title: Ai1: Mtb, A-ALF, after infection, rep1

description:
Sample 9
ALF-Mtb_AOF_raw.txt


title: E16, H4K20me2, WT, rep2

status: Public on Oct 21 2024

type: SRA

city: Ann Arbor

first: Shigeki

last: Iwase

state: Michigan

address: 1241 E. Catherine St.

department: Human Genetics

country: USA

institute: University of Michigan

library_source: genomic

data_processing:
Reads were aligned to the UCSC mm10 genome using Bowtie2. Non-unique alignments (MAPQ > 10) and reads < 140-nt were filtered out.
bigWig files were generated using bamCoverage (deepTools), with files normalized to BPM for each replicate.
Average coverage was calculated from biological replicates within each genotype using bigWigCompare (operation set to “mean”).
To reduce background noise, final normalization to IgG samples was performed using bigWigCompare (operation set to “ratio”).
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

molecule: genomic DNA

organism: Mus musculus

source_name: cortex

extract_protocol:
The digested target chromatin was released and purified by phenol, chloroform, and ethanol.
Sequencing libraries were prepared with NEBNxt Ultra II DNA (NEB #E7645L) and NEB UDI plate 1 (NEB #E6440L)

treatment_protocol: E16.5 cortices are taken from two embryos per genotype (the sex was balanced between genotypes) and washed with HHGN solution78 then washed 4 times with HHGN containing 10% FBS, treated with 0.1 mg/ml DNaseI for 5 mins at RT, triturated using a P1000 pipet. Dissociated cells were precipitated by a centrifugation at 1500 rpm for 5 min, and washed with dPBS (Gibco, 14190). 1 million cells per sample were re-suspended in Wash buffer (20 mM HEPES pH7.5, 150 mM NaCl, 0.5 mM spermidine, 1X protease inhibitor cocktail), and Concanavalin A-coated beads (Bangs Laboratories, Inc., #BP531) were added into the cell suspension and incubated for 10 min. Bead-bound cells were then incubated overnight at 4°C in Wash buffer supplemented with EDtA and digitonin (EMD Millipore, #300410, Wash buffer D) and 1 µg antibody. The beads were then washed three times with Wash buffer D, followed by an incubation with 200 µl pA-MNase (0.7 ng/µl) for 1 hour at 4°C. The beads were washed three times Wash buffer D before 2 mM of CaCl2 were added to activate the pA-MNase for 30 min on ice. The reaction was quenched by 2X stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.02% Digitonin, 50 µg/ml RNase A (QIAGEN, #19101), 50 µg/ml glycogen (Roche, #10901393001) and 2 pg/ml Drosophila spike-in DNA) at 37°C for 10 min.

tag: tissue

value: cortex

tag: genotype

value: WT

tag: cut&run antibody

value: H4K20me2 (Abcam, ab9052)


title: S4KO_EB_Dnmt3b CUT&Tag_1

city: Shanghai

first: yanhua

last: du

address: 227 South Chongqing Road, Huangpu District

department: Shanghai Institute of Immunology

country: China

institute: Shanghai Jiaotong University School of Medicine

data_processing:
Sequencing reads were trimmed by using cutadapt tool with parameters --trim-n  -m 30 -q 20,20.
Sequencing reads were aligned to mm10 genome using Bowtie2 version 2.4.4 with default parameters. Only uniquely and properly paired mapping reads were retained.
Peaks for ChIP-seq data were called using MACS v2.2.7 with the sinificance cut-off P-value <=0.05 and fold change >=3; Peaks for CUT & Tag data were called using MACS v2.2.7 with the sinificance cut-off Q-value <=0.01 and fold change >=4
Assembly: mm10
Supplementary files format and content: bigWig files for each samples.
Library strategy: CUT&Tag

extract_protocol:
For ChIP-Seq sample preparation, ES or EB cells are treated with Activin or SB505124 as indicated, fixed and quenched, sonicated to average fragment size of 250bp in 1% SDS lysis buffer, and incubated with 60ul Dynabeads protein G conjugated with 3-5ug of indicated antibodies. 2% pre-cleared chromatin prior to primary antibody addition was kept as input DNA. Magnetic beads were washed, chromatin was eluted, and reverse crosslinked ChIP DNA was dissolved in 10 mM Tris pH 8.0 buffer for further analysis. For CUT&Tag, 1*10^5 ME cells or EB cells treated either with or without Activin as indicated, were harvested and crosslinked with 0.1% formaldehyde if necessary. Followed steps were performed using a commercially available kit (Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro, Vazyme, TD904).
For ChIP-Seq library construction, ChIP-Seq DNA samples were quantified and quality assessed by Qubit and AATI Fragment Analyzer. DNA fragments range from 200-600bp were selected constructed for ChIP-Seq library with VAHTS® Universal Pro DNA Library Prep Kit for Illumina (Vazyme, ND608) according to manufacturer’s instructions. For CUT&Tag library construction, purified DNA samples were carried out following manual (Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro, Vazyme, TD904)

treatment_protocol: Recombinant human Activin A (R&D Systems, 338-AC) were used at 50ng/ml. SB505124 (10uM, selleck, S2186) were used at 10μM.

tag: cell line

value: Smad4 knockout

tag: treatment

value: LIF removal and form EB for 3.5 days.


title: E16, H3K9me2, KO, rep2


title: UE2: Mtb, unexposed, before infection, rep2

city: San Antonio

first: Anna

last: Allue Guardia

state: Texas

address: 8715 Military Dr W

institute: Texas Biomedical Research Institute

description:
Sample 7
ALF-Mtb_AOF_raw.txt

library_source: transcriptomic

data_processing:
Raw sequencing reads were trimmed and aligned to the M.tb H37Rv reference genome (Genbank NC_000962.3) with the STAR aligner v2.5.3a in the Partek Flow Genomic Analysis software using default settings.
Data were filtered to remove poorly expressed genes and differentially expressed genes (DEGs) were identified using the DESeq2 method with an FDR cut-off of 0.1 and a minimum fold change (FC) of 2 in the iDEP.94 software.
Assembly: H37Rv (Genbank NC_000962.3)
Supplementary files format and content: Raw counts

molecule: total RNA

organism: Mycobacterium tuberculosis

source_name: Bacterial culture

growth_protocol: Before infection: M.tb Erdman were cultured from frozen stocks for 14 days at 37°C in 7H11 agar plates (Remel), supplemented with oleic acid, albumin, dextrose and catalase (OADC). After infection: A549 cell line (ATs) were infected with M.tb Erdman for 72 hours at 37°C with 5% CO2.

extract_protocol:
Bacterial RNA was extracted using the Quick-RNA Fungal/Bacterial Miniprep kit (Zymo Research). Briefly, bacterial pellets were suspended in RNA lysis buffer and transferred to a ZR BashingBead Lysis tube containing 0.1 mm and 0.5 mm ceramic beads. Samples underwent a bead beating procedure in a Disruptor Genie (10 cycles of 1 min at maximum speed with 1 min intervals on ice), facilitating the breaking down of the M.tb cell envelope. RNA in the supernatant was isolated using the Zymo-spin columns, including an in-column DNAse I treatment, and was finally eluted in nuclease-free water. A second DNAse treatment was performed on the extracted RNA using the TURBO DNAse reagent (Thermo Fisher Scientific, Waltham, MA, USA). RNA was further purified using the RNA Clean & Concentrator kit (Zymo Research, Irvine, CA, USA),  MA, USA). Conversely, infected ATs (at 72 hpi) were washed twice with culture media and then lysed with GTC solution (4M guanidinium thiocyanate, 0.5% sodium N-lauryl sarcosine, 25 mM tri-sodium citrate, 0.1M 2-mercaptoethanol, 0.5% Tween 80, pH 7.0) 34, 35 for 5 min at RT and then centrifuged at 5000 x g for 30 min at RT to recover bacteria. M.tb pellets were washed in GTC lysis solution to combine the content from all flasks (4 x 150 cm2 flasks/ condition) into one single tube, centrifuged, and suspended in RNA lysis buffer. RNA was then extracted using the Quick-RNA Fungal/Bacterial Miniprep kit, treated with TURBO DNAse, and purified with the RNA Clean & Concentrator kit, as previously described.
A whole-stranded transcriptome RNA library was generated using the Zymo-Seq RiboFree Total RNA kit (Zymo Research, Irvine, CA, USA), following the manufacturer’s protocol. RNA (250 ng) was used as input to construct the library, which included a rRNA depletion step of 30 min followed by 15 cycles of PCR. Using a NextSeq 500 Mid Output Illumina platform, a 75-bp paired-end (PE) sequencing was conducted. RNA sequencing was performed on three independent experiments (n = 3 per condition), except for E-ALF-exposed M.tb before infection (n=2), where one of the replicates was not included in the study due to low RNA concentration and quality.

treatment_protocol: Single bacterial suspensions were obtained and exposed to human ALFs for 12 ± 2 hours at 37°C. Following exposure, bacteria were thoroughly washed to remove any unbound ALF; the bacterial pellet was either stored at -80°C for further RNA extraction [after incubation in RNAProtect (Qiagen, Hilden, Germany) for 10 min at room temperature, RT] or suspended in culture media for ATs infection. Infected ATs (at 72 hpi) were washed twice with culture media and then lysed with GTC solution (4M guanidinium thiocyanate, 0.5% sodium N-lauryl sarcosine, 25 mM tri-sodium citrate, 0.1M 2-mercaptoethanol, 0.5% Tween 80, pH 7.0) 34, 35 for 5 min at RT and then centrifuged at 5000 x g for 30 min at RT.

tag: strain

value: Erdman

tag: cell type

value: Bacterial culture

tag: condition

value: Before infection


title: UE1: Mtb, unexposed, before infection, rep1

description:
Sample 6
ALF-Mtb_AOF_raw.txt


title: E14_EB_Dnmt3b CUT&Tag_1

value: Wildtype


title: HEK293T_R-M1-1

city: guangzhou

first: Ye

last: Shaotang

address: No. 483, Wushan Road, Tianhe District, Guangzhou

institute: South China Agricultural University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Homo sapiens

source_name: Human embryonic kidney cells

growth_protocol: DMEM with 2% FBS

extract_protocol:
prefrontal cortex were rharvested , flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Transfection by Lipo8000 (Beyotime, China)

value: Human embryonic kidney cells

tag: passages

value: transfected with CIV M1 and canine RIG-I


title: HEK293T_R-M1-2


title: E14_EB_Dnmt3b CUT&Tag_2


title: E16, H3K9me2, KO, rep1


title: HEK293T_M2-2

value: transfected with CIV M2


title: E3: Mtb, E-ALF, before infection, rep3

description:
Sample 5
ALF-Mtb_AOF_raw.txt

value: Elderly ALF


title: HEK293T_M2-3


title: E16, H4K20me2, KO, rep1


title: E16, H3K9me2, WT, rep1


title: aal1OE_BiolRep2

city: London

first: Shajahan

last: Anver

address: Gower Street London

department: Genetics, Evolution and Environment

country: United Kingdom

institute: University College London

data_processing:
Libraries were spiked with 20% PhiX (Illumina) to increase the complexity of the libraries to accommodate clustering and sequenced in an Illumina MiSeq (75 bp, paired-end) instrument.
All quality control steps including quality filtering, demultiplexing and adapter removal were performed with Illumina BaseSpace in-house tools. The quality of the sequences was confirmed with FastQC (ver 0.11.2, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were mapped with Hisat2 (version 2.2.1, code used: hisat2 -x genomeIndex --rna-strandness FR --trim5 8 -1 pair1.fastq.gz -2 pair2.fastq.gz -S out.sam --summary-file summary.txt)
sam files were converted to bam files and sorted/indexed with samtools (ver 1.14) and sorted bam files were used to count reads per gene with htseq (ver. 0.12.3, https://htseq.readthedocs.io/en/master/index.html; code use: htseq-count -s reverse -f bam -t gene -i ID file.bam annotation.gff3  > file.count).
The top aal1-bound RNAs were determined with edgeR (version 3.32.1;  Since there were no significantly enriched RNAs (FDR ≤0.05) in the wild-type relative to aal1∆ cells, we chose the top 30 enriched RNAs which were verified in IGV (ver 2.8.0, https://software.broadinstitute.org/software/igv/). For IGV inspection, strand-specific MiSeq reads were processed further with deepTools (ver 3.5.1, https://deeptools.readthedocs.io/en/develop/) to get normalised gene coverage in counts per million (cpm) per 50 bp bins (bam to bigWig files) for direct comparison.
Assembly: genome build as of January 2020 downloaded from pombase.org
Supplementary files format and content: raw gene counts files combined as a table with counts for each biological replicate as a separate column. In .xlsx format (excel sheet)
Supplementary files format and content: bigwig (.bw) files with normalised gene coverage in counts per million (cpm) per 50 bp bins (bam to bigWig)
Library strategy: ChIRP-RNAseq

