title: LPS853, sgTDP2, 4nM dox, Rep 1

description: Library name: 16_LPS853TDP2__4nM_doxorubicin_1dRep_1


title: peripheral blood 34

status: Public on Feb 12 2026

type: genomic

city: Cusano Milanino

first: Luciano

last: Calzari

state: MI

address: Via Zucchi 18

country: Italy

institute: IRCCS Istituto Auxologico Italiano

description: Case

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 850K EPIC Beadchip using standard Illumina protocol

scan_protocol: Fluorescence intensities were captured by using the fluorescent scanner Illumina HiScan SQ (Illumina).

data_processing: Quality control, pre-processing and generation of β-values matrix were performed by using the ChAMP package (release 2.32.0) package, implemented R environment (version 4.3.1): after the quality control/pre-processing step, 754964 probes and 38 samples were retained.

label: Cy5, Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood lymphocytes

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted from peripheral blood lymphocytes of individuals (Automated Extractor, Tecan Group Ltd. and Wizard Genomic DNA Purification Kit (Ref: A1125), Promega). Quality control and quantification of DNA was assessed by visualization of genomic DNA (gDNA) on 1% agarose gel electrophoresis and by using NanoPhotometer Pearl (Implen GmbH).

tag: tissue

value: Whole Blood

tag: Sex

value: M

tag: age


title: LPS853, sgTDP2, 4nM dox, Rep 2

type: SRA

city: Amsterdam

first: Daniel

last: Peeper

state: Outside the US or Canada

address: Plesmalaan 121

department: Molecular Oncology and Immunology

country: Netherlands

institute: Netherlands Cancer Institute

description: Library name: 17_LPS853TDP2__4nM_doxorubicin_1dRep_2

library_source: transcriptomic

data_processing:
Fastq files were mapped to the human reference genome (Homo.sapiens.GRCh38.102).
Assembly: Homo.sapiens.GRCh38.102
Supplementary files format and content: Gene-level RNA-seq counts matrix  generated using gensum

molecule: total RNA

growth_protocol: Cultured in Advanced DMEM, 9% FCS, 1% Glutamax & 1% Pen/Strep

extract_protocol:
The total RNA was isolated using the RNeasy Mini Kit (Qiagen, 74104), including an on-column DNase digestion (Qiagen, 79254).
cDNA libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina, 20020594)

treatment_protocol: Cells were treated with Doxorubicin (4nM, 24h) +/- peposertib (0.5uM)

tag: cell line

tag: cell type

value: liposarcoma

tag: genotype

value: TDP2 KO

tag: treatment

value: Doxorubicin 4nM


title: human embryo, RNA-Seq, siSP1, 8C, 5

city: hangzhou

first: Hao

last: Jin

address: Nongshenghuan Building E, Zhejiang University, Hangzhou, Zhejiang

country: China

institute: Zhejiang University

description: Library name: h_RNA_siSP1_8C_5

data_processing:
Bulk RNA-Seq data were trimmed and then aligned to the bovine (ARS-UCD1.2) or human (hg19) reference genome by HISAT2 (Version 2.2.1). For scRNA-Seq data, bases 1 - 8 of read 2 were extracted as cell barcodes by UMI-tools (version 1.1.2). Read 1 was trimmed to remove adapter and template switching oligo (TSO) sequences at the 5′ end and poly(A) tails at the 3′ end. Then, aligned reads were split based on their corresponding cell barcodes using Picard (version 2.26.3). The read counts and FPKM values of each gene were calculated by FeatureCounts (version 2.0.1) and StringTie (version 2.1.2).
For CUT&Tag, ChIP-seq, and ATAC-seq data,  Paired end CUT&Tag, ChIP-seq, and ATAC-seq reads were trimmed and then aligned to bovine (ARS-UCD1.2) or human (hg19) genome with Bowtie (version 2.2.5). Low quality reads (MAPQ <20) and PCR duplicated were removed by samtools (version 1.10) and sambamba (version 0.6.6). For downstream analysis, read counts were normalized to RPKM in a 50bp bin by bamCoverage from deepTools (version 3.5.3).
Assembly: bovine (ARS-UCD1.2) or human (hg19)
Supplementary files format and content: excel files include raw counts for scRNA-Seq and FPKM values for bulk RNA-Seq
Supplementary files format and content: bigwig for CUT-Tag, ChIP-Seq and ATAC-Seq signals

