

value: H3K3me3 antibdy (Active Motif, 39159)


title: hESC cells, WT-KRT18P37 rep1


title: hSI60, mock_injected, rep5, seqRun2

description:
Library name: hSI60_none_Mock_j2_R2
unfilt_gene_counts_210125.tsv


title: hSI60, E2_Exposed, rep2, seqRun2

description:
Library name: hSI60_E2_Exposed_j2_R2
unfilt_gene_counts_210125.tsv


title: Normal_1_2_8_3

description: Sample 310


title: hESC cells, ALOX KO rep1

value: ALOX knockout


title: Normal_1_2_7_8

description: Sample 307


title: hESC cells, ALOX KO rep2


title: Normal_1_2_8_2

description: Sample 309


title: D4_double-KO_H3K4me3_repA

description: Library name: Sample 80

value: Differentiated cells

value: Double-KO


title: Normal_1_2_8_1

description: Sample 308


title: D4_double-KO_H3K27me3_repB

description: Library name: Sample 85

value: H3K27me3 antibody (Active Motif, 39155)


title: D4_double-KO_H3K4me2_repA

description: Library name: Sample 78

value: H3K4me2 antibody (Active Motif, 39141)


title: D4_double-KO_H3K4me2_repB

description: Library name: Sample 79


title: hESC cells, TUBBP2 KO rep2

value: hESC

value: TUBBP2 knockout


title: hSI60, E2_Injected, rep2, seqRun2

description:
Library name: hSI60_E2_Injected_j2_R2
unfilt_gene_counts_210125.tsv


title: D4_double-KO_input

description: Library name: Sample 77


title: Normal_1_2_8_5

description: Sample 312

value: male

value: Normal

value: testis


title: D4_WT_H3K27me3_repB

description: Library name: Sample 76

source_name: WT differentiated cells

value: WT differentiated cells


title: hSI60, mock_injected, rep4, seqRun2

description:
Library name: hSI60_none_Mock_j1_R2
unfilt_gene_counts_210125.tsv

value: Terminal Ileum

value: none,Non Inflammed


title: hESC cells, TUBBP2 KO rep1


title: Normal_1_2_7_6

description: Sample 305


title: Normal_1_2_7_7

description: Sample 306


title: hSI60, E2_Exposed, rep1, seqRun2

description:
Library name: hSI60_E2_Exposed_j1_R2
unfilt_gene_counts_210125.tsv

value: organoids


title: hESC cells, WT rep2

value: WT


title: hSI60, E2_Injected, rep1, seqRun2

description:
Library name: hSI60_E2_Injected_j1_R2
unfilt_gene_counts_210125.tsv


title: Normal_1_2_7_5

description: Sample 304


title: hESC cells, WT rep1


title: D4_WT_H3K27ac_repB

description: Library name: Sample 74

value: H3K27ac antibody (Active Motif, 39133)


title: Normal_1_2_7_4

description: Sample 303


title: hSI60, mock_injected, rep3, seqRun2

description:
Library name: hSI60_none_Mock_l2_R2
unfilt_gene_counts_210125.tsv


title: Normal_1_2_7_3

description: Sample 302


title: hSI60, E4_Exposed, rep3, seqRun2

description:
Library name: hSI60_E4_Exposed_l2_R2
unfilt_gene_counts_210125.tsv


title: hESC cells, TUBBP2 KO, input rep2

data_processing:
Clean reads were mapped to human genome version hg19 by bowtie2(v2.2.9) with default settings.
All samples’ sequence depth were scaled to 1 million reads using bamCoverage subcommand of deeptools for visualization.
Uniquely aligned reads were used to call peaks by callpeak subcommand of MACS2(v2.2.6) with a P value ≤ 1 × 10−6 for significant peaks.
Assembly: h19
Supplementary files format and content: BigWig files were generated with the total read normaized to 1 million reads for 20-bp bins.

extract_protocol:
Cells cultured in 10cm dishes were crosslinked in 1% formaldehyde for 15 minutes at room temperature. Crosslinking was quenched with 125 mM glycine. The cells were precipitated with centrifugation at 1000 r.p.m. for 10 minutes and washed with PBS. The pellet was lysed in ChIP buffer 1 (50mM HEPES (Abcam), 140mM NaCl, 1mM EDTA (Invitrogen), 10% Glycerol (Solarbio), 0.5% Igepal (Sigma), 0.5% Triton X-100 and Phenylmethylsulfonyl fluoride (PMSF, Roche)), rotated at 4℃ for 30 minutes and centrifuged at 800g for 10 minutes. The pellet was resuspended in ChIP buffer 2 (200mM NaCl, 1mM EDTA, 0.5mM EGTA, 10mM Tris-HCl (PH 8.0) and PMSF), rotated at 4℃ for 30 minutes and centrifuged at 800g for 10 minutes. Then 200 µl sonication buffer (50mM HEPES, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate (Shanghai Chemical Reagent Factory), 0.3% SDS (Invitrogen) and 1×protease inhibitor cocktail (APE×BIO)) was used to resuspend the pellet and the mixture was sonicated for 13 cycles. The chromatin solution was centrifuged at 4℃ in 10000g for 10 minutes to transfer the supernatant to a new centrifuge tube. 10% of the chromatin solution was saved as an input control, half of the remaining solution was incubated with CTCF antibody (Abcam) and half was incubated with IgG antibody (Abcam). The chromatin solution was rotated at 4℃ overnight with corresponding antibody and protein A/G beads (ThermoFisher) . The next day the sample was taken out and placed on the magnetic adsorption rack (DynaMag™-2 magnet, Thermo Fisher) to remove the supernatant. Then the following four solutions are used successively to clean the chromatin-beads complexes, low-salt solution (0.1% SDS, 1% Triton-X 100, 2mM EDTA, 20mM Tris-HCl (PH 8.0), 150mM NaCl), high-salt solution (0.1% SDS, 1% Triton-X 100, 2mM EDTA, 20mM Tris-HCl (PH 8.0), 500mM NaCl), LiCl solution (250mM LiCl (Sigma), 1% NP40 (ThermoFisher), 1mM EDTA, 10mM Tris-HCl (PH 8.0), 1% sodium deoxycholate), TE buffer (10mM Tris-HCl (PH 8.0), 1mM EDTA). The cleaned sample was eluted with solution (1% SDS, 0.1M NaHCO3 (Sinopharm Chemical Reagent Co.,Ltd.), 0.1mg/ml RNaseA (NEB)) at 37℃ in 1200 r.p.m. for 30 minutes on shaker. Then protease K (1mg/ml, Promega) was added to the input, IP and IgG groups respectively followed by digestion at 50℃ for 45 minutes. DNA was extracted with phenol–chloroform, precipitated with 1/10 volume of 3M sodium acetate (ThermoFisher) and 2.5 volumes of 100% ethanol, dissolved in ddH2O, and stored at -20℃.
extracted DNA was first interrupted by ultrasound into 150-500 bp. After end repair and A-Tailing, PE adapter was ligated.After 2% agarose fragment screening, PCR amplification to obtain the ChIP final library.

value: TUBBP2 KO


title: Normal_1_2_7_2

description: Sample 301


title: hESC cells, TUBBP2 KO, CTCF, ChIP rep2

tag: antibody

value: CTCF


title: D4_WT_H3K27ac_repA

description: Library name: Sample 73

value: Differentiated cells


title: hSI60, E4_Injected, rep3, seqRun2

description:
Library name: hSI60_E4_Injected_l2_R2
unfilt_gene_counts_210125.tsv


title: D4_WT_H3K4me3_repA

description: Library name: Sample 71

value: H3K3me3 antibdy (Active Motif, 39159)


title: Normal_1_2_6_8

description: Sample 300


title: hSI60, mock_injected, rep2, seqRun2

description:
Library name: hSI60_none_Mock_l1_R2
unfilt_gene_counts_210125.tsv


title: D4_WT_H3K4me2_repB

description: Library name: Sample 70


title: hESC cells, TUBBP2 KO, input rep1


title: Normal_1_2_6_7

description: Sample 299


title: D4_WT_H3K27me3_repA

description: Library name: Sample 75

value: H3K27me3 antibody (Active Motif, 39155)


title: D4_WT_H3K4me3_repB

description: Library name: Sample 72


title: hESC cells, WT, CTCF, ChIP rep2


title: D4_WT_H3K4me2_repA

description: Library name: Sample 69

value: H3K4me2 antibody (Active Motif, 39141)


title: hSI60, E4_Exposed, rep2, seqRun2

description:
Library name: hSI60_E4_Exposed_l1_R2
unfilt_gene_counts_210125.tsv


title: hSI60, E4_Injected, rep2, seqRun2

description:
Library name: hSI60_E4_Injected_l1_R2
unfilt_gene_counts_210125.tsv


title: D4_WT_RBBP5_repB

description: Library name: Sample 68

value: RBBP5 antibody (Diagenode, C15410342)


title: hESC cells, WT, input rep2

value: hESC


title: hSI60, mock_injected, rep1, seqRun2

description:
Library name: hSI60_none_Mock_k2_R2
unfilt_gene_counts_210125.tsv


title: Normal_1_2_6_5

description: Sample 297

value: male


title: hSI60, E4_Exposed, rep1, seqRun2

description:
Library name: hSI60_E4_Exposed_k2_R2
unfilt_gene_counts_210125.tsv


title: D4_WT_MLL2_repB

description: Library name: Sample 66

value: GFP antibody (Invitrogen, A11122)


title: hESC cells, WT, input rep1


title: Normal_1_2_6_4

description: Sample 296

value: Normal

value: testis


title: Normal_1_2_6_3

description: Sample 295


title: hESC cells, WT, CTCF, ChIP rep1


title: Normal_1_2_6_6

description: Sample 298


title: D4_WT_RBBP5_repA

description: Library name: Sample 67

value: WT differentiated cells


title: hESC cells,TUBBP2 KO, CTCF, ChIP rep1


title: D4_WT_MLL2_repA

description: Library name: Sample 65


title: SAM24427910_T-47D parental

city: South San Francisco

first: Marc

last: Hafner

state: CA

address: Building 45-1, 1 DNA Way

department: Oncology Bioinformatics

country: USA

institute: Genentech

data_processing:
RNA-Seq reads were first aligned to ribosomal RNA sequences to remove ribosomal reads
remaining reads were aligned to the human reference genome (GRCh38) using GSNAP version 2013-11-1, allowing a maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 —pairmax-rna=200000—clip-overlap)
To quantify gene expression levels, the number of reads mapped to the exons of each RefSeq gene was calculated.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file that include gene counts for each sample

source_name: Breast

growth_protocol: Cells were grown in RPMI (10% serum), and then treated as annotated for 24 hours

extract_protocol:
RNA was extracted using Qiagen RNeasy Plus Mini kit (Cat. No. 74034),
For sequencing library generation, the Truseq Stranded mRNA kit (Illumina) was used with an input of 100-1000 nanograms of total RNA. Libraries were quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and the average library size was determined using D1000 ScreenTape on TapeStation 4200 (Agilent Technologies). Libraries were pooled and sequenced on NovaSeq 6000 (Illumina) to generate 30 million single-end 50-base pair reads for each sample.