organism: Schizosaccharomyces pombe

source_name: cell culture

extract_protocol:
RNA was extracted with QIAzol and RNeasy Mini kit (Qiagen) according to the manufacturer’s recommendations, including a DNase treatment.
RNA quality was assessed in an Agilent 2100 Bioanalyzer and strand-specific cDNA libraries were made NEXTflex Rapid Directional qRNA-Seq Kit (PerkinElmer, formerly BiooScientific). Libraries were quantified in a Qubit, pooled and 4 nM of the pooled library was sequenced

value: cell culture

value: aal1 overexpressed in a plasmid with a thiamine-repressible P41nmt1 promoter in  972h-/leu1-32 background

value: pull down with Dynabeads (Invitrogen, magnetic Streptavidin) and eluted with biotin elution buffer (12.5 mM biotin – Invitrogen, 7.5 mM HEPES pH 7.5, 75 mM NaCl, 1.5 mM EDTA, 0.15% SDS, 0.075% sarkosyl, 0.02% Na-Doc)


title: E16, H3K9me2, WT, rep2


title: A3: Mtb, A-ALF, before infection, rep3

description:
Sample 3
ALF-Mtb_AOF_raw.txt

value: Adult ALF


title: wild type_BiolRep2

value: 972h- wild type


title: wild type_BiolRep1


title: E16, H3K4me2, KO, rep1

value: cortex

value: H3K4me2 (EpiCypher, 13-0027)


title: HEK293T_M1-2

value: transfected with CIV M1


title: E16, H3K4me2, KO, rep2


title: E16, H3K4me2, WT, rep2

value: WT


title: UE3: Mtb, unexposed, before infection, rep3

description:
Sample 8
ALF-Mtb_AOF_raw.txt

value: Erdman


title: aal1D_BiolRep2

value: aal1 deleted with CRISPR-Cas9 in 972h- background


title: A2: Mtb, A-ALF, before infection, rep2

description:
Sample 2
ALF-Mtb_AOF_raw.txt

value: Bacterial culture

value: Before infection


title: E1: Mtb, E-ALF, before infection, rep1

description:
Sample 4
ALF-Mtb_AOF_raw.txt


title: HEK293T_M1-1

value: Human embryonic kidney cells


title: aal1OE_BiolRep1


title: HEK293T_M1-3


title: 5 mM meftormin + 0.6 mM 2DG, dettached, rep 3

status: Public on Oct 20 2024

city: Ljubljana

first: Mojca

last: Pavlin

address: Vrazov Trg 2

country: Slovenia

institute: University of Ljubljana,

data_processing:
Data was processed by Novogene
Assembly: ensembl_homo_sapiens_grch38_p12_gca_000001405_27
Supplementary files format and content: xls -(fpkm and gene count)

source_name: Breast; Mammary gland

growth_protocol: MDA-MB-231 cells were routinely grown in RPMI-1640 medium with 25 mM glucose, 2 mM glutamine and 10 % FBS

extract_protocol:
Cells were washed twice with ice cold PBS, snap freezed in liquid nitrogen, and stored at – 80 °C. Total cell RNA was isolated from cell pellets using PureLink™ RNA Mini Kit (Invitrogen, ThermoFisher Scientific, Waltham, USA)
RNA library was prepared by Novogene

treatment_protocol: For all experiments, cells were seeded in complete RPMI-1640 with 25 mM glucose for 24 h, washed with isotonic NaCl, and subsequently grown in RPMI-1640 medium supplemented with 10% FBS, 2 mM glutamine and 5.6 mM. Cells were treated with 4.8 mM 2DG, 0.6 mM 2DG+5 mM metformin or grown on polyHEMA for 72 h. For cell selection, after 72 hours, detached cells were reseed in compound free media for 72 hours and again treated with the same compounds. We repeated 4 cycles of selection.

value: Breast; Mammary gland

value: cancer, epithelial cell

value: wild type

value: 5 mM meftormin + 0.6 mM 2DG


title: polyHEMA rep 3

value: growth on polyHEMA


title: polyHEMA, rep 2


title: 5 mM meftormin + 0.6 mM 2DG, dettached, rep 1


title: polyHEMA, rep 1


title: 5 mM meftormin + 0.6 mM 2DG, attached, rep 2


title: E16, H3K4me2, WT, rep1


title: 4.8 mM 2DG, dettached, rep 3

value: 4.8 mM 2DG


title: 5 mM meftormin + 0.6 mM 2DG, attached, rep 1


title: 5 mM meftormin + 0.6 mM 2DG, dettached, rep 2


title: 4.8 mM 2DG, attached, rep 2


title: ctrl, rep 3

value: untreated


title: ctrl, rep 1


title: HEK293T_M2-1

value: transfected with CIV M2


title: ctrl, rep 2


title: 4.8 mM 2DG, dettached, rep 2


title: polyHEMA, selected, rep 3

value: selected subpopulation of detached cells


title: 5 mM meftormin + 0.6 mM 2DG, selected, rep 1


title: 5 mM meftormin + 0.6 mM 2DG, selected, rep 3


title: 4.8 mM 2DG, dettached, rep 1


title: 4.8 mM 2DG, selected, rep 2


title: 4.8 mM 2DG, attached, rep 3


title: 4.8 mM 2DG, selected, rep 1


title: 4.8 mM 2DG, attached, rep 1


title: ctrl, selected, rep 1


title: polyHEMA, selected, rep 2


title: 5 mM meftormin + 0.6 mM 2DG, selected, rep 2


title: polyHEMA, selected, rep 1


title: 4.8 mM 2DG, selected, rep 3


title: FHRCC85, primary tumor

city: Sichuan

first: Hao

last: Zeng

address: Department of Urology, Third Inpatient Building, West China Hospital, Sichuan University, Chengdu,

institute: West China Hospital, Sichuan University

data_processing:
FASTP (v0.20.1)
Raw RNA-Seq reads were trimmed the adapter sequences and filtered low-quality bases using FASTP (v0.20.1), followed by mapping to human genome reference hg19 with STAR (v2.7.9a).
During alignment, STAR was supplied with transcript models GENCODE v19 from https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.3.
The quality control metrics were obtained using FastQC (v0.11.9) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and alignment quality metrics of bam files were measured using RSeQC (v4.0.0)
RNA abundance was calculated using RSEM(v1.2.28) and the RSEM results were converted with Bioconductor package tximport (v4.1).
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: kidney

extract_protocol:
RNAs were extracted and purified from FFPE tissues by the RNeasy FFPE Kit (73504, Qiagen, Germany), according to the manufacturer’s instructions, and quantified with Qubit RNA HS Assay Kit (Thermo Fisher Scientific). Purity and quantity of total RNA were measured by Nanodrop. Integrity of RNA was evaluated using the RNA Nano6000 Assay Kit on the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). 1μg RNA of per sample was used as input for the RNA sample preparations.
Strand-specific RNA sequencing libraries were generated using the Whole RNA-seq Lib Prep kit for Illumina (RK20303, ABclonal, Shanghai, China). Library quality was evaluated on the Agilent Bioanalyzer 2100 system (Agilent, USA). Final libraries were sequenced at the Novogene Bioinformatics Institute (Beijing, China) on an Illumina Hiseq X10 platform by 150bp paired-end reads.

value: kidney


title: ctrl, selected, rep 2


title: HiChIP_ALL-SIL_H3K27ac

first: Sunniyat

last: Rahman

address: 72 Huntley Street

institute: UCL

data_processing:
Alignment and generation of mapped read pairs against hg38 was achieved by using bwa, pairtools, and samtools piped with the following command: bwa mem -5SP -T0 -t<cores> <ref.fa> <HiChiP.R1.fastq.gz> <HiChiP.R2.fastq.gz>| \pairtools parse --min-mapq 40 --walks-policy 5unique \--max-inter-align-gap 30 --nproc-in <cores> --nproc-out <cores> --chroms-path <ref.genome> | \pairtools sort --tmpdir=<full_path/to/tmpdir> --nproc <cores>|pairtools dedup --nproc-in <cores> \--nproc-out <cores> --mark-dups --output-stats <stats.txt>|pairtools split --nproc-in <cores> \--nproc-out <cores> --output-pairs <mapped.pairs> --output-sam -|samtools view -bS -@<cores>| \samtools sort -@<cores> -o <mapped.PT.bam>;samtools index <mapped.PT.bam>. Significant loops were identified from the HiChIP data by using FitHiChIP with the following paramaters: IntType=3, BINSIZE=40000, LowDistThr=10000, UppDistThr=2000000, UseP2PBackgrnd=0, BiasType=1, MergeInt=1 and QVALUE=0.01.
Assembly: hg38
Supplementary files format and content: bedpe for IGV
Library strategy: HiChIP

source_name: ALL-SIL

growth_protocol: RPMI + 10% FBS + 1% pen/strep. Cultured at 37oC, 5% CO2

extract_protocol:
HiChIP MNase libraries were prepared using the Dovetail HiChIP MNase Kit according to the manufacturer’s protocol. Briefly, the chromatin was fixed with disuccinimidyl glutarate (DSG) and formaldehyde in the nucleus. The cross-linked chromatin was digested in situ with micrococcal nuclease (MNase) then extracted upon cell lysis. The chromatin fragments were incubated with the H3K27ac antibody (abcam – ab4729) overnight for chromatin immunoprecipitation. The antibody-protein-DNA complex was pulled down with protein A/G-coated beads. Next, the chromatin ends were repaired and ligated to a biotinylated bridge adapter followed by proximity ligation of adapter-containing ends. After proximity ligation, the crosslinks were reversed, the associated proteins were degraded, and the DNA was purified then converted into a sequencing library using Illumina-compatible adaptors. Biotin-containing fragments were isolated using streptavidin beads prior to PCR amplification.
Dovetail HiChIP MNase Kit

value: ALL-SIL

value: T lymphoblast

value: FTO intron 8 deletion


title: FHRCC77, primary tumor


title: FHRCC77, adjacent normal kidney tissue


title: FHRCC78, adjacent normal kidney tissue


title: FHRCC76, primary tumor


title: ctrl, selected, rep 3


title: ATAC-seq_PF-382_FTO_int8del

data_processing:
Paired-end reads were trimmed with cutadapt -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT. Reads were aligned against hg38 with bowtie2 with flags -p 10 in paired-end mode. Duplicates were marked and removed by using picard MarkDuplicates REMOVE_DUPLICATES=true. Peak calling was achieved by using macs2 callpeak function with flags -f BAMPE -g hs --bdg --nolambda. Bedgraph was generated with deeptools bamCoverage --bam -bs 1 -p max -of bedgraph --normalizeUsing RPGC --effectiveGenomeSize 2913022398 --ignoreForNormalization chrX. TDF file of bedgraph was generated with IGVtools.
Assembly: hg38
Supplementary files format and content: bedgraph (TDF)

source_name: PF-382, CRISPR edited bulk line

extract_protocol: First a resuspension buffer was made of 10mM Tris-HCl, pH 7.5, 10mM NaCl, 3mM MgCl2. Briefly, 50,000 cells were washed in ice cold 1X PBS and pelleted by centrifugation. The pellet was lysed in 50 µL of lysis buffer comprised of 48.5 µL resuspension buffer, 0.5 µL 10% NP-40 (Sigma), 0.5 µL 10% Tween-20 (Sigma), 0.5 µL 1% Digitonin (Promega). Following incubation on ice for 3 minutes samples were washed with 1 mL wash buffer comprised of 990µL resuspension buffer, 10 µL 10% Tween-20. Nuclei were retained following centrifugation at 500g for 10 mins at 4oC. Transposition mixes were made with the following reagents 25µL 2X TD/Tagment DNA Buffer (Illumina), 16.5µL 1X PBS, 0.5µL 10% Tween-20 (Sigma), 0.5µL 1% Digitonin (Promega), 2.5µL Tn5 Transposase/Tagment DNA Enzyme 1 (Illumina) and 5µL nuclease-free H2O. Nuclei were gently resuspended in the transposition mix and incubated for 30 minutes at 37oC on a thermomixer at 1,000 rpm. After transposition DNA was purified with AMPure XP beads at a 1.8x ratio. Purified transposed DNA was amplified by PCR by using the NEBNext High-Fidelity 2X PCR Master Mix (NEB) with ATAC-seq primers. PCR cycle number was optimised by spiking in 100X SYBR Green I followed by qPCR to ensure amplification did not reach saturation. Amplified libraries were purified by AMPure XP beads at a 1.8x ratio. Libraries were sequenced at ~30 million paired reads per sample on an NextSeq (Illumina).