molecule: polyA RNA

source_name: human embryo

extract_protocol:
The zona pellucidae of embryos were removed using 0.5% pronase E (Sigma- Aldrich, 107433). Then the embryos were washed in 0.5% BSA (Sigma- Aldrich, SRE0098) and manually transfer into PCR tubes
For RNA-Seq, library construction were performed according to the protocol described previously (Hu et al., 2024). For ChIP-Seq, library construction were performed according to the protocol described previously (Brind’Amour et.al 2015). For ATAC-Seq, library construction were performed according to the protocol described previously (Wu et al., 2018). For CUT-Tag, library construction were performed according to the protocol of Vazyme TD904 kit.

value: 8-cell human embryos

value: wild type


title: human embryo, RNA-Seq, siSP1, 8C, 4

description: Library name: h_RNA_siSP1_8C_4


title: LPS853, sgTDP2, Rep 3

description: Library name: 15_LPS853TDP2__0nM_doxorubicin_1dRep_3


title: LPS853, sgTDP2, Rep 2

description: Library name: 14_LPS853TDP2__0nM_doxorubicin_1dRep_2


title: LPS853, sgTDP2, Rep 1

description: Library name: 13_LPS853TDP2__0nM_doxorubicin_1dRep_1


title: human embryo,RNA-Seq,  siSP1, 8C, 2

description: Library name: h_RNA_siSP1_8C_2


title: human embryo, RNA-Seq, siSP1, 8C, 1

description: Library name: h_RNA_siSP1_8C_1


title: human embryo, RNA-Seq, siSP1, 8C, 3

description: Library name: h_RNA_siSP1_8C_3


title: LPS853, 0.5uM Peposertib, 4nM dox, Rep 2

description: Library name: 11_LPS8530_5_uM_Peposertib_4nM_Doxorubicin_1d_Rep_2

value: WT

value: Peposertib 0.5uM + Doxorubicin 4nM


title: LPS853, 0.5uM Peposertib, 4nM dox, Rep 3

description: Library name: 12_LPS8530_5_uM_Peposertib_4nM_Doxorubicin_1d_Rep_3


title: ER-associated RNA replicate 3

city: New York

first: Shanshan

last: Liu

state: NY

address: 430 East 63rd Street,

country: USA

institute: The Rockefeller University

description:
Library name: ERIP_IP_rep3
RNA isolated from ER-IP fraction

data_processing:
Raw reads were quality checked using standard Illumina pipeline tools.
Reads were pseudoaligned to the mouse reference genome (mm10) using Salmon.
Transcript-level quantifications were imported into R using tximport.
Data were normalized and differential enrichment analysis was performed using limma-voom.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files containing normalized gene-level expression values and differential enrichment statistics. Rows correspond to genes and columns correspond to samples.

growth_protocol: ER-tag Cells were cultured in DMEM supplemented with 10% fetal bovine serum and maintained at 37 °C with 5% CO₂. Cells were harvested at approximately 70–80% confluency for ER immunoprecipitation and RNA extraction.

extract_protocol:
ER fractions were isolated by ER immunoprecipitation (ER-IP) in the presence of RNase inhibitor. RNA was extracted from ER-IP material and from whole-cell lysates using TRIzol reagent according to the manufacturer’s instructions. RNA was precipitated with isopropanol, washed with 70% ethanol, and resuspended in nuclease-free water.
RNA libraries were prepared using an Illumina-compatible RNA-seq library preparation kit according to the manufacturer’s instructions and sequenced on an Illumina platform.