value: Breast

value: T-47D parental

value: Epithelial cell

value: DMSO


title: hSI25, mock_injected, rep6, seqRun2

description:
Library name: hSI25_none_Mock_h1_R2
unfilt_gene_counts_210125.tsv

value: Terminal Ileum

value: organoids

value: Crohns,Inflammed


title: hSI60, E4_Injected, rep1, seqRun2

description:
Library name: hSI60_E4_Injected_k2_R2
unfilt_gene_counts_210125.tsv

value: none,Non Inflammed


title: SAM24427911_T-47D parental


title: D4_WT_input

description: Library name: Sample 64

value: Differentiated cells

value: WT


title: D0_double-KO_RING1B_repB

description: Library name: Sample 63

source_name: Double-KO mESC

value: Double-KO mESC

value: mESC

value: Double-KO

value: RING1B antibody (Cell Signalling, 5694)


title: hSI25, E2_Injected, rep3, seqRun2

description:
Library name: hSI25_E2_Injected_h1_R2
unfilt_gene_counts_210125.tsv


title: Normal_1_2_5_7

description: Sample 292

value: male

value: Normal


title: SAM24427912_T-47D parental


title: Normal_1_2_5_6

description: Sample 291

value: testis


title: SAM24427913_T-47D parental

value: Breast

value: 1uM ARV-471


title: hSI25, mock_injected, rep5, seqRun2

description:
Library name: hSI25_none_Mock_g2_R2
unfilt_gene_counts_210125.tsv


title: D0_double-KO_H3K9me3_repB

description: Library name: Sample 61

value: H3K9me3 antibody (Active Motif, 61014)


title: D0_double-KO_RING1B_repA

description: Library name: Sample 62


title: hSI25, E2_Exposed, rep2, seqRun2

description:
Library name: hSI25_E2_Exposed_g2_R2
unfilt_gene_counts_210125.tsv


title: SAM24427909_T-47D parental

value: T-47D parental

value: Epithelial cell

value: DMSO


title: Normal_1_2_5_4

description: Sample 289


title: D0_double-KO_H3K9me3_repA

description: Library name: Sample 60


title: SAM24427914_T-47D parental


title: hSI25, E2_Injected, rep2, seqRun2

description:
Library name: hSI25_E2_Injected_g2_R2
unfilt_gene_counts_210125.tsv

value: Terminal Ileum

value: organoids

value: Crohns,Inflammed


title: hSI25, mock_injected, rep4, seqRun2

description:
Library name: hSI25_none_Mock_g1_R2
unfilt_gene_counts_210125.tsv


title: Normal_1_2_6_1

description: Sample 293


title: SAM24427916_T-47D parental


title: hSI25, E2_Exposed, rep3, seqRun2

description:
Library name: hSI25_E2_Exposed_h1_R2
unfilt_gene_counts_210125.tsv


title: SAM24427915_T-47D parental


title: Normal_1_2_5_2

description: Sample 287


title: hSI25, E2_Exposed, rep1, seqRun2

description:
Library name: hSI25_E2_Exposed_g1_R2
unfilt_gene_counts_210125.tsv


title: SAM24427917_T-47D parental


title: D0_double-KO_H3K27ac_repB

description: Library name: Sample 57

value: H3K27ac antibody (Active Motif, 39133)


title: Normal_1_2_6_2

description: Sample 294


title: hSI25, E2_Injected, rep1, seqRun2

description:
Library name: hSI25_E2_Injected_g1_R2
unfilt_gene_counts_210125.tsv


title: Normal_1_2_5_3

description: Sample 288


title: D0_double-KO_H3K27me3_repB

description: Library name: Sample 59

value: Double-KO mESC

value: H3K27me3 antibody (Active Motif, 39155)


title: D0_double-KO_H3K27me3_repA

description: Library name: Sample 58

value: mESC

value: Double-KO


title: SAM24427918_T-47D parental


title: Normal_1_2_4_1

description: Sample 285

value: male


title: SAM24427919_T-47D parental


title: Normal_1_2_4_3

description: Sample 286

value: Normal


title: D0_double-KO_H3K4me3_repB

description: Library name: Sample 55

value: H3K3me3 antibdy (Active Motif, 39159)


title: Normal_1_2_5_5

description: Sample 290

value: testis


title: D0_double-KO_H3K27ac_repA

description: Library name: Sample 56


title: hSI25, E4_Exposed, rep3, seqRun2

description:
Library name: hSI25_E4_Exposed_i2_R2
unfilt_gene_counts_210125.tsv


title: Normal_1_2_3_6

description: Sample 283


title: D0_double-KO_H3K4me3_repA

description: Library name: Sample 54


title: hSI25, E4_Injected, rep3, seqRun2

description:
Library name: hSI25_E4_Injected_i2_R2
unfilt_gene_counts_210125.tsv


title: D0_double-KO_H3K4me2_repB

description: Library name: Sample 53

value: H3K4me2 antibody (Active Motif, 39141)


title: Normal_1_2_3_5

description: Sample 282


title: SAM24427921_T-47D parental

value: Breast

value: 1uM AZD9833


title: SAM24427922_T-47D parental

value: T-47D parental

value: Epithelial cell


title: Normal_1_2_3_4

description: Sample 281


title: SAM24427923_T-47D.D538G

value: DMSO


title: hSI25, E4_Injected, rep2, seqRun2

description:
Library name: hSI25_E4_Injected_i1_R2
unfilt_gene_counts_210125.tsv

value: Terminal Ileum

value: organoids


title: hSI25, E4_Exposed, rep2, seqRun2

description:
Library name: hSI25_E4_Exposed_i1_R2
unfilt_gene_counts_210125.tsv

value: Crohns,Inflammed


title: D0_double-KO_H3K4me1_repA

description: Library name: Sample 50

value: Double-KO mESC

value: H3K4me1 antibody (Active Motif, 39297)


title: SAM24427924_T-47D.D538G


title: D0_double-KO_H3K4me1_repB

description: Library name: Sample 51

value: mESC


title: SAM24427925_T-47D.D538G


title: Normal_1_2_3_1

description: Sample 279


title: hSI25, mock_injected, rep3, seqRun2

description:
Library name: hSI25_none_Mock_i2_R2
unfilt_gene_counts_210125.tsv


title: Normal_1_2_3_3

description: Sample 280


title: Normal_1_2_2_4

description: Sample 278


title: SAM24427920_T-47D parental


title: hSI25, mock_injected, rep1, seqRun2

description:
Library name: hSI25_none_Mock_h2_R2
unfilt_gene_counts_210125.tsv


title: SAM24427926_T-47D.D538G


title: Normal_1_2_3_8

description: Sample 284


title: D0_double-KO_RBBP5_repA

description: Library name: Sample 48

value: Double-KO

value: RBBP5 antibody (Diagenode, C15410342)


title: SAM24427927_T-47D.D538G

value: 1uM ARV-471


title: Normal_1_2_2_1

description: Sample 277

value: male

value: Normal


title: D0_double-KO_H3K4me2_repA

description: Library name: Sample 52

value: H3K4me2 antibody (Active Motif, 39141)


title: hSI25, mock_injected, rep2, seqRun2

description:
Library name: hSI25_none_Mock_i1_R2
unfilt_gene_counts_210125.tsv


title: D0_double-KO_input_histmod_RBBP5

description: Library name: Sample 47


title: hSI27, G11_Exposed, rep3, seqRun1

description:
Library name: hSI27_G11_Exposed_c2_R1
unfilt_gene_counts_210125.tsv

value: none,Non Inflammed


title: SAM24427928_T-47D.D538G

value: Breast


title: Normal_1_2_12_8

description: Sample 276

value: testis


title: Normal_1_2_12_7

description: Sample 275


title: D0_Mll2-KO_H3K27me3_repB

description: Library name: Sample 46

value: Mll2-KO mESC

value: H3K27me3 antibody (Active Motif, 39155)


title: hSI27, G11_Injected, rep3, seqRun1

description:
Library name: hSI27_G11_Injected_c2_R1
unfilt_gene_counts_210125.tsv

value: Terminal Ileum


title: Normal_1_2_12_6

description: Sample 274


title: SAM24427929_T-47D.D538G

value: Epithelial cell


title: SAM24427930_T-47D.D538G


title: D0_double-KO_RBBP5_repB

description: Library name: Sample 49


title: SAM24427931_T-47D.D538G


title: D0_Mll2-KO_H3K27ac_repB

description: Library name: Sample 44

value: H3K27ac antibody (Active Motif, 39133)


title: hSI27, mock_injected, rep6, seqRun1

description:
Library name: hSI27_none_Mock_c2_R1
unfilt_gene_counts_210125.tsv

value: organoids


title: hSI25, E4_Exposed, rep1, seqRun2

description:
Library name: hSI25_E4_Exposed_h2_R2
unfilt_gene_counts_210125.tsv

value: Crohns,Inflammed


title: Normal_1_2_12_4

description: Sample 272


title: D0_Mll2-KO_H3K27me3_repA

description: Library name: Sample 45

value: mESC


title: SAM24427932_T-47D.D538G


title: Normal_1_2_12_5

description: Sample 273


title: hSI27, G11_Injected, rep2, seqRun1

description:
Library name: hSI27_G11_Injected_c1_R1
unfilt_gene_counts_210125.tsv


title: D0_Mll2-KO_H3K4me3_repB

description: Library name: Sample 42

value: H3K3me3 antibdy (Active Motif, 39159)