value: PF-382, CRISPR edited bulk line


title: FHRCC85, adjacent normal kidney tissue


title: ATAC-seq_PF-382

value: FTO wild type


title: FHRCC75, primary tumor


title: FHRCC74, primary tumor


title: ATAC-seq_ALL-SIL


title: FHRCC70, primary tumor


title: FHRCC81, primary tumor


title: FHRCC68, primary tumor


title: FHRCC80, primary tumor


title: FHRCC79, primary tumor


title: FHRCC79, adjacent normal kidney tissue


title: FHRCC78, primary tumor


title: FHRCC76, adjacent normal kidney tissue


title: FHRCC65, primary tumor


title: UMI4C_PF-382_IRX3_CTCF5pbait_techrep1

data_processing:
Data was processed by using the UMI4Cats ver 1.14.0 by following the vignette available on Bioconductor. Alignments were against hg19 by using the reference library(BSgenome.Hsapiens.UCSC.hg19) and genes were annotated with library(TxDb.Hsapiens.UCSC.hg19.knownGene).
Assembly: hg19
Library strategy: UMI4C

extract_protocol: 5 µg of 3C template from each experimental condition was sonicated at 4ºC for 20 cycles (30s ON/ 60 s OFF) on a Bioruptor Pi.co (Diagenode). The post-sonication size distribution was checked on a 2200 Tapestation (Agilent) with D1000 Screentape to ensure an ideal peak distribution size of 450 – 550 bp. The sonicated DNA was end-repaired by the End Repair Module (NEB – E6050L) and cleaned up with 2.2x AmpureXP beads (Beckman Coulter) followed by dA-tailing (NEB – E6053L) as per the manufacturers’ reaction conditions and instructions. Following A-tailing, DNA was cleaned up with 2x AmpureXP beads and eluted in 67 µL of EB buffer (Qiagen). Illumina compatible adapters (IDT – xGEN UDI-UMI adapters) were ligated by using T4 ligase (NEB – M0202S) overnight at 16ºC. Two nested PCR reactions were conducted with the following bait sequences for the FTO intron 8 CTCF site, 5’-GAAAGGCTTGTTCTTCCTGGC-3’ for bait 1 (upstream primer), 5’- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTTGGAACTGCTGTTTCCCACTT-3’ for bait 2 (Illumina prefix appended to downstream primer). The bait sequences for the IRX3 proximal promoter were, 5’-AGGAAGAAGTGAAGGGAACGGA-3’ for bait 1 (upstream primer), 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTTGCAGGAGCCCGAAGCA-3’ for bait 2 (Illumina prefix appended to downstream primer). The bait sequences for the CTCF site 5’ to IRX3 were, 5’-GAGAACCTTCCTTGCGCGAC-3’ for bait 1 (upstream primer), 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTCCGGCGCTAACCTCTTTTCT-3’ for bait 2 (Illumina prefix appended to downstream primer). The bait sequences for the CTCF site 3’ to IRX3 were, 5’-TCAACACTGCACACCTTCGA-3’ for bait 1 (upstream primer), 5-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTGGGAGTTCCCTCCGCGAA-3’ for bait 2 (Illumina prefix appended to downstream primer) and 5’-CAAGCAGAAGACGGCATACGA-3’ for the Illumina enrichment primer. The PCR reactions were performed in 50 μl volume with the following reagents: 10 μl GoTaq Flexi buffer (Promga M792A), 3 μl MgCl 25 mM (Promega A3511), 0.2 mM dNTPs, 2 μl 10 mM bait 1/upstream primer (0.4 mM final concentration), 2 μl 10 mM Illumina enrichment primer (0.4 mM final concentration), 1 μl GoTaq Hot Start (Promega M5005) and 200 ng UMI-4C DNA template. PCR program: 2 min 95 °C, 20 cycles of 30 s 95 °C, 30 s 56 °C and 60 s 72 °C and final extension of 5 min 72 °C. Amplified DNA was cleaned with 1x AmpureXP beads, and the eluate was used as a template in the second PCR reaction. Conditions for the second PCR reaction were identical to the first, and the only differences were the use of the bait primer 2. The molarity of the libraries were quantified by using a Qubit dsDNA HS Assay Kit (ThermoFisher – Q32851) together with a Tapestation (Agilent). Libraries were pooled and diluted to 4 nM concentration and multiplexed with other libraries, including a 10% PhiX spike-in (Illumina) and sequenced on a MiSeq (Illumina) with a MiSeq Reagent Nano Kit v2, 300 cycles (Illumina).


title: FHRCC65, adjacent normal kidney tissue


title: UMI4C_PF-382_IRX3_CTCF3pbait_techrep3


title: FHRCC72, primary tumor


title: UMI4C_PF-382_IRX3_CTCF5pbait_techrep3


title: FHRCC64, primary tumor


title: FHRCC71, primary tumor


title: FHRCC72, adjacent normal kidney tissue


title: FHRCC71, adjacent normal kidney tissue


title: FHRCC67, primary tumor


title: FHRCC64, adjacent normal kidney tissue


title: FHRCC61, primary tumor


title: FHRCC70, adjacent normal kidney tissue


title: FHRCC74, adjacent normal kidney tissue


title: UMI4C_PF-382_IRX3_CTCF5pbait_techrep2


title: FHRCC61, adjacent normal kidney tissue


title: FHRCC60, primary tumor


title: FHRCC66, primary tumor


title: UMI4C_PF-382_FTOint8_CTCFdel__clone3_IRX3bait

source_name: PF-382, CRISPR edited single cell derived clone

value: FTO intron 8 CTCF site deletion


title: UMI4C_PF-382_IRX3_CTCF3pbait_techrep2


title: FHRCC63, primary tumor


title: UMI4C_PF-382_WTclone1_IRX3bait

source_name: PF-382, unedited single cell derived clone


title: UMI4C_PF-382_IRX3_CTCF3pbait_techrep1


title: FHRCC57, primary tumor


title: A1: Mtb, A-ALF, before infection, rep1

description:
Sample 1
ALF-Mtb_AOF_raw.txt

value: Erdman

value: Bacterial culture

value: Adult ALF

value: Before infection


title: UMI4C_PF-382_FTOint8_CTCFbait_techrep3


title: FHRCC57, adjacent normal kidney tissue


title: UMI4C_PF-382_FTOint8_CTCFbait_techrep2


title: UMI4C_PF-382_FTOint8_CTCFbait_techrep1


title: FHRCC60, adjacent normal kidney tissue


title: FHRCC59, primary tumor


title: S. Typhimurium 14028s, RpoS, ChIP-mini, heat shock conditions (42°C), replicate 2

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

data_processing:
Sequenced reads of S. Typhimurium 14028s samples were mapped onto NC_016856.1 and NC_016855.1 reference genome sequence using bowtie v1.0.0 with parameters -p 8 -S.
Sigma factors binding sites were identified using DEOCSU(DEep-learning Optimized ChIP-exo peak calling SUite).
Binding intensity of sigma factors was calculated by Signal to Noise ratio (S/N)
Assembly: NC_016856.1, NC_016855.1
Supplementary files format and content: Binding sites and their intensities of ChIP-mini datasets were included.
Library strategy: ChIP-exo

organism: Salmonella enterica subsp. enterica serovar Typhimurium

growth_protocol: S. Typhimurium 14028s and it derivates cells were grown to mid-exponential phase (OD600 ≈ 0.6)  aerobically at 37°C in 50ml of M9 minimal media supplemented with 0.2% glucose. For heat-shock experiments, S. Typhimurium strains were grown to mid-exponential phase at 37°C. and half of the culture was used as a control, while the remaining culture was transferred into pre-warmed (50°C) media and incubated in a 42°C water bath with constant agitation for 15 min.

extract_protocol:
Chromatin Immunoprecipitation (ChIP)
KAPA HiFi HotStart ReadyMix

tag: chip antibody

value: Anti-RpoS

value: WT


title: S. Typhimurium 14028s, RpoS, ChIP-mini, heat shock conditions (42°C), replicate 1


title: FHRCC59, adjacent normal kidney tissue


title: UMI4C_PF-382_IRX3bait


title: UMI4C_ALL-SIL_IRX3bait


title: S. Typhimurium 14028s, RpoS, ChIP-mini, control conditions (37°C), replicate 1


title: FHRCC58, adjacent normal kidney tissue


title: S. Typhimurium 14028s, RpoD, ChIP-mini, heat shock conditions (42°C), replicate 2

value: Anti-RpoD


title: S. Typhimurium 14028s, RpoH, ChIP-mini, heat shock conditions (42°C), replicate 2

value: Anti-c-myc


title: S. Typhimurium 14028s, RpoH, ChIP-mini, heat shock conditions (42°C), replicate 1


title: FHRCC56, primary tumor


title: S. Typhimurium 14028s, RpoH, ChIP-mini, control conditions (37°C), replicate 1


title: FHRCC56, adjacent normal kidney tissue


title: FHRCC53, primary tumor


title: FHRCC58, primary tumor


title: S. Typhimurium 14028s, RpoS, ChIP-mini, control conditions (37°C), replicate 2


title: FHRCC52, primary tumor


title: FHRCC47, primary tumor


title: aal1D_BiolRep1

value: cell culture

value: aal1 deleted with CRISPR-Cas9 in 972h- background

value: pull down with Dynabeads (Invitrogen, magnetic Streptavidin) and eluted with biotin elution buffer (12.5 mM biotin – Invitrogen, 7.5 mM HEPES pH 7.5, 75 mM NaCl, 1.5 mM EDTA, 0.15% SDS, 0.075% sarkosyl, 0.02% Na-Doc)


title: FHRCC52, adjacent normal kidney tissue

value: kidney


title: FHRCC45, primary tumor


title: FHRCC50, primary tumor


title: S. Typhimurium 14028s, RpoD, ChIP-mini, heat shock conditions (42°C), replicate 1


title: S. Typhimurium 14028s, RNA-seq, control conditions (37°C), replicate 2

data_processing:
Sequenced reads of S. Typhimurium 14028s samples were mapped onto NC_016856.1 and NC_016855.1 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S.
Transcript Per Million (TPM) were calculated using featureCounts in R. Differentially expressed genes were identifiec using DEseq2 in R.
Assembly: NC_016856.1, NC_016855.1
Supplementary files format and content: Tab-delimited text files (.tsv) include TPM values and DEGs for samples.

extract_protocol:
The cell culture was treated with the RNAprotect reagent (Qiagen).
RNA libraries were prepared using KAPA RNA Hyper Prep kit for sequencing using standard Illumina protocols

treatment_protocol: Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a Qubit 4.0 (Thermo Scientific Inc., Wilmington, DE, USA).


title: S. Typhimurium 14028s, RpoH, ChIP-mini, control conditions (37°C), replicate 2


title: FHRCC49, primary tumor


title: FHRCC48, primary tumor


title: S. Typhimurium 14028s, RNA-seq, control conditions (37°C), replicate 1


title: FHRCC42, adjacent normal kidney tissue


title: FHRCC48, adjacent normal kidney tissue


title: 5 mM meftormin + 0.6 mM 2DG, attached, rep 3

value: Breast; Mammary gland

value: cancer, epithelial cell

value: wild type

value: 5 mM meftormin + 0.6 mM 2DG


title: FHRCC39, primary tumor


title: FHRCC53, adjacent normal kidney tissue


title: S. Typhimurium 14028s, delta rpoS, RNA-seq, heat shock conditions (42°C), replicate 2

value: delta rpoS


title: S. Typhimurium 14028s, delta rpoS, RNA-seq, heat shock conditions (42°C), replicate 1


title: RKO_input

city: Saint Louis

first: Ting

last: Wang

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in Saint Louis

data_processing:
Adaptor trimming: cutadapt -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA --quality-cutoff=15,10 --minimum-length=36
Alignment: bowtie2 v2.3.4.1 --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Peak calling: MACS2 v 2.2.1  -f BAMPE -q 0.01 --keep-dup all
Bigwig generation: bamCoverage
Assembly: hg38
Supplementary files format and content: bedgraph

source_name: RKO

growth_protocol: A549 cells were cultured in F-12K supplemented with 10% FBS and 1%Pen/Strep (P/S). HCT116 cells were cultured in McCoy's 5A modified supplemented with 10%FBS and 1%P/S. RKO were cultured in RPMI 1640 supplemented with 10%FBS and 1%P/S.

extract_protocol:
P53 ChIP was performed using iDeal ChIP-seq kit for Transcription Factors (Diagenode, C01010055) and 1 µg p53 antibody (Diagenode, C15410083 ) for each IP of 5 million cells
Library construction used Ultra II DNA Library Prep kit (NEB, E7645) following the manufacturer’s instructions.

treatment_protocol: 1uM doxorubicin 24hrs for treatment condition. 0.1% DMSO 24hrs for control condition.