treatment_protocol: Cells stably expressing an ER-targeted tagging construct were generated and used for ER immunoprecipitation experiments. No additional chemical treatments were applied.

value: human embryonic kidney 293 cells

value: ER-tag expression

tag: batch

value: batch 1


title: LPS853, 0.5uM Peposertib, 4nM dox, Rep 1

description: Library name: 10_LPS8530_5_uM_Peposertib_4nM_Doxorubicin_1d_Rep_1


title: ER-associated RNA replicate 1

description:
Library name: ERIP_IP_rep1
RNA isolated from ER-IP fraction


title: LPS853, 0.5uM Peposertib, Rep 3

description: Library name: 9_LPS8530_5_uM_Peposertib_0nM_Doxorubicin_1d_Rep_3

value: Peposertib 0.5uM


title: LPS853, 0.5uM Peposertib, Rep 2

description: Library name: 8_LPS8530_5_uM_Peposertib_0nM_Doxorubicin_1d_Rep_2


title: Whole-cell RNA replicate 3

description:
Library name: ERIP_Input_rep3
RNA isolated from whole-cell lysate


title: LPS853, 0.5uM Peposertib, Rep 1

description: Library name: 7_LPS8530_5_uM_Peposertib_0nM_Doxorubicin_1d_Rep_1


title: Whole-cell RNA replicate 2

description:
Library name: ERIP_Input_rep2
RNA isolated from whole-cell lysate


title: ER-associated RNA replicate 2

description:
Library name: ERIP_IP_rep2
RNA isolated from ER-IP fraction


title: Whole-cell RNA replicate 1

description:
Library name: ERIP_Input_rep1
RNA isolated from whole-cell lysate


title: si_ALDH18A1_3

city: Urumqi City

first: abulajiang·abudoukelimu

middle: abudoukelimu

last: abulajiang

address: 新疆医科大学第三临床医学院

institute: The Third Clinical Medical College of Xinjiang Medical University

description: Library name: Sample6

data_processing:
Raw reads containing more than 2-N bases were first discarded. Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt were also dropped. After that, clean reads were aligned to the GRCm39 genome by tophat2 (Kim et al. 2013) allowing 4 mismatches. Uniquely mapped reads were used for gene reads number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped) (Trapnell et al. 2010).
Assembly: GRCh38
Supplementary files format and content: expressed_gene_FPKM.txt
Supplementary files format and content: expressed_gene_reads.txt

growth_protocol: The  HGC-27 cells were acquired from Procell (Wuhan, China). AGS cells were cultured in Ham’s-F12 medium, whereas HGC-27 cells were incubated in RPMI 1640 medium. All cells were maintained at 37℃ in a humidified atmosphere of 5% CO2.

extract_protocol:
For each sample, 1 µg of total RNA was treated with RQ1 DNase (M6101, Promega, USA) to remove genomic DNA prior to library construction. Directional RNA-seq libraries were prepared using the VAHTS© Universal V8 RNA-seq Library Prep Kit (NR605, Vazyme, China). Poly(A)+ mRNAs were enriched using VAHTS mRNA Capture Beads (N401, Vazyme, China).
Fragmented RNAs were reverse-transcribed into double-stranded cDNA. Following end repair and A-tailing, the cDNA fragments were ligated to VAHTS RNA Multiplex Oligos Set 1 (N323, Vazyme, China). The ligated products were then amplified, purified, quantified, and stored at −80 °C prior to sequencing. The strand marked with dUTP (the second cDNA strand) was not amplified, enabling strand-specific sequencing.  For high-throughput sequencing, libraries were prepared according to the manufacturer’s instructions and sequenced on the DNBSEQ-T7 platform (MGI, China) to generate 150 bp paired-end reads.

treatment_protocol: HGC-27 cells were transfected with si-ALDH18A1 or si-NC. Plasmid transfection of cells was performed using Lipofectamine (Invitrogen, China) according to the manufacturer's protocol. Transfected cells were harvested after 48 h for RT-qPCR and Western blotting analysis.