title: Normal_1_2_12_3

description: Sample 271


title: hSI27, G11_Exposed, rep2, seqRun1

description:
Library name: hSI27_G11_Exposed_c1_R1
unfilt_gene_counts_210125.tsv


title: D0_Mll2-KO_H3K27ac_repA

description: Library name: Sample 43


title: D0_Mll2-KO_H3K4me3_repA

description: Library name: Sample 41


title: Normal_1_2_12_1

description: Sample 270


title: hSI27, mock_injected, rep5, seqRun1

description:
Library name: hSI27_none_Mock_c1_R1
unfilt_gene_counts_210125.tsv


title: hSI25, E4_Injected, rep1, seqRun2

description:
Library name: hSI25_E4_Injected_h2_R2
unfilt_gene_counts_210125.tsv


title: hSI40, B2_Exposed, rep3, seqRun1

description:
Library name: hSI40_B2_Exposed_e1_R1
unfilt_gene_counts_210125.tsv

value: UC,Non Inflammed


title: SAM24427934_T-47D.D538G


title: hSI40, B2_Injected, rep3, seqRun1

description:
Library name: hSI40_B2_Injected_e1_R1
unfilt_gene_counts_210125.tsv


title: SAM24427935_T-47D.D538G

value: 1uM AZD9833


title: Normal_1_2_11_8

description: Sample 269

value: male


title: D0_Mll2-KO_H3K4me2_repB

description: Library name: Sample 40


title: SAM24427936_T-47D.D538G


title: hSI40, mock_injected, rep6, seqRun1

description:
Library name: hSI40_none_Mock_e1_R1
unfilt_gene_counts_210125.tsv


title: Normal_1_2_11_7

description: Sample 268

value: Normal


title: Normal_1_2_11_6

description: Sample 267


title: hSI40, G11_Exposed, rep3, seqRun1

description:
Library name: hSI40_G11_Exposed_f2_R1
unfilt_gene_counts_210125.tsv


title: D0_Mll2-KO_H3K4me1_repB

description: Library name: Sample 38

value: H3K4me1 antibody (Active Motif, 39297)


title: In cellulo-2

city: PRINCETON

first: Danyang

last: Wang

state: NJ

address: 307 Frick Chemistry Laboratory, Washington Road

institute: Princeton University

data_processing:
library strategy: icSHAPE/SHAPE-MaP
remove duplicete reads as icshape pipeline
trimmed reads adaptor as icshape pipeline
mapping reads to human hg38 reference genome with botie2 as default parameters
calculate rpkm as icshape pipeline
calulate reverse transcript stop sites as icshape pipeline
Assembly: calculate icSHAPE score as icshape pipeline
Supplementary files format and content: hg38
Supplementary files format and content: tab-delimited text files for icshape file

source_name: Kidney

growth_protocol: Human HEK293T cells were cultured in DMEM supplemented with 10% FBS at 37°C with 5% CO2 in 10-cm plates. Cells were cultured to 70~80% confluency, treated with 1 mM 2’-aminodeoxycytidine for 16 hrs

extract_protocol:
The  RNA or modified RNA was extracted by TRIazol
100 µg of total RNA from HEK293T cells was used for polyA enrichment  using the mouse/human ribominus kit (Invitrogen). IcSHAPE sequencing libraries were then constructed from these RNA samples as icSHAPE protocol. Libraries were sequenced on the Illumina NovaSeq to ~200 million reads per replicate.

treatment_protocol: For in cellular treatment, cells was incubated with isoS-N3 at 37°C for 15min. For in vitro treatment, RNA was extracted by TRIzol and treated with isoS-N3 for 15 minutes at 37°C.

value: Kidney

value: human embryonic kidney cells

value: Wide Type

value: 2’-aminodeoxycytidine+ isoSN3


title: D0_Mll2-KO_H3K4me1_repA

description: Library name: Sample 37

value: Mll2-KO mESC


title: hSI40, G11_Injected, rep3, seqRun1

description:
Library name: hSI40_G11_Injected_f2_R1
unfilt_gene_counts_210125.tsv

value: Terminal Ileum


title: hSI40, mock_injected, rep5, seqRun1

description:
Library name: hSI40_none_Mock_f2_R1
unfilt_gene_counts_210125.tsv


title: D0_Mll2-KO_MLL1_repB

description: Library name: Sample 36

value: MLL1 antibody (Active Motif, 61295)


title: In vitro-2


title: D0_Mll2-KO_MLL1_repA

description: Library name: Sample 35


title: Normal_1_2_11_4

description: Sample 265

value: testis


title: Normal_1_2_11_5

description: Sample 266


title: hSI40, B2_Exposed, rep2, seqRun1

description:
Library name: hSI40_B2_Exposed_d2_R1
unfilt_gene_counts_210125.tsv

value: organoids


title: In vitro-1


title: Normal_1_2_11_2

description: Sample 263


title: hSI40, B2_Injected, rep2, seqRun1

description:
Library name: hSI40_B2_Injected_d2_R1
unfilt_gene_counts_210125.tsv


title: Normal_1_2_11_3

description: Sample 264


title: D0_Mll2-KO_input_histmod_MLL1

description: Library name: Sample 34


title: D0_Mll1-KO_H3K27me3_repB

description: Library name: Sample 33

value: Mll1-KO mESC

value: H3K27me3 antibody (Active Motif, 39155)


title: DMSO-2


title: D0_Mll2-KO_H3K4me2_repA

description: Library name: Sample 39

value: mESC

value: H3K4me2 antibody (Active Motif, 39141)


title: SAM24427933_T-47D.D538G

value: Breast

value: Epithelial cell


title: D0_Mll1-KO_H3K27me3_repA

description: Library name: Sample 32


title: Normal_1_2_11_1

description: Sample 262

value: male

value: Normal


title: hSI40, mock_injected, rep4, seqRun1

description:
Library name: hSI40_none_Mock_d2_R1
unfilt_gene_counts_210125.tsv

value: UC,Non Inflammed


title: Normal_1_2_10_8

description: Sample 261


title: D0_Mll1-KO_H3K27ac_repB

description: Library name: Sample 31

value: H3K27ac antibody (Active Motif, 39133)


title: hSI40, G11_Injected, rep2, seqRun1

description:
Library name: hSI40_G11_Injected_f1_R1
unfilt_gene_counts_210125.tsv


title: Normal_1_2_10_7

description: Sample 260


title: In cellulo-1

value: Kidney

value: human embryonic kidney cells

value: Wide Type


title: D0_Mll1-KO_H3K27ac_repA

description: Library name: Sample 30


title: hSI40, G11_Exposed, rep2, seqRun1

description:
Library name: hSI40_G11_Exposed_f1_R1
unfilt_gene_counts_210125.tsv

value: Terminal Ileum


title: D0_Mll1-KO_H3K4me3_repB

description: Library name: Sample 29

value: H3K3me3 antibdy (Active Motif, 39159)


title: hSI40, mock_injected, rep3, seqRun1

description:
Library name: hSI40_none_Mock_f1_R1
unfilt_gene_counts_210125.tsv


title: Normal_1_2_10_5

description: Sample 259

value: testis


title: hSI40, B2_Exposed, rep1, seqRun1

description:
Library name: hSI40_B2_Exposed_d1_R1
unfilt_gene_counts_210125.tsv

value: organoids


title: Normal_1_2_10_4

description: Sample 258


title: clone23_att_exp1

city: Geneva

first: Vasilis

last: Dionellis

address: 30, quai Ernest-Ansermet

country: Switzerland

institute: University of Geneva

description:
ID37
MiDAS

data_processing:
library strategy: EdU-seq
100-bp single end reads were aligned to the reference human genome Human GRCh37/hg19 using bwa v.0.7.17, retaining only the reads with the highest quality score.
CSV processed files have been generated as described in the section "Sequence alignment and calculation of sigma values" of Methods published in https://doi.org/10.1038/nature25507
Assembly: GRCh37/hg19

source_name: HeLa

extract_protocol:
EdU-labelled DNA isolation and sequencing were performed as described in Mailler, Padayachy & Halazonetis, 2021, and Macheret & Halazonetis, 2019. Briefly, fixed cells were permeabilized in PBS-0.2% Triton X (PanReac, AppliChem, Cat. No. A1388,2500) and resuspended in click-it reaction mix (85.5mM Tris pH8, 4mM CuSO4, 100mM Sodium Ascorbate and 50µM biotin-azide, Jena Biosciences, Cat. No. CLK-A2112-10) for 30 minutes for biotinilation of EdU-labelled DNA. Each sample was then incubated over-night in a solution of 10mM Tris pH 8, 10mM EDTA, 0.5% SDS and proteinase K (Roche, Cat. No. 03115844001) 0.2mg/mL. The next day, proteins and other contaminants were eliminated by phenol-chlorophorm extraction, and purified DNA was precipitated over night at -20°C by adding 0.2M NaCl and two volumes of ethanol to the solution. DNA pellet was washed in 70% ethanol, resuspended in 1xTE (10mM Tris pH 8, 1mM EDTA) and quantified by Qubit ® dsDNA BR assay kit (Invitrogen, Cat. No. Q32853) using a Qubit ® 2.0 Fluorometer (Invitrogen, Cat. No. Q32866). 10μg of DNA from each samples were sonicated by Bioruptor ® Pico sonication device (Diagenode, cat. no. B01060003) to get 100-500bp fragments (6-8 cycles, 15 seconds on, 90 seconds off). EdU-biotin-labelled DNA was isolated by using Dynabeads™ MyOne™ Streptavidin C1 (Invitrogen, Cat. No. 65002) and eluted in Tris 10mM pH8 additioned with 2% β-mercaptoethanol.
TruSeq ChIP Sample Prep Kit (Illumina, Cat. No. IP-202-1012)

value: HeLa

value: tumor

tag: group


title: D0_Mll1-KO_H3K4me3_repA

description: Library name: Sample 28

value: Mll1-KO mESC

value: mESC


title: clone23_mit_exp1

description:
ID36
MiDAS


title: hSI40, B2_Injected, rep1, seqRun1

description:
Library name: hSI40_B2_Injected_d1_R1
unfilt_gene_counts_210125.tsv


title: D0_Mll1-KO_H3K4me2_repB

description: Library name: Sample 27

value: H3K4me2 antibody (Active Motif, 39141)


title: Normal_1_2_10_3

description: Sample 257


title: Normal_1_2_10_2

description: Sample 256


title: hSI40, mock_injected, rep2, seqRun1

description:
Library name: hSI40_none_Mock_d1_R1
unfilt_gene_counts_210125.tsv


title: clone2C4_mit_exp4

description:
ID33
MiDAS


title: clone2E4_mit_exp6

description:
ID32
MiDAS


title: DMSO-1


title: D0_Mll1-KO_H3K4me2_repA

description: Library name: Sample 26


title: hSI40, G11_Exposed, rep1, seqRun1

description:
Library name: hSI40_G11_Exposed_e2_R1
unfilt_gene_counts_210125.tsv


title: clone3D1_mit_exp5

description:
ID31
MiDAS


title: hSI40, G11_Injected, rep1, seqRun1

description:
Library name: hSI40_G11_Injected_e2_R1
unfilt_gene_counts_210125.tsv