value: RKO

value: input


title: FHRCC46, primary tumor


title: FHRCC46, adjacent normal kidney tissue


title: S. Typhimurium 14028s, delta rpoS, RNA-seq, control conditions (37°C), replicate 2


title: FHRCC38, adjacent normal kidney tissue


title: S. Typhimurium 14028s, RNA-seq, heat shock conditions (42°C), replicate 2


title: S. Typhimurium 14028s, delta rpoS, RNA-seq, control conditions (37°C), replicate 1


title: S. Typhimurium 14028s, RpoD, ChIP-mini, control conditions (37°C), replicate 2


title: FHRCC35, primary tumor


title: HCT116_WT_DMSO

value: DMSO


title: S. Typhimurium 14028s, RNA-seq, heat shock conditions (42°C), replicate 1


title: S. Typhimurium 14028s, RpoD, ChIP-mini, control conditions (37°C), replicate 1


title: FHRCC43, primary tumor


title: A549_WT_DOX

value: DOX


title: FHRCC32, primary tumor


title: FHRCC42, primary tumor


title: FHRCC39, adjacent normal kidney tissue


title: RKO_WT_DMSO


title: FHRCC30, primary tumor


title: FHRCC29, primary tumor


title: RKO_WT_DOX


title: RKO_WT_DOX_WGBS_BRep2

data_processing:
Adaptor trimming: Cutadapt v1.18
Alignment was done using Bismark v0.20.0, follwoed by deduplication using (deduplicate_bismark) and DNA methylation levels were calculated using (bismark_methylation_extractor).
Assembly: hg38
Supplementary files format and content: bedgraph

extract_protocol:
Genome DNA was extracted using Quick-DNA Microprep Kit (Zymo Research, R3020).
DNA was sheared to produce 350 bp DNA fragments. 100 ng of DNA fragments were then bisulfite converted using EZ DNA Methylation-Gold Kit (Zymo, D5005) for subsequent WGBS library construction, with xGen Methyl-Seq DNA Library Prep Kit (IDT, 10009860).


title: FHRCC38, primary tumor


title: FHRCC35, adjacent normal kidney tissue


title: RKO_WT_DOX_WGBS_BRep1


title: HCT116_WT_DOX


title: A549_input


title: RKO_WT_DMSO_WGBS_BRep2


title: RKO_KO_DOX_WGBS_BRep1

value: KO


title: FHRCC26, primary tumor


title: RKO_KO_DOX_WGBS_BRep2


title: FHRCC28, primary tumor


title: RKO_WT_DMSO_WGBS_BRep1

value: WT


title: FHRCC23, primary tumor


title: FHRCC30, adjacent normal kidney tissue


title: FHRCC26, adjacent normal kidney tissue


title: FHRCC27, adjacent normal kidney tissue


title: FHRCC27, primary tumor


title: FHRCC28, adjacent normal kidney tissue


title: HCT116_input


title: HCT116_WT_DOX_WGBS_BRep2


title: A549_WT_DMSO


title: FHRCC19, primary tumor


title: RKO_KO_DMSO_WGBS_BRep2


title: FHRCC23, adjacent normal kidney tissue


title: HCT116_WT_DOX_WGBS_BRep1


title: RKO_KO_DMSO_WGBS_BRep1


title: HCT116_WT_DMSO_WGBS_BRep2


title: FHRCC16, adjacent normal kidney tissue


title: HCT116_WT_DMSO_WGBS_BRep1


title: FHRCC16, primary tumor


title: HCT116_KO_DOX_WGBS_BRep2


title: FHRCC09, adjacent normal kidney tissue


title: FHRCC15, adjacent normal kidney tissue


title: HCT116_KO_DMSO_WGBS_BRep1


title: HCT116_KO_DOX_WGBS_BRep1


title: HCT116_KO_DMSO_WGBS_BRep2


title: FHRCC06, primary tumor


title: FHRCC08, adjacent normal kidney tissue


title: FHRCC07, primary tumor


title: A549_WT_DMSO_WGBS_BRep2


title: A549_WT_DMSO_WGBS_BRep1


title: FHRCC09, primary tumor


title: A549_KO_DOX_WGBS_BRep1


title: A549_KO_DMSO_WGBS_BRep2


title: A549_WT_DOX_WGBS_BRep2


title: FHRCC04, adjacent normal kidney tissue


title: FHRCC08, primary tumor


title: FHRCC15, primary tumor


title: A549_WT_DOX_WGBS_BRep1


title: A549_KO_DOX_WGBS_BRep2


title: FHRCC06, adjacent normal kidney tissue


title: RKOWT_DOX_RNA-seq_BRep1

description:
RKO_R1_gene_count_matrix.csv
all_samples_teprof3_RKO_WT_vs_KO_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv
DOX_RKO_WT_vs_KO_DETranscript.csv
DMSO_DOX_WT_KO_teprof3_tier1_quantification.tsv
DMSO_DOX_WT_KO_teprof3_tier1.tsv

data_processing:
Cutadapt for adapter trimming: cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --minimum-length 50
Alignmeng: STAR v2.6.1b --outSAMtype BAM   SortedByCoordinate   --outSAMstrandField intronMotif   --outSAMattributes NH HI NM MD AS XS --outSAMunmapped Within --outSAMheaderHD @HD VN:1.4 --outFilterMultimapNmax 20 --outFilterScoreMinOverLread 0.33 --outFilterMatchNminOverLread 0.33  --alignIntronMax 500000  --alignMatesGapMax 1000000 --twopassMode Basic
De novo assembly: Stringtie2 version 2.2.1
Quantification: Stringtie2 version 2.2.1
Assembly: hg38
Supplementary files format and content: csv files include raw count for each sample
Supplementary files format and content: tsv files include custom transcript reference and quantification from each sample
Supplementary files format and content: csv files include DESeq2 differentially expressed transcripts using custom reference

extract_protocol:
Total RNA was extracted with the RNAeasy mini kit (Qiagen, 74104) using 5-10M cells. 1ug high quality RNA was used for sequencing library construction.
The cDNA libraries were prepared using a TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) according to the manufacturer’s instructions.


title: FHRCC05, primary tumor


title: A549_KO_DMSO_WGBS_BRep1


title: FHRCC04, primary tumor


title: FHRCC03, primary tumor


title: RKOWT_DOX_RNA-seq_BRep2

description:
RKO_R2_gene_count_matrix.csv
all_samples_teprof3_RKO_WT_vs_KO_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv
DOX_RKO_WT_vs_KO_DETranscript.csv
DMSO_DOX_WT_KO_teprof3_tier1_quantification.tsv
DMSO_DOX_WT_KO_teprof3_tier1.tsv


title: RKOKO_WT_DOX_RNA-seq_BRep2

description:
RKO_R2_gene_count_matrix.csv
all_samples_teprof3_RKO_KOWT_vs_KOEV_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: RKOWT_DMSO_RNA-seq_BRep2

description:
RKO_R2_gene_count_matrix.csv
all_samples_teprof3_RKO_WT_vs_KO_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv
DMSO_RKO_WT_vs_KO_DETranscript.csv
DMSO_DOX_WT_KO_teprof3_tier1_quantification.tsv
DMSO_DOX_WT_KO_teprof3_tier1.tsv


title: FHRCC02, primary tumor


title: RKOKO_WT_DMSO_RNA-seq_BRep1

description:
RKO_R1_gene_count_matrix.csv
all_samples_teprof3_RKO_KOWT_vs_KOEV_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: RKOKO_R273H_DOX_RNA-seq_BRep1

description:
RKO_R2_gene_count_matrix.csv
all_samples_teprof3_RKO_KO273_vs_KOWT_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: FHRCC02, adjacent normal kidney tissue


title: CD2-iCre CD2-Lmo2 Psip1 KO, thymoma, CDNA004063

city: Gent

first: Igor

last: Fijalkowski

address: Sint-Pietersnieuwstraat 33

country: Belgium

institute: Ugent

description:
CDNA004063
Lmo2_countMatrix_GEO.txt

data_processing:
alignment by STAR 2.7.10
quantified on Gencode v44
Assembly: GRCh38 or GRCm39
Supplementary files format and content: tab-delimited text file includes the raw counts for each sample (column name specified for each sample under description).

source_name: Thymus

growth_protocol: Tumors were collected, dissociated into a single cell suspension by using a 40 µM cell strainer (Novolab, A09360), treated with red blood cell lysis buffer (Gibco, A1049201), washed in phosphate-buffered saline (PBS) (Gibco, 10010023), and stored as a pellet and/or viable cells in 10% DMSO in heat-inactivated fetal bovine serum (FBS) (HyClone GE, SV3016003). Jurkat cells were maintained in in RPMI 1640 medium (Gibco, 52400025) supplemented with 10% FBS, 100 U/mL penicillin and 100 µg/mL streptomycin (Gibco, 15140163), and 2 mM L-glutamine (L-Glu)(Gibco, 25030081) at 37°C and 5% CO2.

extract_protocol:
RNA was extracted from the samples by using the RNeasy Plus Micro Kit (Qiagen, 74034) according to the manufacturer’s instructions.
RNAseq libraries were prepared with the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, 015.96) according to the manufacturer’s instructions.

value: Thymus

value: T-ALL


title: RKOKO_R175H_DMSO_RNA-seq_BRep1

description:
RKO_R1_gene_count_matrix.csv
all_samples_teprof3_RKO_KO175_vs_KOWT_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: RKOKO_EV_DOX_RNA-seq_BRep2

description:
RKO_R2_gene_count_matrix.csv
all_samples_teprof3_RKO_KOEV_vs_KOWT_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: Jurkat, IgG (H3K36me3-matched control), CUT&RUN

description:
instrument model: AVITI
diff_peaks_H3K36me3_vs_IgG.MAPQ30_keepdupauto_hg38_peaks.broadPeak

data_processing:
Adapter sequences were trimmed using Trim-Galore v0.6.5
Reads were aligned to GRCh38 or GRCm39 using bowtie2 v2.3.1.
Sorted and quality filtered (MAPQ30) aligned files were deduplicated using picard v2.25.1.
Peak calling was performed using MACS2 v2.1.0
Significant peaks were further processed using the ChIPseeker R package (v1.38.0).
Assembly: GRCh38 or GRCm39
Supplementary files format and content: BigWig files containing RPM normalized signal, peaklist files containing significant MACS2 peaks
Library strategy: CUT&RUN

source_name: Jurkat

growth_protocol: Murine thymi were collected, dissociated into a single cell suspension by using a 40 µM cell strainer (Novolab, A09360), treated with red blood cell lysis buffer (Gibco, A1049201), washed in phosphate-buffered saline (PBS) (Gibco, 10010023), and stored as a pellet and/or viable cells in 10% DMSO in heat-inactivated fetal bovine serum (FBS) (HyClone GE, SV3016003). Jurkat cells were maintained in in RPMI 1640 medium (Gibco, 52400025) supplemented with 10% FBS, 100 U/mL penicillin and 100 µg/mL streptomycin (Gibco, 15140163), and 2 mM L-glutamine (L-Glu)(Gibco, 25030081) at 37°C and 5% CO2.

extract_protocol:
CUT&RUN was performed using CUTANA pA/G-MNase (Epicypher, 15-1016) according to manufacturer’s instructions except for minor adaptations. Per sample, nuclei of 0.5M cells were extracted (20mM HEPES-KOH pH 7.9, 10mM KCl, 0.1% Triton X-100, 20% glycerol 1mM MnCl2, 0.5mM spermidine and protease inhibitors), incubated for 10 min at 4°C on a rotator with activated concanavalin A beads, resuspended in antibody buffer (150mM NaCl, 20mM HEPES-KOH pH 7.5, 2mM EDTA, 0.5mM spermidine and protease inhibitors) and incubated overnight at 4°C with rotation with 1:100 dilution of antibody recognizing PSIP1 (Bethyl, A300-848A), H3K27me3 (Cell Signaling Technology, 97335), H3K36me3 (Abcam, ab9050) or a rabbit anti-IgG (Cell Signaling Technology, 3900S). Targeted chromatin digestion and release was performed with 2.5 µl CUTANA pA/G-MNase and 100 mM CaCl2. The reaction was terminated with STOP buffer (340 mM NaCl, 4mM EGTA, 20mM EDTA, RNAase (0.05 mg/ml) and glycogen (0.05 µg/ml). For the mice samples, 0.01 ng/ml spike-in E.Coli DNA (Epicypher, 18-1401) was added. Retrieved genomic DNA was purified with the CUTANA DNA purification kit V2 (Epicypher, 14-0050).
Smples were library prepped using the NEBNext Ultra II DNA Library Prep Kit according to the manufacturing’s instructions, but NEBNext Endprep was conducted at 50°C for 1h. Sequencing was done on the AVITI, 2x75 (Element Biosciences).