value: ALDH18A1 knockdown transfected with si-ALDH18A3


title: LPS853, sgNTC, 4nM dox, Rep 3

description: Library name: 6_LPS853NTC_4nM_Doxorubicin_1d_Rep_3

value: NTC


title: LPS853, sgNTC, 4nM dox, Rep 2

description: Library name: 5_LPS853NTC_4nM_Doxorubicin_1d_Rep_2


title: peripheral blood 21

description: Case


title: LPS853, sgNTC, 4nM dox, Rep 1

description: Library name: 4_LPS853NTC_4nM_Doxorubicin_1d_Rep_1


title: LPS853, sgNTC, Rep 2

description: Library name: 2_LPS853NTC_0nM_Doxorubicin_1d_Rep_2


title: LPS853, sgNTC, Rep 3

description: Library name: 3_LPS853NTC_0nM_Doxorubicin_1d_Rep_3


title: Ms877_Sham

city: Tuscaloosa

first: Sergei

last: Bombin

address: 739 University Blvd

institute: The University of Alabama

description: Library name: Ms877

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, and gene counting were made using Parse Biosciences pipeline v0.9.6
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: liver

extract_protocol:
fixed cells processed in Evercode Whole Transcriptome kit (Parse Biosciences), per manufacturer protocol
Evercode Whole Transcriptome kit (Parse Biosciences), 100K cells. Split-pool combinatorial barcoding on fixed/frozen whole cells; random hexamer and oligo (dT) primers for reverse transcription

value: liver

value: biliary epithelial cells

value: 7d post Sham surgery


title: Ms840_BDL

description: Library name: Ms840

value: 7d post bile duct ligation surgery


title: Ms805_BDL

description: Library name: Ms805


title: 9_KRAS_DoxInfliximab_biStellate_run2

city: Ulm

first: Alexander

last: Kleger

address: Albert-Einstein-Allee 23, 89071 Ulm

department: Institute of Molecular Oncology and Stem Cell Biology

country: Germany

institute: University Hospital Ulm

description: Library name: 9_KRAS_DoxInfliximab_biStellate_run2

data_processing:
Sequencing was performed on a NovaSeq 6000 instrument (Illumina). Flow cell demultiplexing was achieved by using the BCLConvert tool (v4.2.4, Illumina), followed by further processing with the CellRanger Multi -pipeline (v9.0.0, 10x Genomics).
To minimize potential bias due to variable probe performance, the raw probe matrix was filtered to exclude probes with mean raw counts (across all cells) below 20% of the mean raw counts of the best-performing probe for that gene. The raw counts of the remaining probes were then aggregated by computing the mean count per gene and cell.
Assembly: Chromium Human Transcriptome Probe Set v1.1.0
Supplementary files format and content: tab-separated barcodes and features files, and matrix files

extract_protocol:
Cells were fixed using the GEM-X Flex Sample Preparation v2 Kit (10x Genomics) according to the manufacturer's protocol (CG000782).
Multiplexed libraries were prepared following the 10x Genomics user guide “GEM-X Flex Gene Expression for Multiplexed Samples” (CG000787) using the Chromium X (10x Genomics) and the Chromium Human Transcriptome Probe Set v1.1.0 (10x Genomics). A self-designed customized probe was added, targeting the sequence of the mCherry reporter of the KRASG12D construct (LHS-CCTTGGCACCCGAGAATTCCAATTACGGGGCCGTCGGAGGGGAAGT and RHS-phospho-TGGTGCCGCGCAGCTTCACCTTGTA-ACGCGGTTAGCACGTA-NN-XXXXXXXX-CGGTCCTAGCAA). Two independent sequencing runs were conducted. The first run included all samples of mono- and bi-cultures, while bi-cultures were additionally sequenced in a second run.

treatment_protocol: Doxycline was added to induce KRASG12D expression, infliximab was added to neutralize soluble TNFa.