title: Normal_1_1_9_8

description: Sample 254


title: clone23_mit_exp2

description:
ID35
MiDAS


title: clone3D1_mit_exp6

description:
ID30
MiDAS


title: Normal_1_1_9_7

description: Sample 253


title: Normal_1_2_10_1

description: Sample 255


title: clone23_mit_exp3

description:
ID34
MiDAS


title: clone3H2_mit_exp6

description:
ID29
MiDAS


title: D0_Mll1-KO_input_histmod

description: Library name: Sample 23


title: Normal_1_1_9_6

description: Sample 252


title: hSI27, G11_Exposed, rep1, seqRun1

description:
Library name: hSI27_G11_Exposed_b2_R1
unfilt_gene_counts_210125.tsv

value: none,Non Inflammed


title: Normal_1_1_9_5

description: Sample 251

value: male


title: WT_att_exp1

description:
ID28
MiDAS


title: hSI27, G11_Injected, rep1, seqRun1

description:
Library name: hSI27_G11_Injected_b2_R1
unfilt_gene_counts_210125.tsv


title: WT_mit_exp1

description:
ID27
MiDAS


title: Normal_1_1_9_4

description: Sample 250

value: Normal


title: hSI27, mock_injected, rep4, seqRun1

description:
Library name: hSI27_none_Mock_b2_R1
unfilt_gene_counts_210125.tsv


title: WT_mit_exp2

description:
ID26
MiDAS


title: D0_WT_RING1B_repA

description: Library name: Sample 21

value: WT mESC

value: WT

value: RING1B antibody (Cell Signalling, 5694)


title: D0_Mll1-KO_H3K4me1_repA

description: Library name: Sample 24

value: H3K4me1 antibody (Active Motif, 39297)


title: hSI27, B2_Injected, rep3, seqRun1

description:
Library name: hSI27_B2_Injected_b1_R1
unfilt_gene_counts_210125.tsv


title: D0_Mll1-KO_H3K4me1_repB

description: Library name: Sample 25


title: Normal_1_1_9_3

description: Sample 249


title: D0_WT_RING1B_repB

description: Library name: Sample 22


title: Normal_1_1_9_2

description: Sample 248


title: D0_WT_H3K9me3_repA

description: Library name: Sample 19

value: H3K9me3 antibody (Active Motif, 61014)


title: WT_mit_exp3

description:
ID25
MiDAS


title: WT_mit_exp4

description:
ID24
MiDAS


title: hSI40, mock_injected, rep1, seqRun1

description:
Library name: hSI40_none_Mock_e2_R1
unfilt_gene_counts_210125.tsv

value: Terminal Ileum

value: UC,Non Inflammed


title: D0_WT_H3K9me3_repB

description: Library name: Sample 20


title: Normal_1_1_9_1

description: Sample 247

value: testis


title: D0_WT_H3K27me3_repB

description: Library name: Sample 18

value: H3K27me3 antibody (Active Motif, 39155)


title: D0_WT_H3K27me3_repA

description: Library name: Sample 17


title: hSI27, B2_Injected, rep2, seqRun1

description:
Library name: hSI27_B2_Injected_a2_R1
unfilt_gene_counts_210125.tsv

value: organoids


title: Normal_1_1_8_2

description: Sample 246


title: WT_mit_exp6

description:
ID22
MiDAS

value: HeLa

value: tumor


title: WT_mit_exp5

description:
ID23
MiDAS


title: D0_WT_H3K27ac_repB

description: Library name: Sample 16

value: mESC

value: H3K27ac antibody (Active Motif, 39133)


title: Normal_1_1_8_1

description: Sample 245


title: hSI27, B2_Injected, rep1, seqRun1

description:
Library name: hSI27_B2_Injected_a1_R1
unfilt_gene_counts_210125.tsv

value: none,Non Inflammed


title: hSI27, mock_injected, rep1, seqRun1

description:
Library name: hSI27_none_Mock_a1_R1
unfilt_gene_counts_210125.tsv


title: D0_WT_H3K27ac_repA

description: Library name: Sample 15


title: Normal_1_1_7_7

description: Sample 243

value: male


title: clone23_forkprogr_45mins_exp1

description:
ID20
fork progression


title: RT112_Talazoparib_4

city: Duesseldorf

first: Michèle

middle: J

last: Hoffmann

state: NRW

address: Moorenstr. 5

department: Urology

country: Germany

institute: Heinrich Heine University, Medical Faculty

description:
Library name: 1016-72
1016-72_RPKM

data_processing:
Illumina BCL Convert Tool (version 3.8.4) was used for basecalling.
Sequenced reads were adapter trimmed and quality trimmed (using the default parameters: bases below Q13 were trimmed from the end of the reads, ambiguous nucleotides maximal 2). Mapping was done against the Homo sapiens (hg38; GRCh38.107) (July 20, 2022) genome sequence using CLC Genomics Workbench v23.0.5 with standard parameters.
Reads Per Kilobase and per Megabase (RPKM) were calculated using CLC Genomics Workbench v23.0.5 with standard parameters. Multi-group comparisons were calculated using the CLC Differential Expression for RNA-Seq tool (version 2.8, Qiagen, Venlo, Netherlands). The resulting p values were corrected for multiple testing by FDR and Bonferroni-correction. A p value of ≤ 0.05 was considered significant. Cut-off for differential gene expression was set to 1.5 fold.
Assembly: hg38
Supplementary files format and content: The excel file includes RPKM values for each sample

growth_protocol: UC cell lines were cultivated in Dulbecco’s Modified Eagle’s Medium (DMEM; 4.5 g/L glucose) with GlutaMAX, Pyruvate, and 10 % fetal bovine serum (FBS). Cells were maintained at 37 °C in a humidified atmosphere containing 5 % CO2.

extract_protocol:
Rneasy Mini Kit, Qiagen, according to manufacturer with optional DNAse treatment
Library preparation was performed according to the manufacturer’s protocol using the Lexogen® QuantSeq 3’ mRNA-Seq Library Prep Kit FWD with UMI’s. The Input mount was 200 ng totalRNA. Bead purified libraries were normalized and finally sequenced on the NextSeq2000 system (Illumina Inc. San Diego, CA, USA) with a read setup of 1x100 bp.

treatment_protocol: Indicated cell lines were treated with reduced dosage (as indicated in publication, additional file 1) with PARP inhibitor Olaparib or Talazoparib for 72h. Solvent control cells were treated with DMSO.

value: urothelial carcinoma cell line

value: Talazoparib


title: clone23_forkprogr_45mins_exp3

description:
ID19
fork progression


title: D0_WT_H3K4me3_repA

description: Library name: Sample 13

value: WT mESC

value: WT

value: H3K3me3 antibdy (Active Motif, 39159)


title: Normal_1_1_7_8

description: Sample 244

value: Normal


title: RT112_Talazoparib_3

description:
Library name: 1016-71
1016-71_RPKM


title: clone23_forkprogr_90mins_exp1

description:
ID18
fork progression


title: hSI27, mock_injected, rep3, seqRun1

description:
Library name: hSI27_none_Mock_b1_R1
unfilt_gene_counts_210125.tsv

value: Terminal Ileum


title: D0_WT_H3K4me2_repB

description: Library name: Sample 12

value: H3K4me2 antibody (Active Motif, 39141)


title: Normal_1_1_7_5

description: Sample 241

value: testis


title: RT112_Talazoparib_1

description:
Library name: 1016-70
1016-70_RPKM


title: hSI27, mock_injected, rep2, seqRun1

description:
Library name: hSI27_none_Mock_a2_R1
unfilt_gene_counts_210125.tsv


title: clone23_forkprogr_90mins_exp2

description:
ID17
fork progression


title: D0_WT_H3K4me2_repA

description: Library name: Sample 11


title: Normal_1_1_7_4

description: Sample 240


title: RT112_DMSO_4

description:
Library name: 1016-69
1016-69_RPKM

value: DMSO


title: Normal_1_1_7_3

description: Sample 239


title: clone23_forkprogr_135mins_exp2

description:
ID21
fork progression


title: RT112_DMSO_2

description:
Library name: 1016-68
1016-68_RPKM


title: D0_WT_H3K4me1_repB

description: Library name: Sample 10

value: H3K4me1 antibody (Active Motif, 39297)


title: D0_WT_H3K4me1_repA

description: Library name: Sample 9


title: clone23_orifir_exp1

description:
ID15
fork progression

value: HeLa


title: Normal_1_1_7_1

description: Sample 238


title: clone23_orifir_exp2

description:
ID14
fork progression

value: tumor


title: D0_WT_H3K4me3_repB

description: Library name: Sample 14

value: mESC


title: Normal_1_1_7_6

description: Sample 242


title: clone2C4_forkprogr_45mins_exp3

description:
ID12
fork progression


title: J82LTT_Talazoparib_3

description:
Library name: 1016-62
1016-62_RPKM


title: RT112_DMSO_1

description:
Library name: 1016-67
1016-67_RPKM


title: Normal_1_1_6_7

description: Sample 236


title: D0_WT_MLL1_repB

description: Library name: Sample 7

value: MLL1 antibody (Active Motif, 61295)


title: clone23_orifir_exp3

description:
ID13
fork progression


title: Normal_1_1_6_6

description: Sample 235


title: Normal_1_1_6_8

description: Sample 237


title: D0_WT_RBBP5_repB

description: Library name: Sample 5

value: RBBP5 antibody (Diagenode, C15410342)


title: J82LTT_Talazoparib_4

description:
Library name: 1016-63
1016-63_RPKM


title: D0_WT_MLL1_repA

description: Library name: Sample 6


title: Normal_1_1_6_4

description: Sample 234

value: male


title: clone2C4_forkprogr_90mins_exp3

description:
ID11
fork progression


title: D0_WT_input_histmod_1

description: Library name: Sample 8


title: J82LTT_Talazoparib_2

description:
Library name: 1016-61
1016-61_RPKM

value: urothelial carcinoma cell line


title: J82LTT_DMSO_4

description:
Library name: 1016-57
1016-57_RPKM


title: D0_WT_RBBP5_repA

description: Library name: Sample 4


title: Normal_1_1_5_6

description: Sample 232


title: J82LTT_DMSO_2

description:
Library name: 1016-56
1016-56_RPKM


title: J82LTT_DMSO_1

description:
Library name: 1016-55
1016-55_RPKM


title: clone2C4_orifir_exp3

description:
ID10
fork progression


title: D0_WT_MLL2_repB

description: Library name: Sample 3

value: GFP antibody (Invitrogen, A11122)