value: Jurkat

value: E.Coli spike-in control

tag: antibody

value: IgG (Cell Signaling Technology, 3900S)


title: Jurkat, H3K36me3, CUT&RUN

value: H3K36me3 (Abcam, ab9050)


title: RKOKO_WT_DOX_RNA-seq_BRep1

description:
RKO_R1_gene_count_matrix.csv
all_samples_teprof3_RKO_KOWT_vs_KOEV_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: RKOKO_EV_DOX_RNA-seq_BRep1

description:
RKO_R1_gene_count_matrix.csv
all_samples_teprof3_RKO_KOEV_vs_KOWT_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: Jurkat, IgG (PSIP1-matched control), CUT&RUN

description:
instrument model: AVITI
diff_peaks_PSIP_Jurkat_vs_IgG_Jurkat.MAPQ30_keepdupauto_hg38_peaks.narrowPeak


title: RKOKO_DOX_RNA-seq_BRep2


title: CD2-iCre CD2-Lmo2 Psip1 WT, thymoma, CDNA004056

description:
CDNA004056
Lmo2_countMatrix_GEO.txt

value: CD2-iCre_+/+_CD2-LMO2_tg/+_Psip fl/fl


title: FHRCC01, primary tumor

value: kidney


title: RKOKO_WT_DMSO_RNA-seq_BRep2

description:
RKO_R2_gene_count_matrix.csv
all_samples_teprof3_RKO_KOWT_vs_KOEV_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: CD2-iCre CD2-Lmo2 Psip1 KO, thymoma, CDNA004066

description:
CDNA004066
Lmo2_countMatrix_GEO.txt


title: Jurkat, PSIP1, CUT&RUN

value: PSIP1 (Bethyl, A300-848A)


title: CD2-iCre CD2-Lmo2 Psip1 WT, thymoma, CDNA004057

description:
CDNA004057
Lmo2_countMatrix_GEO.txt


title: RKOKO_EV_DMSO_RNA-seq_BRep2

description:
RKO_R2_gene_count_matrix.csv
all_samples_teprof3_RKO_KOEV_vs_KOWT_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: CD2-iCre CD2-Lmo2 Psip1 KO, thymoma, CDNA004062

description:
CDNA004062
Lmo2_countMatrix_GEO.txt


title: CD2-iCre CD2-Lmo2 Psip1 KO, thymoma, CDNA004061

description:
CDNA004061
Lmo2_countMatrix_GEO.txt


title: RKOKO_R175H_DOX_RNA-seq_BRep1

description:
RKO_R2_gene_count_matrix.csv
all_samples_teprof3_RKO_KO175_vs_KOWT_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: CD2-iCre CD2-Lmo2 Psip1 WT, thymoma, CDNA004055

description:
CDNA004055
Lmo2_countMatrix_GEO.txt


title: CD2-iCre CD2-Lmo2 Psip1 KO, thymoma, CDNA004060

description:
CDNA004060
Lmo2_countMatrix_GEO.txt


title: RKOWT_DMSO_RNA-seq_BRep1

description:
RKO_R1_gene_count_matrix.csv
all_samples_teprof3_RKO_WT_vs_KO_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv
DMSO_RKO_WT_vs_KO_DETranscript.csv
DMSO_DOX_WT_KO_teprof3_tier1_quantification.tsv
DMSO_DOX_WT_KO_teprof3_tier1.tsv


title: CD2-iCre CD2-Lmo2 Psip1 KO, thymoma, CDNA004059

description:
CDNA004059
Lmo2_countMatrix_GEO.txt


title: CD2-iCre CD2-Lmo2 Psip1 WT, thymoma, CDNA004058

description:
CDNA004058
Lmo2_countMatrix_GEO.txt


title: RKOKO_EV_DMSO_RNA-seq_BRep1

description:
RKO_R1_gene_count_matrix.csv
all_samples_teprof3_RKO_KOEV_vs_KOWT_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: RKOKO_DOX_RNA-seq_BRep1

description:
RKO_R1_gene_count_matrix.csv
all_samples_teprof3_RKO_WT_vs_KO_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv
DOX_RKO_WT_vs_KO_DETranscript.csv
DMSO_DOX_WT_KO_teprof3_tier1_quantification.tsv
DMSO_DOX_WT_KO_teprof3_tier1.tsv


title: Blood, HU-MTD, HU50

city: Atlanta

first: Varsha

last: Bhat

state: Georgia

address: 950 Atlantic Drive, EBB1

institute: Georgia Institute of Technology

data_processing:
Quality control of the paired-end reads was performed using FastQC (version 0.11.9).
Read alignment was performed using STAR (version 2.7.10b)12 with the GRCh38 primary assembly and GENCODE annotation (release 42)
The number of reads per gene was quantified using HTSeq (version 2.0.2) with the same GENCODE annotation as reference.
Genes with zero expression in at least 10% of the samples were removed, and the raw read counts were normalized for library size with the TMM method implemented in edgeR.
The washout samples were excluded for differential gene expression analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes normalized counts for each sample

source_name: Blood

extract_protocol:
A total of 3 mL of whole blood was collected in EDTA tubes for each patient during either baseline or HU washout, and at HU MTD and processed within four hours of collection.
RNA sequencing (RNA-seq) libraries were prepared using the Illumina TruSeq RNA Library Prep Kit and sequenced on the Illumina HiSeq 4000 with a paired-end 150-bp reads protocol

value: Blood

tag: age in_yrs

tag: Sex

value: F

value: HU-MTD


title: RKOKO_R273H_DMSO_RNA-seq_BRep1

description:
RKO_R1_gene_count_matrix.csv
all_samples_teprof3_RKO_KO273_vs_KOWT_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv

value: RKO


title: CD2-iCre CD2-Lmo2 Psip1 WT, thymoma, CDNA004052

description:
CDNA004052
Lmo2_countMatrix_GEO.txt


title: Blood, HU-MTD, HU48


title: Blood, HU-MTD, HU46

value: M


title: RKOKO_175_DMSO_RNA-seq_BRep2

value: DMSO


title: RKOKO_DMSO_RNA-seq_BRep2

value: KO


title: HCT116WT_DOX_RNA-seq_BRep1

description:
HCT116_R1_gene_count_matrix.csv
all_samples_teprof3_HCT116_WT_vs_KO_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv
DOX_HCT116_WT_vs_KO_DETranscript.csv
DMSO_DOX_WT_KO_teprof3_tier1_quantification.tsv
DMSO_DOX_WT_KO_teprof3_tier1.tsv

value: WT

value: DOX


title: Blood, HU-MTD, HU42


title: HCT116WT_DMSO_RNA-seq_BRep2

description:
HCT116_R2_gene_count_matrix.csv
all_samples_teprof3_HCT116_WT_vs_KO_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv
DMSO_HCT116_WT_vs_KO_DETranscript.csv
DMSO_DOX_WT_KO_teprof3_tier1_quantification.tsv
DMSO_DOX_WT_KO_teprof3_tier1.tsv


title: CD2-iCre CD2-Lmo2 Psip1 WT, thymoma, CDNA004054

description:
CDNA004054
Lmo2_countMatrix_GEO.txt

value: Thymus

value: T-ALL


title: RKOKO_273_DMSO_RNA-seq_BRep2


title: Lck-Cre Pten Psip1 KO, thymoma, L17

description:
L17.A7_S17ReadsPerGene.out.tab
Pten_countMatrix_GEO.txt


title: Lck-Cre Pten Psip1 KO, thymoma, L20

description:
L20.D7_S20ReadsPerGene.out.tab
Pten_countMatrix_GEO.txt


title: HCT116WT_DMSO_RNA-seq_BRep1

description:
HCT116_R1_gene_count_matrix.csv
all_samples_teprof3_HCT116_WT_vs_KO_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv
DMSO_HCT116_WT_vs_KO_DETranscript.csv
DMSO_DOX_WT_KO_teprof3_tier1_quantification.tsv
DMSO_DOX_WT_KO_teprof3_tier1.tsv


title: Blood, HU-MTD, HU38


title: Blood, HU-MTD, HU44


title: RKOKO_175_DOX_RNA-seq_BRep2


title: Lck-Cre Pten Psip1 KO, thymoma, L19

description:
L19.C7_S19ReadsPerGene.out.tab
Pten_countMatrix_GEO.txt


title: HCT116KO_WT_DOX_RNA-seq_BRep2

description:
HCT116_R2_gene_count_matrix.csv
all_samples_teprof3_HCT116_KOWT_vs_KOEV_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: RKOKO_273_DOX_RNA-seq_BRep2

description:
RKO_R2_gene_count_matrix.csv
all_samples_teprof3_RKO_KO273_vs_KOWT_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: Lck-Cre Pten Psip1 KO, thymoma, L16

description:
L16.H6_S16ReadsPerGene.out.tab
Pten_countMatrix_GEO.txt


title: HCT116WT_DOX_RNA-seq_BRep2

description:
HCT116_R2_gene_count_matrix.csv
all_samples_teprof3_HCT116_WT_vs_KO_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv
DOX_HCT116_WT_vs_KO_DETranscript.csv
DMSO_DOX_WT_KO_teprof3_tier1_quantification.tsv
DMSO_DOX_WT_KO_teprof3_tier1.tsv


title: Blood, HU-MTD, HU40


title: HCT116KO_WT_DOX_RNA-seq_BRep1

description:
HCT116_R1_gene_count_matrix.csv
all_samples_teprof3_HCT116_KOWT_vs_KOEV_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: RKOKO_DMSO_RNA-seq_BRep1


title: Blood, HU-MTD, HU34


title: HCT116KO_WT_DMSO_RNA-seq_BRep2

description:
HCT116_R2_gene_count_matrix.csv
all_samples_teprof3_HCT116_KOWT_vs_KOEV_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: Blood, HU-MTD, HU32


title: HCT116KO_WT_DMSO_RNA-seq_BRep1

description:
HCT116_R1_gene_count_matrix.csv
all_samples_teprof3_HCT116_KOWT_vs_KOEV_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: Lck-Cre Pten Psip1 KO, thymoma, L13

description:
L13.E6_S13ReadsPerGene.out.tab
Pten_countMatrix_GEO.txt


title: Blood, HU-MTD, HU36


title: MC38-iPM nanovax-3

city: Beijing

last: Li

address: Zhongguancun street

institute: NCNST

data_processing:
Basecalls performed using fastp
RNA-seq reads were aligned to the  genome assembly using HiSat2.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include TPM values for each sample.

source_name: MC38 tumor tissue

extract_protocol:
The total RNA from tumor tissues were extracted through MJZol extraction kit.
Libraries were prepared according to Illumina's instructions accompanying Stranded mRNA Prep.

value: MC38 tumor tissue

value: MC38 cell

value: tumor cell

value: iPM nanovax


title: MC38-Lipoadjuvant-3

value: Lipo-adjuvant


title: Lck-Cre Pten Psip1 KO, thymoma, L15

description:
L15.G6_S15ReadsPerGene.out.tab
Pten_countMatrix_GEO.txt


title: Blood, HU-MTD, HU30


title: Lck-Cre Pten Psip1 KO, thymoma, L18

description:
L18.B7_S18ReadsPerGene.out.tab
Pten_countMatrix_GEO.txt


title: MC38-Lipoadjuvant-2


title: HCT116KO_EV_DOX_RNA-seq_BRep1

description:
HCT116_R1_gene_count_matrix.csv
all_samples_teprof3_HCT116_KOEV_vs_KOWT_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: Lck-Cre Pten Psip1 WT, thymoma, L6

description:
L6.F5_S6ReadsPerGene.out.tab
Pten_countMatrix_GEO.txt


title: Lck-Cre Pten Psip1 KO, thymoma, L14

description:
L14.F6_S14ReadsPerGene.out.tab
Pten_countMatrix_GEO.txt


title: Blood, HU-MTD, HU26


title: MC38-Lipoadjuvant-1


title: MC38-iPM nanovax-2


title: Blood, HU-MTD, HU24


title: Blood, HU-MTD, HU22


title: FOXA2_NT_rep2

city: WuHan

first: chenchao

last: yan

state: Hubei Province

address: Donghu Road, No. 115

institute: WuHan university

data_processing:
The raw reads were quality-controlled using FastQC (v0.11.8) with default parameters.
Adapter and reads with low-quality base were removed using trim_galore (0.6.4).
The resulting clean RNA-seq reads were aligned to human genome (hg38) using HISAT2 (v2.1.0), sorted and indexed using Samtools (v1.9).
The number of reads (raw_counts) per gene was determined using FeatureCounts (v1.6.4).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.

extract_protocol:
ThecellswerewashedbyDPBSandharvestedbybufferRL.TheHiPureTotalRNAMiniKit(Magen,Cat#R4111-03)wasusedtoextracttotalRNAfollowingthemanufacturer’sinstructionsandtheRNAwasquantitatedwithnanodrop2000(ThermoFisher).
cDNA libraries for each sample were constructed as reported previously. Libraries were sequenced on DNBSEQ-T7 platform (BGI-Shenzhen, China), using 150 bp paired-end reads.