value: stem-cell derived pancreatic duct-like organoid + stellate cells

value: 3µg/ml Doxycycline + 10µg/ml Infliximab


title: Ms802_Sham

description: Library name: Ms802


title: E18 Cortex single cell RNA-seq

city: Shanghai

first: Guoping

address: 138 Yi Xue Yuan Road

institute: Fudan University

description:
Library name: sample1
10x Genomics

data_processing:
High quality sequences (clean reads) were obtained by removing low quality sequences and joints. The clean reads were then processed with Cell Ranger software to obtain quantitative information on gene expression.
Assembly: mm10
Supplementary files format and content: matrix

source_name: cortex

extract_protocol:
FlashTag (CellTrace Yellow, Life Technologies, #C34567, 0.5 μl of 10 mM) was injected into the cortical lateral ventricle of  hGFAP-Cre; EGFR-cko mice at E16.0. E18 pups were sacrificed, and the brains were immediately removed and submerged in fresh ice-cold Hanks’ balanced salt solution (Gibco 14175-095). The dorsal cortices were cut into small pieces and dissociated into a single-cell suspension using a Papain Cell Dissociation Kit by following the manufacturer’s instruction. The tdTomato+ (tdT+) cells were captured and harvested through fluorescence-activated cell sorting (FACS).
The Chromium droplet-based sequencing platform (10X Genomics) was used to generate scRNA-Seq libraries, following the manufacturer’s instructions (manual document part number: CG00052 Rev C). The cDNA libraries were purified, quantified using an Agilent 2100 Bioanalyzer, and sequenced on an Illumina Novaseq 6000.

value: cortex


title: miR-1 KO 3

city: Fayetteville

first: Pieter

middle: Jan

last: Koopmans

state: AR

address: 155 N Stadium Drive

department: Cell and Molecular Biology

institute: University of Arkansas - Fayetteville

description:
Library name: M3_M1KO_PLT
Middle Aged Mice treated with 5 days consecutive days of 2mg/day IP tamoxifen followed by an 8 weeks washout

data_processing:
For total RNA-Seq, raw FASTQ files were imported into Partek Cloud Platfor aligned to mm39 with STAR 2.7.8a with default parameters. Aligned reads were quantified to annovation model and filtered to exclude genes with maximum count of less than 5. Normalized with DESeq2 median ratio. Tested for significance using DESeq2, with lowest average coverage filter of 1 prior to false discovery correction.
For myonuclear DNA RRBS (methylation), Base calling with Illumina Software. Raw FASTQ files were adapter, filled-in nucleotides, and quality trimmed using TrimGalore. The effect of trimming and overall quality distribution was determined using FastQC. Alignment was performed using Bismark. Read totals were called using Bismark Methylation Extractor. Bismark coverage data (.cov files) are generated from Bismark Methylation Extractor and contains the methylated count and total count at each position within the genome
Following library construction, libraries were sequenced on the Illumina Nova NextSeq X Plus System by Novogene to 200 million reads per sample. Raw FASTQ files were imported into Cell Ranger 9.0 for alignment to reference transcriptome, and report of UMIs/reads/nuclei barcodes. h5 files were exported and imported into Python environment, where ambient RNA correction tool CellBender was used. Processed files were imported into Seurat v5, and data quality control was performed by removing nuclei with <200 UMIs, nuclei with >5% of mitochondrial reads, and genes expressed in <3 nuclei.
Assembly: mm39
Supplementary files format and content: For total RNA-seq, DESeq2 Normalized Counts. For RRBS, bismark files.
Supplementary files format and content: For single myonucleus RNA-seq, .h5 Cell Ranger files