title: WT_forkprogr_45mins_exp1

description:
ID8
fork progression


title: WT_forkprogr_135mins_exp2

description:
ID9
fork progression


title: Normal_1_1_6_3

description: Sample 233


title: WT_forkprogr_45mins_exp3

description:
ID7
fork progression


title: D0_WT_MLL2_repA

description: Library name: Sample 2

value: WT mESC


title: clone23_forkprogr_90mins_exp3

description:
ID16
fork progression


title: Normal_1_1_5_5

description: Sample 231


title: J82_Tala_4

description:
Library name: 1016-51
1016-51_RPKM

value: Talazoparib


title: D0_WT_input_MLL2_RBBP5_MLL1

description: Library name: Sample 1

value: WT


title: J82_Tala_3

description:
Library name: 1016-50
1016-50_RPKM


title: WT_forkprogr_90mins_exp1

description:
ID6
fork progression


title: Normal_1_1_5_3

description: Sample 229

value: Normal


title: J82_Tala_2

description:
Library name: 1016-49
1016-49_RPKM


title: Normal_1_1_5_2

description: Sample 228


title: WT_forkprogr_90mins_exp2

description:
ID5
fork progression


title: RAW264.7 cells, LCCL 10ug treated for 24 hours-2

city: Seoul

first: Seung Hyun

last: Jang

address: Yonsei-ro 50-1

department: College of Medicine

country: South Korea

institute: Yonsei University

description:
Library name: 10ug-24hr-2
Column name in raw_count.csv; 10ug-24hr-2

data_processing:
CLC Genomics Workbench 9.5.3 software (QIAGEN)
Sequence reads were trimmed for adapter sequences and low-quality reads were filtered out in CLC Genomics Workbench (Quality limit: 0.05)
Filtered reads were mapped to GRCm39 in CLC Genomics Workbench (Mismatch cost 2, Insertion cost 2, Deletion cost 3, Length fraction 0.8, Similarity fraction 0.8, maximum number of hits for a read 10)
Total gene read counts were quantified in CLC Genomics Workbench
Assembly: GRCm39
Supplementary files format and content: A CSV file of raw read counts per each sample

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen, Cat# 15596026) and purified with the Rneasy mini kit (QIAGEN, Cat# 74106).
Libraries were constructed from 1ug of total RNA per sample using the Illumina TruSeq stranded mRNA sample prep kit (Illumina, Cat# RS-122-2101)

value: murine macrophage

value: LCCL 10ug for 24 hours


title: WT_forkprogr_90mins_exp3

description:
ID4
fork progression


title: RAW264.7 cells, LCCL 10ug treated for 24 hours-1

description:
Library name: 10ug-24hr-1
Column name in raw_count.csv; 10ug-24hr-1


title: J82_DMSO_3

description:
Library name: 1016-44
1016-44_RPKM


title: Normal_1_1_4_8

description: Sample 227

value: testis


title: WT_orifir_exp1

description:
ID3
fork progression


title: Normal_1_1_4_4

description: Sample 226


title: RAW264.7 cells, LCCL 10ug treated for 6 hours-3

description:
Library name: 10ug-6hr-3
Column name in raw_count.csv; 10ug-6hr-3

value: LCCL 10ug for 6 hours


title: RAW264.7 cells, LCCL 10ug treated for 6 hours-2

description:
Library name: 10ug-6hr-2
Column name in raw_count.csv; 10ug-6hr-2


title: RAW264.7 cells, LCCL 10ug treated for 6 hours-1

description:
Library name: 10ug-6hr-1
Column name in raw_count.csv; 10ug-6hr-1


title: WT_orifir_exp3

description:
ID1
fork progression


title: Normal_1_1_4_3

description: Sample 225


title: CAMA-1 RNA-Seq

city: Toronto

first: Scott

middle: Victor

last: Bratman

state: ON

address: 101 College Ave.

department: Medical Biophysics

country: Canada

institute: Princess Margaret Cancer Centre

data_processing:
Expression matrices were constructed via a custom pipeline (https://github.com/elsamah/rna-Seq-star-deseq2).
FASTQ files were aligned to hg38 using STARv2 (v2.7.8a) aligner.
Gene expression levels were quantified using RSEM (v1.3.0).
Assembly: hg38
Supplementary files format and content: counts matrix for CAMA-1

source_name: Breast; Mammary gland

extract_protocol:
RNA was extracted from CAMA-1 cells with NucleoSpin RNA kit (Machery Nagel).
The RNA library was prepared by polyA capture and reverse transcription of cDNA (conducted by Novogene Corporation).

value: Breast; Mammary gland

value: Epithelial


title: Normal_1_1_4_2

description: Sample 224


title: J82_DMSO_1

description:
Library name: 1016-43
1016-43_RPKM

value: DMSO


title: WT_orifir_exp2

description:
ID2
fork progression

value: HeLa

value: tumor


title: RAW264.7 cells, LCCL 10ug treated for 24 hours-3

description:
Library name: 10ug-24hr-3
Column name in raw_count.csv; 10ug-24hr-3


title: T24LTT_Olaparib_3

description:
Library name: 1016-35
1016-35_RPKM

value: Olaparib


title: Normal_1_1_5_4

description: Sample 230

value: male


title: RAW264.7 cells, LCCL 1ug treated for 24 hours-3

description:
Library name: 1ug-24hr-3
Column name in raw_count.csv; 1ug-24hr-3

value: LCCL 1ug for 24 hours


title: T24LTT_Olaparib_1

description:
Library name: 1016-34
1016-34_RPKM

value: urothelial carcinoma cell line


title: Normal_1_1_3_8

description: Sample 222


title: T24LTT_Tala_4

description:
Library name: 1016-24
1016-24_RPKM


title: Normal_1_1_3_5

description: Sample 221


title: Normal_1_1_4_1

description: Sample 223


title: RAW264.7 cells, LCCL 1ug treated for 24 hours-1

description:
Library name: 1ug-24hr-1
Column name in raw_count.csv; 1ug-24hr-1


title: RAW264.7 cells, LCCL 1ug treated for 24 hours-2

description:
Library name: 1ug-24hr-2
Column name in raw_count.csv; 1ug-24hr-2


title: CAMA-1 cf-chromatin, cfMNase-Seq, 5 min MNase digestion

library_source: other

data_processing:
Paired-end sequencing reads were trimmed using Cutadapt (v3.0), utilizing a list of UMIs as input.
Trimmed reads were aligned to the hg38 human genome build using Bowtie2 (v2.4.1).
Duplicate reads were removed using Samtools (v1.9), using a combination of samtools sort (before and after samtools fixmate), samtools fixmate with the -m option, and samtools markdup with the -r option. Low-quality mapped reads were removed using samtools view with the -bq option, with a minimum mapping quality of 25-30.
Counts per 10,000 bp bin were calculated from BAM files (in bigWig format), using DeepTools. bigWig files were generated with Reads Per Kilobase per Million mapped reads (RPKM) normalization, centered and extended read options.
Assembly: hg38
Supplementary files format and content: bigWig, for all samples
Library strategy: cfMNase-Seq

molecule: other

growth_protocol: HCT116 was cultured in X and CAMA-1 in Dulbecco's Modified Eagle Medium (DMEM), both supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin solution. Both cell lines  were grown in adherent dishes and in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Conditioned media was collected in exponential growth phase. The media was spun at 2500g for 10 min at 4 °C, transferred to a new tube, and spun again at 16100g for 10 min at 4 °C. The supernatant was transferred to a new tube and kept at 4 °C until MNase digestion.
Processed media samples were subject to either no MNase digestion, or a 1, 2, 5, 10 or 30 minute digestion, using an MNase master mix. The MNase master mix was prepared at 3000 Units/mL (U/mL) by combining 440 μL of ddH20, 50 μL of MNase buffer, 5 μL of BSA, and 5 μL of 300,000 U/mL MNase (New England Biolabs, CAT #M0247S). MNase was added to the processed media samples at a final concentration of 20 U/mL and incubated in a 37 ºC water bath for corresponding digestion time. The reaction was halted with 5 mM EDTA (Invitrogen, CAT #15575020).
After Mnase digestion, purification of DNA from cell-free chromatin was performed using the Qiagen Circulating Nucleic Acid kit (CAT #55114). The DNA was quantified using the Qubit High Sensitivity dsDNA kit (Life Technologies, CAT #Q33231) and analyzed with a Agilent 2100 Bioanalyzer using the High Sensitivity DNA kit (CAT #5067-4626).
Libraries were prepared from 20 ng of purified DNA using the KAPA Hyperprep Kit with Library Amplification Primer Mix (Roche, CAT #07962363001) and adapters containing unique molecular identifiers from Integrated DNA Technologies. The libraries were cleaned-up using Beckman Coulter AMPure XP beads (CAT #A63882) with a 0.8× cleanup before library amplification and a 0.9X cleanup afterward. The libraries were amplified with six PCR cycles. Quality control was performed with a Qubit High Sensitivity dsDNA kit and  Agilent 2100 Bioanalyzer.