title: Blood, HU-MTD, HU28


title: HCT116KO_EV_DMSO_RNA-seq_BRep2

description:
HCT116_R2_gene_count_matrix.csv
all_samples_teprof3_HCT116_KOEV_vs_KOWT_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: MC38-iPM nanovax-1


title: Lck-Cre Pten Psip1 WT, thymoma, L3

description:
L3.C5_S3ReadsPerGene.out.tab
Pten_countMatrix_GEO.txt


title: HCT116KO_DOX_RNA-seq_BRep2


title: Lck-Cre Pten Psip1 KO, thymoma, L12

description:
L12.D6_S12ReadsPerGene.out.tab
Pten_countMatrix_GEO.txt


title: Lck-Cre Pten Psip1 WT, thymoma, L5

description:
L5.E5_S5ReadsPerGene.out.tab
Pten_countMatrix_GEO.txt


title: HCT116KO_EV_DOX_RNA-seq_BRep2

description:
HCT116_R2_gene_count_matrix.csv
all_samples_teprof3_HCT116_KOEV_vs_KOWT_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: Blood, HU-MTD, HU18


title: HCT116KO_EV_DMSO_RNA-seq_BRep1

description:
HCT116_R1_gene_count_matrix.csv
all_samples_teprof3_HCT116_KOEV_vs_KOWT_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: HCT116KO_DOX_RNA-seq_BRep1

description:
HCT116_R1_gene_count_matrix.csv
all_samples_teprof3_HCT116_WT_vs_KO_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv
DOX_HCT116_WT_vs_KO_DETranscript.csv
DMSO_DOX_WT_KO_teprof3_tier1_quantification.tsv
DMSO_DOX_WT_KO_teprof3_tier1.tsv


title: FOXA2_dox_rep2


title: Lck-Cre Pten Psip1 WT, thymoma, L2

description:
L2.B5_S2ReadsPerGene.out.tab
Pten_countMatrix_GEO.txt


title: HCT116KO_DMSO_RNA-seq_BRep2

description:
HCT116_R2_gene_count_matrix.csv
all_samples_teprof3_HCT116_WT_vs_KO_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv
DMSO_HCT116_WT_vs_KO_DETranscript.csv
DMSO_DOX_WT_KO_teprof3_tier1_quantification.tsv
DMSO_DOX_WT_KO_teprof3_tier1.tsv


title: Lck-Cre Pten Psip1 WT, thymoma, L1

description:
L1.A5_S1ReadsPerGene.out.tab
Pten_countMatrix_GEO.txt


title: Blood, HU-MTD, HU16


title: FOXA2_dox_rep1


title: Lck-Cre Pten Psip1 WT, thymoma, L4

description:
L4.D5_S4ReadsPerGene.out.tab
Pten_countMatrix_GEO.txt


title: i33-BM-C2plus-Pamc4-3SL_S9

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

institute: University of Oxford

description:
PAM3CSK4 100 µg/ml and 3SL 100 µl/ml - 6hr
BM_Pamc4w3SL_C2plus

data_processing:
Analysis of the data was performed using CGAT tools and pipelines (https://github.com/cgat-developers)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.1.0 with parameters --score-min L,0.0,-0.2
Reads were counted to features using featurecounts (part of the subreads package) v2.0.1
Genome_build: Hg38
Supplementary_files_format_and_content: comma-delimited text files of read counts for each sample

source_name: Bone marrow-derived macrophages

extract_protocol:
RNA from cells was harvested using Trizol reagent. Libraries were constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®
RNA libraries were prepared for sequencing using standard NEB protocols

value: Bone marrow


title: Blood, HU-MTD, HU20

value: Blood


title: snpGG_pp2_rep2


title: FOXA2_NT_rep1


title: HCT116KO_273_DOX_RNA-seq_BRep2

description:
HCT116_R2_gene_count_matrix.csv
all_samples_teprof3_HCT116_KO273_vs_KOWT_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: snpAA_pp2_rep1


title: Blood, HU-MTD, HU12

value: F


title: i32-BM-B2plus-Pamc4-3SL_S8

description:
PAM3CSK4 100 µg/ml and 3SL 100 µl/ml - 6hr
BM_Pamc4w3SL_B2plus


title: snpGG_pp2_rep1


title: cow.bulk.esc.4

first: Jianyong

last: Han

address: 2rd, Yuanmingyuan West Road

department: State Key Laboratory of Agrobiotechnology

institute: China Agricultural University

data_processing:
For RNA-seq, Expression levels of protein coding genes were quantified as transcripts per million (TPM) using kallisto (v-0.46.0). DEGs between different cell types were identified using the DEseq2 tool (v-1.30.1). We used Benjamini-Hochberg adjusted false discovery rate (FDR) < 0.05 and absolute log2 (fold change) >2 as cut-offs for statistical significance.
Assembly:Bos_taurus.ARS_UCD1.2
Supplementary files format and content: txt

organism: Bos taurus

source_name: Embryonic epiblast

extract_protocol:
For bulk RNA-seq, total RNA was extracted separately from four bEpiSCs samples using the RNeasy Mini Kit (Qiagen, 74106).
For bulk RNA-seq, for constructing strand-specific RNA-seq libraries, we employed a rRNA depletion protocol (Globin-Zero Gold rRNA Removal Kit, Illumina, GZG1224) in conjunction with the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, E7420S). All libraries were quantified using the Qubit dsDNA High Sensitivity Assay Kit (Invitrogen, Life Technologies, Q32851) and sequenced on an Illumina HiSeq 4000 platform.

value: Embryonic epiblast


title: cow.bulk.esc.3


title: i31-BM-A2plus-Pamc4-3SL_S7

description:
PAM3CSK4 100 µg/ml and 3SL 100 µl/ml - 6hr
BM_Pamc4w3SL_A2plus


title: snpAA_pp2_rep2


title: HCT116KO_273_DOX_RNA-seq_BRep1

description:
HCT116_R1_gene_count_matrix.csv
all_samples_teprof3_HCT116_KO273_vs_KOWT_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: Blood, HU-MTD, HU14

value: HU-MTD


title: cow.bulk.esc.2


title: Blood, HU-MTD, HU10

value: M


title: i30-BM-D3-Pamc3_S6

description:
PAM3CSK4 100 µg/ml - 6hr
BM_Pamc3_D3


title: HCT116KO_273_DMSO_RNA-seq_BRep2

description:
HCT116_R2_gene_count_matrix.csv
all_samples_teprof3_HCT116_KO273_vs_KOWT_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv

value: DMSO


title: HCT116KO_273_DMSO_RNA-seq_BRep1

description:
HCT116_R1_gene_count_matrix.csv
all_samples_teprof3_HCT116_KO273_vs_KOWT_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: HCT116KO_DMSO_RNA-seq_BRep1

description:
HCT116_R1_gene_count_matrix.csv
all_samples_teprof3_HCT116_WT_vs_KO_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv
DMSO_HCT116_WT_vs_KO_DETranscript.csv
DMSO_DOX_WT_KO_teprof3_tier1_quantification.tsv
DMSO_DOX_WT_KO_teprof3_tier1.tsv

value: KO


title: i29-BM-D2-Pamc3_S5

description:
PAM3CSK4 100 µg/ml - 6hr
BM_Pamc3_D2


title: cow.bulk.esc.1


title: cow.sc.esc.2

library_source: transcriptomic single cell

data_processing:
For STRT-seq, raw reads from scRNA-seq were split by 8 bp cell barcodes located on the Read 2 allowed 2 mismatches, besides, the 8pb unique molecular identifiers(UMIs) located on the Read 2 were switched to the identifier line of paired Read 1. Then the Read 1 were processed to remove the template switch oligo (TSO) primer, low quality bases and polyA sequence. The trimmed reads were aligned to the  Bos_taurus.ARS_UCD1.2 reference genomes. The unique molecular identifier (UMI) counts using kallisto (v-0.46.0)
Assembly:Bos_taurus.ARS_UCD1.2
Supplementary files format and content: txt

molecule: polyA RNA

extract_protocol:
For STRT-seq, a modified Smart-seq2 protocol (Gao et al., 2018; Wang et al., 2018)
For STRT-seq, single cell was transferred into prepared lysis buffer contained an 8bp barcode. Then, the first-strand cDNA was reversed-synthesized and amplified in a reverse transcription (RT) mixture containing 4U RNase inhibitor, 100U SuperScript II reverse transcriptase (Invitrogen, Cat. 18064071), 1 mM dNTPs (TAKARA, Cat. 4019), 60 mM MgCl2, 3 µM RT primer with 10 µM TSO primer. After PCR incubation, the product was purified by 0.8×AMPure XP beads (Beckman, Cat. A63882). Biotin PCR was carried out and enriched. The single cell RNA-seq library was constructed according to the KAPA Hyper Prep Kits with PCR Library Amplication/Illumina series (KAPA, KK8054).


title: Blood, HU-MTD, HU6


title: HCT116KO_175_DOX_RNA-seq_BRep2

description:
HCT116_R2_gene_count_matrix.csv
all_samples_teprof3_HCT116_KO175_vs_KOWT_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: Blood, HU-MTD, HU2


title: cow.embryo.7

source_name: Embryos

value: Embryos

tag: developmental stage

value: multiplexed sample (mixture of stages)


title: i28-BM-D1-Pamc3_S4

description:
PAM3CSK4 100 µg/ml - 6hr
BM_Pamc3_D1


title: HCT116KO_175_DOX_RNA-seq_BRep1

description:
HCT116_R1_gene_count_matrix.csv
all_samples_teprof3_HCT116_KO175_vs_KOWT_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv

value: DOX


title: HCT116KO_175_DMSO_RNA-seq_BRep2

description:
HCT116_R2_gene_count_matrix.csv
all_samples_teprof3_HCT116_KO175_vs_KOWT_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: Blood, HU-MTD, HU4


title: cow.sc.esc.1

source_name: Embryos & Embryonic epiblast

value: Embryos & Embryonic epiblast


title: i27-BM-C2-Blank_S3

description:
untreated - PBS - 6h
BM_Blank_C2

value: Blank


title: i26-BM-B2-Blank_S2

description:
untreated - PBS - 6h
BM_Blank_B2


title: i25-BM-A2-Blank_S1

description:
untreated - PBS - 6h
BM_Blank_A2


title: cow.embryo.5


title: Blood, pre-HU, HU49

value: pre-HU


title: HCT116KO_175_DMSO_RNA-seq_BRep1

description:
HCT116_R1_gene_count_matrix.csv
all_samples_teprof3_HCT116_KO175_vs_KOWT_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: cow.embryo.6


title: Blood, HU-MTD, HU8


title: Blood, pre-HU, HU43


title: cow.embryo.4


title: Blood, pre-HU, HU47


title: RKO_WT_DMSO_ATAC-seq_BRep2

data_processing:
Adaptor trimming: cutadapt -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA --quality-cutoff=15,10 --minimum-length=36
Alignment: bowtie2 v2.3.4.1  --very-sensitive -p 4 -X 2000
Peak calling: MACS2 v 2.2.1 --nomodel --shift 37 --extsize 73 -B --keep-dup all
Bigwig generation: bedGraphToBigWig
Assembly: hg38
Supplementary files format and content: Bigwig
Supplementary files format and content: Bedgraph

extract_protocol:
Extraction from nuclei followed Omni-ATAC protocol. Specific steps are described in Wu et al. 2020
Library construction followed Omni-ATAC protocol. Specific steps are described in Wu et al. 2020

value: RKO

value: WT


title: A549WT_DOX_RNA-seq_BRep2

description:
A549_R2_gene_count_matrix.csv
all_samples_teprof3_A549_WT_vs_KO_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv
DOX_A549_WT_vs_KO_DETranscript.csv
DMSO_DOX_WT_KO_teprof3_tier1_quantification.tsv
DMSO_DOX_WT_KO_teprof3_tier1.tsv


title: Blood, pre-HU, HU41


title: Blood, pre-HU, HU45


title: A549WT_DMSO_RNA-seq_BRep2

description:
A549_R2_gene_count_matrix.csv
all_samples_teprof3_A549_WT_vs_KO_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv
DMSO_A549_WT_vs_KO_DETranscript.csv
DMSO_DOX_WT_KO_teprof3_tier1_quantification.tsv
DMSO_DOX_WT_KO_teprof3_tier1.tsv


title: A549WT_DOX_RNA-seq_BRep1

description:
A549_R1_gene_count_matrix.csv
all_samples_teprof3_A549_WT_vs_KO_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv
DOX_A549_WT_vs_KO_DETranscript.csv
DMSO_DOX_WT_KO_teprof3_tier1_quantification.tsv
DMSO_DOX_WT_KO_teprof3_tier1.tsv