title: CAMA-1 cf-chromatin, cfMNase-Seq, 10 min MNase digestion


title: Normal_1_1_3_4

description: Sample 220


title: J82_DMSO_4

description:
Library name: 1016-45
1016-45_RPKM


title: T24LTT_Tala_1

description:
Library name: 1016-22
1016-22_RPKM


title: RAW264.7 cells, LCCL 1ug treated for 6 hours-2

description:
Library name: 1ug-6hr-2
Column name in raw_count.csv; 1ug-6hr-2

value: LCCL 1ug for 6 hours


title: CAMA-1 cf-chromatin, cfMNase-Seq, 2 min MNase digestion


title: T24LTT_Tala_3

description:
Library name: 1016-23
1016-23_RPKM

value: Talazoparib


title: RAW264.7 cells, LCCL 1ug treated for 6 hours-1

description:
Library name: 1ug-6hr-1
Column name in raw_count.csv; 1ug-6hr-1

value: WT


title: RAW264.7 cells, untreated control-3

description:
Library name: control3
Column name in raw_count.csv; control3


title: CAMA-1 cf-chromatin, cfMNase-Seq, 30 min MNase digestion


title: RAW264.7 cells, LCCL 1ug treated for 6 hours-3

description:
Library name: 1ug-6hr-3
Column name in raw_count.csv; 1ug-6hr-3


title: Normal_1_1_2_7

description: Sample 218

value: Normal


title: CAMA-1 cf-chromatin, cfMNase-Seq, 1 min MNase digestion


title: T24LTT_DMSO_4

description:
Library name: 1016-21
1016-21_RPKM


title: T24LTT_DMSO_3

description:
Library name: 1016-20
1016-20_RPKM


title: HCT116 cf-chromatin, cfMNase-Seq, 30 min MNase digestion

source_name: Large intestine; Colon

value: Large intestine; Colon


title: CAMA-1 cf-chromatin, no MNase digestion


title: RAW264.7 cells, untreated control-2

description:
Library name: control2
Column name in raw_count.csv; control2

value: murine macrophage


title: T24LTT_DMSO_2

description:
Library name: 1016-19
1016-19_RPKM


title: Normal_1_1_2_6

description: Sample 217

value: testis


title: HCT116 cf-chromatin, cfMNase-Seq, 10 min MNase digestion


title: Normal_1_1_2_2

description: Sample 216


title: RAW264.7 cells, untreated control-1

description:
Library name: control1
Column name in raw_count.csv; control1


title: T24_Olaparib_3

description:
Library name: 1016-15
1016-15_RPKM


title: HCT116 cf-chromatin, cfMNase-Seq, 5 min MNase digestion


title: Normal_1_1_12_2

description: Sample 215


title: T24_Olaparib_2

description:
Library name: 1016-14
1016-14_RPKM


title: T24LTT_Olaparib_4

description:
Library name: 1016-36
1016-36_RPKM


title: Normal_1_1_3_1

description: Sample 219


title: WT_PD1_A7_A14 CD45+ tumor-infiltrating leukocytes (TILs) from MC38 tumors

first: Suraj

last: Bansal

state: Ontario

address: 101 College Street

institute: Princess Margaret Cancer Centre, UHN

description:
Library name: WT_PD1_A7_A14
10X Genomics

data_processing:
Sequencing data for 38,994 total cells from isotype control (n=3 Tet2wt and n=3 Tet2het) and anti-PD-1 treated mice (n=5 Tet2wt and n=5 Tet2het) were analyzed using Seurat v4.3 (Hugo et al., Cell, 2016) in the R programming environment (Snyder el al., Engl. J. Med., 2014). The SCTransform method was used with “glmGamPoi” for data normalization and correction of technical variation, with principal component analysis applied for dimensionality reduction.
Data was projected into 2-dimensional space using the UMAP algorithm, and cells were grouped into 20 clusters using Seurat’s FindNeighbors and FindClusters functions.
We performed Milo differential abundance analysis (Dann et al., Nat. Biotechnol., 2021). Cells were assigned to partially overlapping neighborhoods using a k-nearest neighbor graph using a neighborhood size of n=30. We performed multiple hypothesis correction following a weighted FDR procedure that accounts for spatial overlapping of the neighborhoods, as recommended by the Milo framework. Applying a spatial FDR cutoff of 0.1, we identified cell neighborhoods that were differentially enriched between our experimental conditions. AUcell was used to score gene expression signatures within neighborhoods between different conditions.
We performed VDJ recombination analysis using the R entropy package to calculate the Shannon Diversity Index of Tet2wt and Tet2het CD8 exhausted and CD8 memory T cells from isotype control or anti-PD-1 treated MC38 tumors.
We applied the consensus-based LIANA (Dimitrov et al., Nat. Commun., 2022) framework to estimate ligand-ligand interactions for sender cell populations, comprising cells in myeloid neighborhoods (macrophages, monocytes, dendritic cells, and MDSCs) and receiver T cell populations: CD4, CD8, or other T cell neighborhoods, to identify interactions significantly enriched in Tet2het PD1-treated compared to TET2wt PD1-treated TILs.
Assembly: Clusters were annotated based on prior knowledge, published gene expression signatures from MC38 TILs (Zhang et al., Cell, 2020), and similarities to human LM22 leukocyte gene expression programs. We projected our dataset onto the MetaTiME platform which provides pretrained meta-components from 1.7 million single cells across 79 tumor datasets to automatically annotate fine-grained cell states and plot signature continuum across our dataset (Zhang et al., Nat. Commun., 2023).
Supplementary files format and content: UMAP projection of annotated clusters; bar graphs for Milo neighborhood analysis, enrichment signature and Shannon diversity index; dot plots of mean gene expression and fraction of cells expressing each gene; GSEA plots; dot plots of LIANA consensus cell-cell communication analysis between sender and receiver cells
Supplementary files format and content: RDS object with rawcounts, normalized expression data, and sample-level annotations

source_name: Subcutaneous MC38 tumor (right flank)

growth_protocol: C57Bl6/J mice between 6-10 weeks of age were lethally irradiated. One day post-irradiation mice were rescued by tail-vein injection of 1-1.5 million bone marrow cells from donor mice, sex and aged matched between 8-16 weeks of age, with wild type Tet2 or were heterozygous for a deletion in Tet2 exons 8-11, including the catalytic domain, which leads to a loss of detectable gene product in homozygotes. 9 weeks after bone marrow transplant, 250,000 MC-38 cells were subcutaneously implanted into the right flank of rescued mice.

extract_protocol:
Mice were euthanized 48 hours after the final dose and tumors were dissected and dissociated with 1X Collagenase and Hyaluronidase in DMEM with 0.1 mg/mL DNAse for 1 hour at 37 C. Fragments were then washed in DMEM with 2% fetal calf serum, filtered through 70 μm and 40 μm filters and subjected to 5 minute ammonium chloride lysis at room temperature. Live, CD45+ tumor-infiltrating leukocytes were isolated using Fluorescence-Activated Cell Sorting.
Single cells were processed using Chromium 10X 5’ Single Cell and Chromium Single Cell Mouse TCR Amplification kits at the Princess Margaret Cancer Centre Genomics Facility according to the manufacturer’s instructions.

treatment_protocol: 17 days post-tumor implantation Tet2wt or Tet2het rescued mice were matched by tumor-size and assigned to receive 300 μg of anti-PD-1 blocking antibody (5 mice per genotype) or rat IgG2a isotype control (3 mice per genotype) every 2 days for 3 doses.

value: Subcutaneous MC38 tumor (right flank)

value: MC-38 (colon adenocarcinoma)

value: CD45+ tumor-infiltrating leukocytes

value: Tet2wt (wild-type)

value: anti-PD-1 checkpoint blockade (BioXcell clone RMP1-14)

tag: Sex

value: female

tag: host strain


title: Normal_1_1_11_6

description: Sample 213


title: WT_PD1_A11 CD45+ tumor-infiltrating leukocytes (TILs) from MC38 tumors

description:
Library name: WT_PD1_A11
10X Genomics


title: T24_Olaparib_1

description:
Library name: 1016-13
1016-13_RPKM

value: Olaparib


title: HCT116 cf-chromatin, cfMNase-Seq, 1 min MNase digestion

value: Epithelial


title: T24_Talazoparib_4

description:
Library name: 1016-12
1016-12_RPKM


title: WT_ISO_A2 CD45+ tumor-infiltrating leukocytes (TILs) from MC38 tumors

description:
Library name: WT_ISO_A2
10X Genomics

value: isotype control (rat IgG2a)


title: HCT116 cf-chromatin, no MNase digestion


title: Normal_1_1_11_4

description: Sample 212

value: male


title: WT-PD1_7 CD45+ tumor-infiltrating leukocytes (TILs) from MC38 tumors

description:
Library name: WT-PD1_7
10X Genomics


title: Normal_1_1_11_3

description: Sample 211


title: T24_Talazoparib_2

description:
Library name: 1016-11
1016-11_RPKM

value: urothelial carcinoma cell line


title: SU-DHL-6 cf-chromatin, 300ng input, ChIP-Seq, H3K27me3, rep2

data_processing:
Paired-end sequencing reads were trimmed using Cutadapt (v3.0), utilizing a list of UMIs as input.
Trimmed reads were aligned to the hg38 human genome build using Bowtie2 (v2.4.1).
Duplicate reads were removed using Samtools (v1.9), using a combination of samtools sort (before and after samtools fixmate), samtools fixmate with the -m option, and samtools markdup with the -r option. Low-quality mapped reads were removed using samtools view with the -bq option, with a minimum mapping quality of 25-30.
Counts per 50bp bin were calculated from BAM files (in bigWig format), using DeepTools. bigWig files were generated with Reads Per Kilobase per Million mapped reads (RPKM) normalization.
For BAM files, peaks were called using MACS2, specifying --broad options for broadPeak files, or default for narrowPeak files. Files that were subsampled were also generated with a p-value cutoff of 1x10^-6 for increased stringency, while unsampled files were called using default parameters.
Assembly: hg38
Supplementary files format and content: bigWig, BAM
Library strategy: cfChIP-Seq

source_name: Peritoneal effusion

growth_protocol: SU-DHL-6 was grown in suspension dishes in RPMI supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin solution in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Processed media samples were subject to either no MNase digestion, or a 1, 2, 5, 10 or 30 minute digestion, using an MNase master mix. The MNase master mix was prepared at 3000 Units/mL (U/mL) by combining 440 μL of ddH20, 50 μL of MNase buffer, 5 μL of BSA, and 5 μL of 300,000 U/mL MNase (New England Biolabs, CAT #M0247S). MNase was added to the processed media samples at a final concentration of 20 U/mL and incubated in a 37 ºC water bath for corresponding digestion time. The reaction was halted with 5 mM EDTA (Invitrogen, CAT #15575020). Cell-free ChIP-Seq was performed on the media cf-chromatin using specific antibodies against H3K4me3 (Abcam, ab1012) and H3K27me3 (Cell Signaling Technology, 9733S, lot 21), respectively.
Libraries were prepared using an on-bead ligation protocol published in Sadeh et al (Nature Biotechnology, 2021). All library preparation steps were performed on Dynabead M270-Epoxy beads (Invitrogen, CAT #14301), up until the chromatin elution step was performed. Library preparation was otherwise conducted according to the KAPA Hyperprep Kit with Library Amplification Primer Mix (Roche, CAT #07962363001), utilizing sequencing adapters containing unique molecular identifiers (UMIs) from Integrated DNA Technologies. The libraries were cleaned-up using Beckman Coulter AMPure XP beads (CAT #A63882) with a 0.8× cleanup before library amplification and a 0.9X cleanup afterward. H3K4me3 libraries were amplified to 16 cycles, and H3K27me3 libraries were amplified to 12 cycles for 10 ng and 30 ng cf-chromatin input, and 11 cycles for 300 ng input. Quality control was performed with a Qubit High Sensitivity dsDNA kit and Agilent 2100 Bioanalyzer.