title: cow.embryo.3


title: Blood, pre-HU, HU39


title: RKO_WT_DMSO_ATAC-seq_BRep1


title: A549WT_DMSO_RNA-seq_BRep1

description:
A549_R1_gene_count_matrix.csv
all_samples_teprof3_A549_WT_vs_KO_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv
DMSO_A549_WT_vs_KO_DETranscript.csv
DMSO_DOX_WT_KO_teprof3_tier1_quantification.tsv
DMSO_DOX_WT_KO_teprof3_tier1.tsv


title: A549KO_WT_DOX_RNA-seq_BRep2

description:
A549_R2_gene_count_matrix.csv
all_samples_teprof3_A549_KOWT_vs_KOEV_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: RKO_KO_DOX_ATAC-seq_BRep2


title: RKO_WT_DOX_ATAC-seq_BRep2


title: cow.embryo.1


title: Blood, pre-HU, HU37


title: A549KO_WT_DMSO_RNA-seq_BRep2

description:
A549_R2_gene_count_matrix.csv
all_samples_teprof3_A549_KOWT_vs_KOEV_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: RKO_KO_DMSO_ATAC-seq_BRep2


title: Blood, pre-HU, HU33


title: cow.embryo.2


title: RKO_KO_DMSO_ATAC-seq_BRep1


title: Blood, HU-Washout, HU35

value: HU-Washout


title: A549KO_WT_DMSO_RNA-seq_BRep1

description:
A549_R1_gene_count_matrix.csv
all_samples_teprof3_A549_KOWT_vs_KOEV_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: scRNA_seq_day12_organoids_clone4

city: New York

first: Daniel

last: Medina Cano

email: medinacd@mskcc.org, dmcdmc156@gmail.com

state: New York

address: 411E 67th St

department: Developmental Biology

institute: MSKCC

description: scRNA-seq on day12 cortical organoids from F1 cell lines, clone 4 (cultured with 20% KSR from day4)

data_processing:
The fastq files were processed using the 10x cloud (CellRanger), using as reference the mm10 genome
The CellRanger output files were processed using scanpy
Clusters with excessive mitochondrial reads to too low number of reads per cell were excluded from further analyses
Assembly: mm10
Supplementary files format and content: Scanpy files containing all the background, gene counts, cell type and clone information required to reconstitute the images and perform further analyses

source_name: Mouse brain organoids

growth_protocol: Epiblast stem cells were grown as previously described (Medina-Cano et al, Development 2022) and the organoids generated as described in the associated article

extract_protocol:
Epiblast stem cells were extracted as previously described (Medina-Cano et al, Development 2022)
10x library (3' scRNA-seq)

treatment_protocol: Epiblast stem cells were treated as previously described (Medina-Cano et al, Development 2022) and the organoids treated as described in the associated article

value: Mouse brain organoids


title: A549KO_WT_DOX_RNA-seq_BRep1

description:
A549_R1_gene_count_matrix.csv
all_samples_teprof3_A549_KOWT_vs_KOEV_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: A549KO_EV_DOX_RNA-seq_BRep2

description:
A549_R2_gene_count_matrix.csv
all_samples_teprof3_A549_KOEV_vs_KOWT_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: RKO_WT_DOX_ATAC-seq_BRep1


title: RKO_KO_DOX_ATAC-seq_BRep1


title: snRNA_seq_day18 organoids_batch2

description: snRNA-seq on day18 cortical organoids from F1 cell lines


title: snRNA_seq_day18 organoids_batch1


title: Blood, pre-HU, HU29

value: Blood


title: Blood, pre-HU, HU31


title: HCT116_WT_DOX_ATAC-seq_BRep2


title: A549KO_EV_DOX_RNA-seq_BRep1

description:
A549_R1_gene_count_matrix.csv
all_samples_teprof3_A549_KOEV_vs_KOWT_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: scRNA_seq_day12_organoids_clone3

description: scRNA-seq on day12 cortical organoids from F1 cell lines, clone 3 (cultured with 20% KSR from day4)


title: Blood, pre-HU, HU27

value: F


title: scRNA_seq_day12_organoids_clone2

description: scRNA-seq on day12 cortical organoids from F1 cell lines, clone 2 (cultured without 20% KSR from day4)


title: A549KO_EV_DMSO_RNA-seq_BRep2

description:
A549_R2_gene_count_matrix.csv
all_samples_teprof3_A549_KOEV_vs_KOWT_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: A549KO_EV_DMSO_RNA-seq_BRep1

description:
A549_R1_gene_count_matrix.csv
all_samples_teprof3_A549_KOEV_vs_KOWT_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: HCT116_WT_DMSO_ATAC-seq_BRep1


title: HCT116_WT_DMSO_ATAC-seq_BRep2


title: HCT116_WT_DOX_ATAC-seq_BRep1


title: scRNA_seq_day12_organoids_clone1

description: scRNA-seq on day12 cortical organoids from F1 cell lines, clone 1 (cultured without 20% KSR from day4)


title: Blood, pre-HU, HU23


title: A549KO_DOX_RNA-seq_BRep2

description:
A549_R2_gene_count_matrix.csv
all_samples_teprof3_A549_WT_vs_KO_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv
DOX_A549_WT_vs_KO_DETranscript.csv
DMSO_DOX_WT_KO_teprof3_tier1_quantification.tsv
DMSO_DOX_WT_KO_teprof3_tier1.tsv


title: Blood, HU-Washout, HU21


title: scRNA_seq_on_F1_EpiSCs

description: scRNA_seq on F1 EpiSCs

source_name: Mouse epiblast stem cells

value: Mouse epiblast stem cells


title: Blood, pre-HU, HU25


title: scATAC_seq_on_day_18_cortical_organoids_batch1

description: scATAC_seq on day 18 cortical organoids

data_processing:
The fastq files were processed using the 10x pipeline (CellRanger), using as reference the mm10 genome
The CellRanger output files were processed using ArchR, following the recommended guidelines
Assembly: mm10
Supplementary files format and content: The ArchR output file contains clone, backgorund, cell type and reads information

source_name: Cortical organoids

extract_protocol:
Epiblast stem cells were extracted as previously described (Medina-Cano et al, Development 2022)
10x library (scATAC-seq)

value: Cortical organoids


title: A549KO_DOX_RNA-seq_BRep1


title: HCT116_KO_DMSO_ATAC-seq_BRep1


title: A549KO_DMSO_RNA-seq_BRep2

description:
A549_R2_gene_count_matrix.csv
all_samples_teprof3_A549_WT_vs_KO_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv
DMSO_A549_WT_vs_KO_DETranscript.csv
DMSO_DOX_WT_KO_teprof3_tier1_quantification.tsv
DMSO_DOX_WT_KO_teprof3_tier1.tsv


title: HCT116_KO_DOX_ATAC-seq_BRep1


title: HCT116_KO_DOX_ATAC-seq_BRep2


title: HCT116_KO_DMSO_ATAC-seq_BRep2


title: UPEC_Bladder_Immune cells

city: Jinan

first: Zizhuo

last: Yang

state: Shandong

address: 44 Wenhua West Road, Lixia District

institute: Shandong University

data_processing:
Raw reads were processed with fastQC and fastp to remove low quality reads. Poly-A tails and adaptor sequences were removed by cutadapt.
After quality control, reads were mapped to the reference genome GRCh38 (ensembl version 92 annotation) using STAR.
Assembly: GRCh38
Supplementary files format and content: Expression matrix files for subsequent analyses were generated based on gene counts and UMI counts.

source_name: bladder

extract_protocol:
The concentration of single-cell suspension was adjusted to 1×105 cells/mL in PBS.
Single cell suspension was then loaded onto a microfluidic chip (part of Singleron GEXSCOPETM Single Cell RNAseq Kit, Singleron Biotechnologies) and single cell RNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron Biotechnologies).

value: bladder

value: Immune cells

value: UPEC


title: Blood, pre-HU, HU15


title: A549_WT_DOX_ATAC-seq_BRep2


title: A549KO_DMSO_RNA-seq_BRep1

value: KO

value: DMSO


title: bladder, DTA_UPEC_rep3

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Mus_musculus.GRCm38.v101
Supplementary files format and content: Excel file includes FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: A549KO_273_DOX_RNA-seq_BRep2

description:
A549_R2_gene_count_matrix.csv
all_samples_teprof3_A549_KO273_vs_KOWT_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv

value: DOX


title: bladder, DTA_UPEC_rep2


title: scATAC_seq_on_day_18_cortical_organoids_batch2

description: scATAC_seq on day 18 cortical organoids


title: Blood, pre-HU, HU13

value: M


title: A549_WT_DOX_ATAC-seq_BRep1


title: A549KO_273_DOX_RNA-seq_BRep1

description:
A549_R1_gene_count_matrix.csv
all_samples_teprof3_A549_KO273_vs_KOWT_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: Blood, pre-HU, HU11


title: bladder, DTA_UPEC_rep1


title: Blood, pre-HU, HU9


title: Blood, pre-HU, HU19


title: bladder, Il33KO_UPEC_rep3


title: A549KO_273_DMSO_RNA-seq_BRep2

description:
A549_R2_gene_count_matrix.csv
all_samples_teprof3_A549_KO273_vs_KOWT_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: A549_WT_DMSO_ATAC-seq_BRep2


title: A549_WT_DMSO_ATAC-seq_BRep1


title: A549KO_273_DMSO_RNA-seq_BRep1

description:
A549_R1_gene_count_matrix.csv
all_samples_teprof3_A549_KO273_vs_KOWT_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: Blood, pre-HU, HU17


title: Blood, pre-HU, HU7


title: bladder, Il33KO_UPEC_rep2


title: A549_KO_DOX_ATAC-seq_BRep2


title: A549_KO_DOX_ATAC-seq_BRep1


title: Blood, pre-HU, HU5


title: A549KO_175_DOX_RNA-seq_BRep1

description:
A549_R1_gene_count_matrix.csv
all_samples_teprof3_A549_KO175_vs_KOWT_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: Blood, pre-HU, HU3


title: A549_KO_DMSO_ATAC-seq_BRep2


title: Blood, pre-HU, HU1


title: A549KO_175_DMSO_RNA-seq_BRep2

description:
A549_R2_gene_count_matrix.csv
all_samples_teprof3_A549_KO175_vs_KOWT_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: bladder, WT_UPEC_rep4


title: bladder, Il33KO_UPEC_rep4


title: A549KO_175_DMSO_RNA-seq_BRep1

description:
A549_R1_gene_count_matrix.csv
all_samples_teprof3_A549_KO175_vs_KOWT_DMSO_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: A549_KO_DMSO_ATAC-seq_BRep1


title: SNU-484 cells, T-DXd / biol rep 3

city: Seoul

first: Kyoung-Seok

last: Oh

address: 101 Daehak-ro, Jongno-gu

institute: Seoul National University Cancer Research Institute

data_processing:
The raw reads were trimmed using Trimmomatic 0.38 and aligned to the Homo sapiens reference genome (GRCh38) using HISAT v2.1.0.
StringTie v2.1.3b was used to assemble the mapped reads into transcripts and calculate read counts per gene.
DESeq2 was used to identify differentially expressed genes (DEGs) with a | fold change | ≥ 2 and raw p < 0.05. Hierarchical clustering analysis was performed using complete linkage and Euclidean distance as similarity measures.
Functional and pathway analyses were performed using gProfiler software.
Assembly: GRCh38
Supplementary files format and content: Excel file (xlsx) containing count (FPKM, TPM) and normalized expression values, along with DEGs and their respective fold-changes between biological groups.

growth_protocol: Cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum and 10 µg/ml gentamycin at 37°C in 5% CO2.

extract_protocol:
Total RNA was isolated using TRIzol, and RNA integrity was calculated using the TapeStation RNA screentape (Agilent, #5067-5576). Only high-quality RNA samples (RIN greater than 7.0) were used for RNA library construction. RNA-seq libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina, lnc., San Diego, CA, USA, #RS-122-2101).
Only high-quality RNA samples (RIN greater than 7.0) were used for RNA library construction. RNA-seq libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina, lnc., San Diego, CA, USA, #RS-122-2101). The libraries were quantified using KAPA Library Quantification kits and qualified using a TapeStation D1000 ScreenTape (Agilent Technologies, #5067-5582) before sequencing on an Illumina NovaSeq platform.