value: Peritoneal effusion

tag: disease

value: Diffuse Large B-cell lymphoma

value: B Lymphocyte

tag: chip antibody

tag: chip input_concentration


title: Tet2het_PD-1_m144 CD45+ tumor-infiltrating leukocytes (TILs) from MC38 tumors

description:
Library name: Tet2het_PD-1_m144
10X Genomics

tag: cell line


title: Normal_1_1_11_2

description: Sample 210

tag: age

value: Normal


title: SU-DHL-6 cf-chromatin, 300ng input, ChIP-Seq, H3K27me3, rep1

tag: cell type

value: Cell Signaling Technology, 9733S, lot 21


title: Tet2het_ISO_A31 CD45+ tumor-infiltrating leukocytes (TILs) from MC38 tumors

description:
Library name: Tet2het_ISO_A31
10X Genomics

tag: genotype

tag: treatment


title: SU-DHL-6 cf-chromatin, 30ng input, ChIP-Seq, H3K27me3, rep2

tag: tissue


title: T24_DMSO_3

description:
Library name: 1016-2
1016-2_RPKM

value: DMSO


title: Normal_1_1_10_5

description: Sample 209

value: testis


title: Normal_1_1_10_4

description: Sample 208


title: Normal_1_1_11_7

description: Sample 214


title: HCT116 cf-chromatin, cfMNase-Seq, 2 min MNase digestion

value: Large intestine; Colon


title: SU-DHL-6 cf-chromatin, 30ng input, ChIP-Seq, H3K27me3, rep1


title: Normal_1_1_10_3

description: Sample 207


title: P3,  mRNA-derived cDNA

city: Seattle

middle: N

last: Furlan

state: WA

address: 1100 Fairview Ave N

department: TST

institute: Fred Hutchinson Cancer Research Center

description:
Library name: Sample 3 RNA
10x genomics

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression) was performed using the 10x genomics Cell Ranger pipeline  and aligning to the GRCm38 genome build and Ensembl 93 annotations.
Further processing was done with Seurat v3.0.0 (cell and gene filtering, clustering, differential gene expression analysis).
The demultiplexing, barcode processing, cell counting were made using cellranger count software -3.1.0
Assembly: GRCm38
Supplementary files format and content: normalized RNA  count matrices, cell metadata.csv, genes.csv,  cellranger bams
Supplementary files format and content: Tab separated values files (barcodes, features), Comma- separated values files (metadata, filtered contig annotations) and matrix files.

source_name: spleen

extract_protocol:
Spleens (n = 4) were taken on day +14 and pooled. CD4+ T cells were enriched with MACS selection, stained with CD90.2 Pacific Blue, CD4 APC/Cy7, H2Dd AF647 and FACS sorted to P1 (Eomes- IL10-), P2 (Eomes+ IL10-) and P3 (Eomes+ IL10+) based on the expression of mCherry and GFP.
Samples were resuspended at 1000 cells/uL and libraries  were  generated  using  the Chromium Single Cell 3' Reagent Kits User Guide (v3 Chemistry ). Final library quality was assessed using the Tapestation 4200 (Agilent, Santa Clara, CA) and libraries were quantified by Qubit dsDNA kit on Denovix( spectrometer/flurometer) .Pooled libraries were then subjected to paired-end Illumina sequencing according  to the  manufacturer’s  protocol

treatment_protocol: B6D2F1 recipients were transplanted with TCD BM (5x106) and naive CD4+ T cells (CD44loCD62Lhi 0.5x106) from EomesmCherry/IL-10GFP donors.

value: spleen

value: splenic CD4+ T cells

value: Mice transplanted with BM + T cells from allogeneic Ifng KO donors


title: Normal_1_1_10_1

description: Sample 206


title: SU-DHL-6 cf-chromatin, 10ng input, ChIP-Seq, H3K27me3, rep2


title: TET2_HET_PD1_28 CD45+ tumor-infiltrating leukocytes (TILs) from MC38 tumors

description:
Library name: TET2_HET_PD1_28
10X Genomics

value: Subcutaneous MC38 tumor (right flank)

value: MC-38 (colon adenocarcinoma)

value: CD45+ tumor-infiltrating leukocytes

value: anti-PD-1 checkpoint blockade (BioXcell clone RMP1-14)

value: female


title: Tet2het_ISO_A18 CD45+ tumor-infiltrating leukocytes (TILs) from MC38 tumors

description:
Library name: Tet2het_ISO_A18
10X Genomics

value: isotype control (rat IgG2a)


title: SU-DHL-6 cf-chromatin, 10ng input, ChIP-Seq, H3K27me3, rep1

value: Peritoneal effusion


title: Liver tissue, CD163WT, Western diet, rep O

city: Odense M

first: Jonas

last: Graversen

address: Campusvej 55

department: Health, IMM

country: Denmark

institute: University of Southern Denmark

description: Library name: D435

data_processing:
Reads were aligned to the mouse gene assembly (GRCm39) using STAR (v.2.7.8a) and FeatureCounts (v.2.0) was used for exon read quantification. FastQC and MultiQC was used to assess quality of raw sequencing.
Assembly: GRCm39
Supplementary files format and content: Raw counts supplied as a txt file.

source_name: Liver

extract_protocol:
RNA was extracted from snap-frozen liver tissue. The tissue was homogenized in TRI reagent (T9424, Sigma-Aldrich) using the FastPrep-24 5G bead beating grinder. 1-bromo-3-chloropropane was added and vortexed thoroghly and incubated for 15min at RT followed by centrifugation (10000g, 10min, 4oC). The aqueous phase containing the RNA was mixed with cold 96% ethanol and loaded on a EconoSpin column (1920-250, Epoch Life Science) by centrifugation (13000g, 30sec, RT). After three washes with RPE buffer, the column was spinned dry for 2 minutes (13000g, RT) followed by 5 minutes to allow evapuration of ethanol. RNA was eluted by DEPC-treated water and centrifugation (16000g, 1min, RT).
Libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) and RNA was paired-end sequenced on the NovaSeq 6000 Sequencing System (Illumina).

treatment_protocol: Male CD163 knockout and littermate wildtype mice were generated by crossing heterozygous C57BL/6NTac (CD163tm1(KOMP)Vlcg) mice. At six-weeks of age, mice were allocated randomly to receive either Western diet with fructose-supplemented water (n=15 per genotype) or control chow diet (Chow; #1320 maintenance diet, Altromin) with normal drinking water (n=4-5 per genotype) ad libitum for 8 weeks.

value: Liver

value: Western diet, 8 weeks


title: NOA_3_7_7

description: Sample 205

value: male

value: nonobstructive azoospermia (NOA)


title: Liver tissue, CD163WT, Western diet, rep N

description: Library name: D434


title: P1,  mRNA-derived cDNA

description:
Library name: Sample 1 RNA
10x genomics

value: Mice transplanted with TCD BM from allogeneic WT donors


title: P2,  mRNA-derived cDNA

description:
Library name: Sample 2 RNA
10x genomics

value: Mice transplanted with BM + T cells from allogeneic WT donors


title: T24_DMSO_4

description:
Library name: 1016-3
1016-3_RPKM

value: urothelial carcinoma cell line

value: DMSO


title: NOA_3_7_6

description: Sample 204

value: testis


title: T24_Talazoparib_1

description:
Library name: 1016-10
1016-10_RPKM

value: Talazoparib


title: SU-DHL-6 cf-chromatin, 300ng input, ChIP-Seq, H3K4me3, rep2

description: These are all chromatin immunoprecipitation  experiments utilizing cell-free chromatin (cf-chromatin) from culture media. Conditions differ in the cf-chromatin input concentration per ChIP experiment.

value: Diffuse Large B-cell lymphoma

value: B Lymphocyte

value: Abcam, ab1012


title: NOA_3_7_5

description: Sample 203


title: Liver tissue, CD163WT, Western diet, rep M

description: Library name: D433


title: SU-DHL-6 cf-chromatin, 30ng input, ChIP-Seq, H3K4me3, rep2


title: CAMA-1 xenograft plasma cfDNA WGS, replicate 2

description: Library name: CAMA1_xeno_plasma_C6M4

data_processing:
*library strategy: plasma cfDNA WGS
Reads were processed with UMI-tools (v1.1.1) to extract UMIs, and then we followed a previously described protocol to remove mouse reads.
Briefly, reads were aligned to a human (hg38) and mouse (mm10) concatenated genome using Bowtie2.
Only read pairs where both reads aligned to the human reference genome were kept, and were realigned to a human-only reference
Counts per 10,000 bp bin were calculated from BAM files (in bigWig format), using DeepTools. bigWig files were generated with Reads Per Kilobase per Million mapped reads (RPKM) normalization, centered and extended read options.
Assembly: hg38
Supplementary files format and content: bigWig, for all samples

source_name: Plasma cfDNA from xenograft

growth_protocol: CAMA-1 was cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin solution. CAMA-1 was cultured in adherent dishes and in a humidified atmosphere with 5% CO2 at 37C. NOD/SCID IL2R-gamma-null (NSG, CAT #005557) female mice were purchased from Jackson Laboratory, and five million cells were injected in a 50% matrigel (Corning CAT #356231) solution into the mammary fat pad.

extract_protocol:
At endpoint (maximum tumor size of 1.5 cm), blood was collected by terminal cardiac exsanguination under anesthesia (isoflurane inhalant) into K2 EDTA tubes (CAT #BD 365974). Blood was spun at 2500g for 10 min at 4 °C, and plasma was transferred to 1.5 mL DNA LoBind Eppendorf tubes (CAT #022-43-102-1) and spun at 16100g for 10 min at 4 °C. The double-spun plasma was transferred to a new 1.5 mL tube and stored at -80 °C until cfDNA isolation.
Xenograft plasma cfDNA was performed using the Qiagen Circulating Nucleic Acid kit (CAT #55114) and quantified using the Qubit High Sensitivity dsDNA kit (Life Technologies, CAT #Q33231) according to kit instructions. DNA fragment length distributions were analyzed on an Agilent 2100 Bioanalyzer with the High Sensitivity DNA kit (CAT #5067-4626) according to the manufacturer’s instructions. Purified cfDNA was stored at either 4°C (<3 days) or -20°C (>3 days).
Illumina-compatible sequencing libraries were prepared from less than 10 ng of purified cfDNA. Libraries were prepared using the KAPA Hyperprep Kit with Library Amplification Primer Mix (Roche, CAT #07962363001) and six or seven cycles of PCR amplification. Sequencing adapters containing unique molecular identifiers (UMIs) were obtained from Integrated DNA Technologies39. Library clean-ups were performed using Beckman Coulter AMPure XP beads (CAT #A63882) with a 0.8X cleanup before library amplification and a 0.9X cleanup afterward. The library concentration was determined using the Qubit High Sensitivity dsDNA kit, and the fragment length distribution was assessed with an Agilent 2100 Bioanalyzer.