treatment_protocol: Cells were treated with 1 µg/ml of vehicle (10 mM acetate buffer-5% sorbitol, pH 5.5) or trastuzumab or T-DXd for 72 h

value: Gastric adenocarcinoma

value: T-DXd 1 ug/ml


title: bladder, WT_UPEC_rep3


title: shCtrl, sample 15, replicate 5

description:
sample_15
KD_countMatrix_GEO.txt

value: Jurkat

value: T-ALL


title: SpretB6_S5

description: Ribodepleted bulk RNA_seq

data_processing:
The fastq files were processed using salmon to generate the "quant" files
The "quant" files were used as input for Rstudio (deseq2 package)
Assembly: mm10
Supplementary files format and content: Salmon-outputs and sample description (samples_info.txt)

organism: Mus

growth_protocol: Epiblast stem cells were grown as previously described (Medina-Cano et al, Development 2022)

extract_protocol:
Epiblast stem cells were extracted as previously described (Medina-Cano et al, Development 2022)
The libraries were constucted as described in Medina-Cano et al, Development 2022

treatment_protocol: Epiblast stem cells were treated as previously described (Medina-Cano et al, Development 2022)


title: SNU-484 cells, T-DXd / biol rep 2

value: WT


title: A549KO_175_DOX_RNA-seq_BRep2

description:
A549_R2_gene_count_matrix.csv
all_samples_teprof3_A549_KO175_vs_KOWT_DOX_DETranscript.csv
all_samples_teprof3_tier1_quantification.tsv
all_samples_teprof3_tier1.tsv


title: shPSIP1 2, sample 14, replicate 5

description:
sample_14
KD_countMatrix_GEO.txt


title: shPSIP1 1, sample 13, replicate 5

description:
sample_13
KD_countMatrix_GEO.txt


title: SpretB6_S6

description: Ribodepleted bulk RNA_seq


title: bladder, WT_UPEC_rep2


title: SNU-484 cells, T-DXd / biol rep 1


title: bladder, WT_UPEC_rep1


title: SpretB6_S1

description: Ribodepleted bulk RNA_seq


title: SNU-484 cells, vehicle control / biol rep 3

value: vehicle control


title: shCtrl, sample 12, replicate 4

description:
sample_12
KD_countMatrix_GEO.txt


title: bladder, Il33KO_UPEC_rep1


title: bladder, WT_PBS_rep2

value: PBS


title: bladder, WT_PBS_rep3


title: SNU-484 cells, vehicle control / biol rep 2


title: PwkB6_P6

description: Ribodepleted bulk RNA_seq


title: bladder, WT_PBS_rep1


title: shPSIP1 1, sample 10, replicate 4

description:
sample_10
KD_countMatrix_GEO.txt


title: shCtrl, sample 9, replicate 3

description:
sample_9
KD_countMatrix_GEO.txt


title: PwkB6_P5

description: Ribodepleted bulk RNA_seq


title: SpretB6_S3

description: Ribodepleted bulk RNA_seq


title: SNU-484 cells, vehicle control / biol rep 1


title: Klf11KO_DDC

city: Ann Arbor

first: Guizhen

last: Zhao

address: 2800 Plymouth Road

department: Internal Medicine

institute: University of Michigan

description: mice developed diabetic atherosclerosis after 12-week DDC

data_processing:
The Cell Ranger Single Cell Software Suite, version 5.0.1 was used to perform sample de-multiplexing, barcode ad UMI processing, and single-cell 3′ gene counting. A detailed description of the pipeline and specific instructions to run it can be found at: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger.
Cloupe files were generated using the Cell Ranger 5.0.1 version. A description of the pipeline and instructions can be found at: https://support.10xgenomics.com/single-cell-gene-expression/software/visualization/latest/cellranger
The CellRanger count command was run on the individual Fastq datasets to produce expression data
R package Seurat v4.0 was used for cell filtration, normalization, principal component analysis, variable genes finding, clustering analysis, and Uniform Manifold Approximation and Projection (UMAP) dimensional reduction.Data were then log-normalized for the subsequent analyses. Principal component analysis (PCA) was used for dimension reduction, followed by clustering analysis in principal component analysis space using a graph-based clustering approach. UMAP was then used for the two-dimensional visualization of the identified clusters. The Seurat functions Vlnplot, FeaturePlot, DotPlot and DoHeatmap were used to visualize the gene expression with violin plot, feature plot, dot plot and heatmap, respectively. Markers for a specific cluster against all remaining cells were found by using the Seurat function FindAllMarkers.
Assembly: Data were mapped to the pre-build mouse reference genome (mm10-2020-A), and the mapping rate of the reads mapped to genome for the two samples was more than 82%.
Supplementary files format and content: UMAP was then used for the two-dimensional visualization of the identified clusters. The Seurat functions Vlnplot, FeaturePlot, DotPlot and DoHeatmap were used to visualize the gene expression with violin plot, feature plot, dot plot and heatmap,

source_name: mouse endothelial cells from aorta and heart

extract_protocol:
The aorta and heart of three mice in each group were digested with enzyme solution [2mg/ml collagenase I (Worthington Biochemical Corporation, LS004196), 60 U/ml DNase I (Roche Diagnostics, 1010459001)] at 37°C for 30-45 minutes with shaking. The cell suspension was filtered through a 40 μm strainer and enriched for endothelial cells using CD31 MicroBeads (Miltenyi Biotec, 130097418) according to the manufacturer’s instructions. The CD31-enriched single cell suspension was washed with WB and stained with Viable dye eFluor 450 (Thermo Fisher Scientific, 50-112-8817). Doublets were gated out prior to FACS sorting, and the viable cells were sorted into a collecting tube with DMEM containing 20% FBS. The cell suspensions were loaded on a 10x Genomics Chromium instrument to generate single cell gel beads in emulsion (GEMs).
Libraries were prepared using the Chromium Single cell 3' Reagent Kits v3.1 (CG000204): Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (PN-1000128), Chromium Single Cell 3’ Chip Kit v2 (PN-1000127) and Single Index Kit Set A (PN-1000213). Libraries were sequenced on an Illumina NovaSeq 6000 using paired-end sequencing with approximately >90% sequencing saturation.

value: mouse arterial endothelial cells

value: Ldlr null and KLF11 deficiency in endothelial cells

value: Klf11ECKO-Ldlr-/- mice fed DDC for 12 weeks


title: PwkB6_P3

description: Ribodepleted bulk RNA_seq

value: Mouse epiblast stem cells


title: NCI-N87 cells, T-DXd / biol rep 3

value: Gstric carcinoma


title: PwkB6_P1

description: Ribodepleted bulk RNA_seq


title: NCI-N87 cells, T-DXd / biol rep 1


title: MolfB6_M3

description: Ribodepleted bulk RNA_seq


title: MolfB6_M6

description: Ribodepleted bulk RNA_seq


title: CD2-iCre PSIP1 KO, IgG, CUT&RUN, KO2

description:
instrument model: AVITI
diff_peaks_nrCP4_H3K27me3_vs_nrCP4_IgG.MAPQ30_keepdupauto_mm10_peaks.broadPeak

source_name: thymus

value: thymus

value: T-cell

value: IgG (Cell Signaling Technology, 3900S)


title: shPSIP1 1, sample 7, replicate 3

description:
sample_7
KD_countMatrix_GEO.txt


title: CD2-iCre PSIP1 KO, H3K27me3, CUT&RUN, KO2

value: H3K27me3 (Cell Signaling Technology, 97335)


title: shCtrl, sample 6, replicate 2

description:
sample_6
KD_countMatrix_GEO.txt


title: shPSIP1 2, sample 5, replicate 2

description:
sample_5
KD_countMatrix_GEO.txt


title: shPSIP1 2, sample 11, replicate 4

description:
sample_11
KD_countMatrix_GEO.txt


title: MolfB6_M1

description: Ribodepleted bulk RNA_seq


title: CD2-iCre PSIP1 KO, H3K27me3, CUT&RUN, KO1

description:
instrument model: AVITI
diff_peaks_nrCP1_H3K27me3_vs_nrCP1_IgG.MAPQ30_keepdupauto_mm10_peaks.broadPeak


title: CD2-iCre PSIP1 KO, IgG, CUT&RUN, KO1


title: NCI-N87 cells, trastuzumab / biol rep 2

value: trastuzumab 1 ug/ml


title: shPSIP1 1, sample 4, replicate 2

description:
sample_4
KD_countMatrix_GEO.txt


title: NCI-N87 cells, trastuzumab / biol rep 1


title: CD2-iCre PSIP1 WT, IgG, CUT&RUN, WT2

description:
instrument model: AVITI
diff_peaks_nrCP6_H3K27me3_vs_nrCP6_IgG.MAPQ30_keepdupauto_mm10_peaks.broadPeak


title: Klf11flox_DDC

value: mouse endothelial cells from aorta and heart

value: Ldlr null

value: Klf11f/f-Ldlr-/- mice fed DDC for 12 weeks


title: shCtrl, sample 3, replicate 1

description:
sample_3
KD_countMatrix_GEO.txt

value: Jurkat

value: T-ALL


title: CD2-iCre PSIP1 WT, H3K27me3, CUT&RUN, WT2


title: NCI-N87 cells, T-DXd / biol rep 2

value: WT

value: T-DXd 1 ug/ml


title: shPSIP1 2, sample 8, replicate 3

description:
sample_8
KD_countMatrix_GEO.txt


title: NCI-N87 cells, vehicle control / biol rep 3

value: vehicle control


title: NCI-N87 cells, vehicle control / biol rep 2


title: CD2-iCre PSIP1 WT, IgG, CUT&RUN, WT1

description:
instrument model: AVITI
diff_peaks_nrCP3_H3K27me3_vs_nrCP3_IgG.MAPQ30_keepdupauto_mm10_peaks.broadPeak


title: shPSIP1 2, sample 2, replicate 1

description:
sample_2
KD_countMatrix_GEO.txt


title: MolfB6_M2

description: Ribodepleted bulk RNA_seq


title: CastB6_C3

description: Ribodepleted bulk RNA_seq


title: NCI-N87 cells, vehicle control / biol rep 1


title: shPSIP1 1, sample 1, replicate 1

description:
sample_1
KD_countMatrix_GEO.txt


title: HGC-27 cells, shGXYLT2 rep3,10%FBS

status: Public on Oct 19 2024

city: Shanghai

first: Yang

middle: jia

last: le

state: Shanghai

address: No. 501, Haike Road, Pudong New Area

institute: Chinese Academy of Sciences University

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

growth_protocol: HGC-27 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum(FBS) and atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted from the cell using TRIzol® Reagent according the manufacturer's instructions.
RNA purification,reverse transcription,library construction and sequencig were performed at ShanghalMajorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer's instructions . The RNA-seq transcriptome librariy was prepared following llumina® Stranded mRNA Prep, Ligation (San Diego,CA) using 1μg of total RNA.

value: Gastric cancer cell

value: GXYLT2 knockdown


title: HGC-27 cells, shGXYLT2 rep2,10%FBS


title: NCI-N87 cells, trastuzumab / biol rep 3


title: HGC-27 cells, shGXYLT2 rep1,10%FBS


title: CD2-iCre PSIP1 WT, H3K27me3, CUT&RUN, WT1


title: HGC-27 cells, shControl rep3,10%FBS


title: HGC-27 cells, shControl rep1,10%FBS


title: CastB6_C6

description: Ribodepleted bulk RNA_seq

value: Mouse epiblast stem cells


title: CastB6_C1

description: Ribodepleted bulk RNA_seq


title: HGC-27 cells, shControl rep2,10%FBS


title: CastB6_C5

description: Ribodepleted bulk RNA_seq


title: VB270

city: Paris

first: Clarice

last: Groeneveld

address: 11 rue de Pierre et Marie Curie

country: France

institute: Institut Curie

data_processing:
We applied the CurieCoreTech RNA-seq pipeline v 3.1.8 (https://github.com/bioinfo-pf-curie/RNA-seq) with standard parameters to align and quantify the RNA-seq.
ComBat-seq for batch correction
log2 counts per million normalization
Assembly: GRCh38
Supplementary files format and content: tab delimited file containing log2 counts per million normalized expression
Supplementary files format and content: tab delimited file containing raw counts data

source_name: urothelial carcinoma

extract_protocol:
Using an annotated hematoxylin-eosin-saffron stained slide for reference, each tumor area was individually macrodissected from the corresponding FFPE tissue block. One to 10 10-µm thick sections were cut from each tumor area using a microtome and then processed using commercially available FFPE kits, Maxwell Rapid Sample Concentrator (RSC) RNA FFPE Kit (Cat. #AS1440) and Maxwell RSC microRNA (miRNA) Tissue Kit (Cat. #AS1460), and a Maxwell RSC device from Promega. RNA isolation was performed according to the manufacturer’s protocol (Total RNA and miRNA purification from FFPE samples using FFPE preprocessing and the Maxwell RSC miRNA Tissue Kit) provided by Promega.
RNA libraries for RNA-seq were prepared using the Lexogen QuantSeq 30 mRNA-Seq Library PrepKit FWD

value: urothelial carcinoma

tag: sample type

value: TURBT

value: neoadjuvant chemotherapy


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title: VB489


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title: VB056_z3


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title: VB122_A_z1


title: VB286


title: VB275