treatment_protocol: A 90-day slow-release estrogen pellet (0.72 mg of 17b-estradiol, Innovative Research of America, CAT #NE-121) was implanted between the ear and shoulder of the mouse to help ER+ cancer cell line growth.

value: Plasma cfDNA from xenograft

value: Epithelial


title: Liver tissue, CD163WT, Western diet, rep L

description: Library name: D432


title: CAMA-1 xenograft plasma cfDNA WGS, replicate 1

description: Library name: CAMA1_xeno_plasma_C6M1


title: SU-DHL-6 cf-chromatin, 30ng input, ChIP-Seq, H3K4me3, rep1


title: KU50 cultivar, heat (42°C), 5 hours

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

country: Japan

institute: RIKEN

description:
Library name: KU50_Heat
total RNA

data_processing:
base-calling:bcl2fastq
adapter trim: trimmomatic
alignment: Bowtie2
In order to identify the transcription start site, the RECLU pipeline was used.
Assembly: Mesculenta_671_v8.0
Supplementary files format and content: bed

organism: Manihot esculenta

source_name: Leaf and stem

growth_protocol: Cassava (Manihot esculenta) plants (cultivars ECU72 and KU50) were propagated from stem cuttings and grown in controlled environment chambers under a 12-hour light/12-hour dark photoperiod at 25°C. One-month-old plants were used for stress treatments.

extract_protocol:
Total RNA was extracted using RNeasy Plant Mini Kit (QIAGEN) with DNaseI treatment. RNA quality was verified via Bioanalyzer (RIN >7.5).
nAnT-iCAGE-seq libraries were prepared with the previously described protocol (https://doi.org/10.1007/978-1-4939-0805-9_7).

treatment_protocol: Control: Plants were maintained at 25°C for 5 hours. Heat stress: Plants were transferred to 42°C chambers for 5 hours. Cold stress: Plants were transferred to 4°C chambers for 5 hours. After treatment, the youngest leaves and shoot apices were immediately harvested, flash-frozen in liquid nitrogen, and stored at –80°C until RNA extraction.

value: Leaf and stem

value: Heat

value: WT


title: KU50 cultivar, cold (4°C), 5 hours

description:
Library name: KU50_Cold
total RNA

value: Cold


title: Liver tissue, CD163KO, Western diet, rep O

description: Library name: D431

value: Liver

value: Western diet, 8 weeks


title: CAMA-1 ATAC-Seq, biol rep2

data_processing:
The analytical pipeline can be found on the CoBE platform (www.pmcobe.ca/pipeline/60a4336aaf7a3251ac7e152d).
TrimGalore (v0.6.5) was used to trim FASTQ files.
Bowtie2 (v2.3.5.1) was used for alignment to hg38.
MACS2 (v2.2.6) was used for peak calling and narrowPeak files were saved.
Assembly: hg38
Supplementary files format and content: narrowPeak, for both biological replicates

growth_protocol: CAMA-1 was cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin solution. CAMA-1 was cultured in adherent dishes and in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Two biological replicates of 50,000 CAMA-1 cells were lysed to prepare nuclei for the transposition reaction.
A Tn5 enzyme was used for the transposition reaction and samples were cleaned up with the Qiagen MinElute PCR Purification Kit (CAT #28004) with 250 μL of buffer PB for each 50 μL sample. The libraries were amplified for 7-8 PCR cycles. The libraries were then cleaned-up with the Qiagen MinElute PCR Purification Kit and size selected with Beckman Coulter AMPure beads. Library quality control was performed by ensuring greater than ten fold enrichment for open chromatin with a qPCR for two constitutively open (GAPDH and KAT6B) and closed regions (QML93 and SLC22A3) . Further library quality control was performed with a Qubit High Sensitivity dsDNA kit and Agilent 2100 Bioanalyzer.

value: Breast; Mammary gland


title: KU50 cultivar, control (25°C), 5 hours

description:
Library name: KU50_Control
total RNA

value: Control


title: NOA_3_7_3

description: Sample 201

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
For bisulfite-seq data, Trim Galore (v0.3.3) was used to remove the first 6 bases of random primer, adaptor sequences and low quality bases; for RNA-seq data, each single cell was separated by unique cell barcode, then template switch oligo (TSO), ployA tails, adaptors and low quality bases were removed.
For bisulfite-seq data, clean reads were first mapped to human reference genome hg19 with Bismark (v0.7.6) in paired-end and non-directional module, and then the unmapped reads were realigned to the same reference genome in single-end and non-directional module; for RNA-seq data, clean reads were mapped to human genome hg19 with Tophat (v2.0.14), and then unique UMI counts were calculated by HTSeq.
WCG and GCH methylation level of cytosines was estimated using comstomized scripts.
Genome_build: hg19
Supplementary_files_format_and_content: UMI_count.txt files include UMI counts of RefSeq genes. While WCG.txt and GCH.txt files include the read counts of cytosines in WCG and GCH context respectively. The columns in WCG.txt or GCH.txt files represent "chr" "position" "unmethylated read counts" "methylated read counts".

source_name: testis

extract_protocol:
An individual cell was picked into the cell lysis buffer with vitro methylation (IVM) mixture containing 4 U RNase inhibitor (TAKARA, Cat. 2313B), 0.25% IGEPAL CA-630 (SIGMA, Cat. I3021), 1X GC reaction buffer and 2 U M. CviPI (NEB, Cat. M0227L). After gently vortexed for 10 sec, the cell lysate was incubated at 37 °C for 20 min and then at 65 °C for 25 min. Then, the cell lysate could be directly processed for RNA/DNA separation or stored at -80 °C.
For RNA part, a modified Smart-seq2 protocol was applied for single-cell RNA-seq. For DNA part, Bisulfite-converted DNA was amplified with biotinylated random primer and klenow exo– polymerase (NEB, M0212L) for 7 rounds and excess primer was removed by exonuclease I (NEB, M0293L). After second strands synthesis, the library was amplified by KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602) for 14 cycles.

value: male

value: nonobstructive azoospermia (NOA)


title: Tet2het_ISO_A16 CD45+ tumor-infiltrating leukocytes (TILs) from MC38 tumors

description:
Library name: Tet2het_ISO_A16
10X Genomics

value: Subcutaneous MC38 tumor (right flank)

value: MC-38 (colon adenocarcinoma)

value: CD45+ tumor-infiltrating leukocytes

value: isotype control (rat IgG2a)

value: female


title: CAMA-1 ATAC-Seq, biol rep1


title: Liver tissue, CD163KO, Western diet, rep N

description: Library name: D430


title: ECU72 cultivar, cold (4°C), 5 hours

description:
Library name: ECU72_Cold
total RNA


title: SU-DHL-6 cf-chromatin, 300ng input, ChIP-Seq, H3K4me3, rep1

value: Peritoneal effusion

value: Diffuse Large B-cell lymphoma

value: B Lymphocyte

value: Abcam, ab1012


title: ECU72 cultivar, control (25°C), 5 hours

description:
Library name: ECU72_Control
total RNA

value: Leaf and stem

value: WT


title: NOA_3_6_5

description: Sample 197

value: testis


title: SA00799_MGUS_529

city: Liège

first: Jo

last: Caers

address: Avenue de l'Hôpital

country: Belgium

institute: CHU de Liège

description:
5' barcoded RNA + Antibody-derived oligonucleotide library
The file name is constructed based on SampleID_Cohort_ExperimentID

data_processing:
Sample demultiplexing, barcode processing, alignment to the human transcriptome (GRCh38), single-cell 5′ gene, V(D)J and feature barcode counting were performed using Cell Ranger Single-Cell Software Suite (cellranger-4.0.0, 10x Genomics). Each data type (RNA, ADT, BCR) was then pre-processed per sample independently and subsequently concatenated into a single dataset for further downstream analysis. Unless stated otherwise, for each data analysis step, related functions from the scanpy (v1.6.1) Python package were used with default parameters.
Empty droplets and dying cells were filtered out based on UMI counts < 650, minimum number of genes < 300 and mitochondrial gene expression > 20%. Doublet detection was conducted by Scrublet (v0.2.1). Droplets with a Scrublet doublet score > 0.3 and genes expressed in <3 cells were excluded. Following the initial filtering, a cell per million (CPM) normalization was applied with a scale factor of 10^4 and the data were log transformed. Highly variable genes were detected with Seurat flavor. For the downstream analyses, immunoglobulin genes (IG) were removed from the dataset. Cell cycle scores were calculated using score_genes_cell_cycle function from scanpy using the gene sets identified by Kowalczyk et al..
Droplets with UMI counts  500 were excluded. The data were normalized using centered log-ratio (CLR) transformation
Cell Ranger filtered BCR-seq output contig files from individual samples were concatenated into a single file. Using the scirpy (v0.6.1) library, with parameters receptor_arms=all and dual_ir=primary only, observed clonotypes were defined based on CDR3 nucleic acid sequences. To assess clonal expansion, per-sample-clonotype definitions were generated using both CDR3 nucleic acid sequences and sample IDs. Per-sample-clonotypes observed in  10 cells were considered expanded malignant clonotypes.
Gene expression based principal component analysis (PCA) and Harmony (v1.0) batch correction, using theta=0, was performed. Nearest neighborhood networks were constructed using a cosine distance. Each integrated dataset was projected onto 2D space applying the UMAP algorithm based on the standard settings of scanpy. Cell typing was performed as described in the publication.
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: raw_feature_bc_matrix.h5. Integrated_processed_data.h5ad file includes the following information: batch (SampleID), cohort, experimentID, clonotype, isExpandedClonotype (expansion status), cellType, isLowQuality (high mito or low nr of genes within the same cell type), highly_variable, gene_ids, feature_types, cohort_colors, X_umap (RNa based), log (log counts).

source_name: BM aspirate mononuclear cells mRNA-derived cDNA and ADT-derived cDNA

extract_protocol:
BM-MNCs were isolated from BM aspirate using Ficoll-plaque gradient separation and processed for single cell 10x Genomics 5' Chromium single cell V(D)J with Feature Barcoding protocol.
The library was constructed using single cell 10x Genomics 5' Chromium single cell V(D)J with Feature Barcoding protocol.

tag: sample id

tag: cohort

value: monoclonal gammopathy of unknown significance (MGUS)

value: Bone Marrow

value: BM aspirate mononuclear cells

tag: library type

value: mRNA and ADT