source_name: Skeletal Muscle, Plantaris

extract_protocol:
Total RNA was extracted via Trizol-Chloroform precpitiation of RNA using Zymo Direct-Zol RNA extraction kit. Genomic DNA was extracted from myonuclei isolated from the plantaris muscle via fluorescent activated nuclear sorting. The Quick-DNA™ Miniprep Plus kit (Zymo Research, D4068) was used as specified in the protocol. For single myonucleus RNA-seq, myonuclei were isolated from plantaris muscle chunks were minced with scissors in homogenization buffer (500 µl HEPES (1 M) 3 ml KCl (1 M) 250 µl spermidine (100 mM) 750 µl spermine tetrahydrochloride (10 mM) 10 ml EDTA (10 mM) 250 µl EGTA (100 mM) 2.5 ml MgCl (100 mM) 5.13 g sucrose, Dounce homogenized on ice with a plastic pestle in homogenization buffer, then passed through a 40 µm and 20 µm filter into directly into the MACSQuant High Speed Tyto Cardtridge. PI was added to label nuclei. Fluorescently labeled nuclei (GFP+/PI+) were purified via Fluorescence-activated nuclear sorting (FANS) and sorted into re-suspension buffer (1X PBS, 1% BSA, 0.2U/uL RNase inhibitors).
Total RNA-seq libraries were prepared for seqeuencing using standard Illumina protocols and underwent 150 bp PE sequencing. The DNA RRBS was rered to Zymo Research Corporation (RRBS Basic Srvise Package, 15-20 million read pairs per sample). Myouclei were mixed with reverse transcriptase buffer and loaded into the 10X Chromium system using the Single Cell 3’ Reagent Kit v4 according to the manufacturer’s protocol. Following library construction, libraries were sequenced on the Illumina NovaSeq X Plus System at the Novogene.

treatment_protocol: Mice were treated with doxycycline for 7 days to label myonuclei with green fluorescent protein, followed by a 7-13 day washout period. Then mice underwent 72 hours of ambulation after synergist ablation mechanical overload (MOV) surgery.

value: Skeletal Muscle, Plantaris

value: 5 days tamoxifen IP, 8 weeks washout


title: 6_KRAS_Dox_biStellate_run2

description: Library name: 6_KRAS_Dox_biStellate_run2

value: 3µg/ml Doxycycline


title: miR-1 CON 3

description:
Library name: M3_M1CON_PLT
Middle Aged Mice treated with 5 days consecutive days of 2mg/day IP tamoxifen followed by an 8 weeks washout

value: miR-1 fl/fl


title: LPS853, sgNTC, Rep 1

description: Library name: 1_LPS853NTC_0nM_Doxorubicin_1d_Rep_1

value: liposarcoma


title: miR-1 KO 2

description:
Library name: M2_M1KO_PLT
Middle Aged Mice treated with 5 days consecutive days of 2mg/day IP tamoxifen followed by an 8 weeks washout


title: 5_KRAS_Dox_biTcells_run2

description: Library name: 5_KRAS_Dox_biTcells_run2

value: stem-cell derived pancreatic duct-like organoid + T cells


title: miR-1 CON 2

description:
Library name: M2_M1CON_PLT
Middle Aged Mice treated with 5 days consecutive days of 2mg/day IP tamoxifen followed by an 8 weeks washout


title: 2_KRAS_noDox_biTcells_run2

description: Library name: 2_KRAS_noDox_biTcells_run2

value: wildtype

value: no treatment


title: 3_KRAS_noDox_biStellate_run2

description: Library name: 3_KRAS_noDox_biStellate_run2


title: miR-1 CON 1

description:
Library name: M1_M1CON_PLT
Middle Aged Mice treated with 5 days consecutive days of 2mg/day IP tamoxifen followed by an 8 weeks washout


title: 9_KRAS_DoxInfliximab_biStellate_run1

description: Library name: 9_KRAS_DoxInfliximab_biStellate_run1


title: miR-1 KO 1

description:
Library name: M1_M1KO_PLT
Middle Aged Mice treated with 5 days consecutive days of 2mg/day IP tamoxifen followed by an 8 weeks washout


title: Young Sham5

description:
Library name: YSH5
Young adult mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload sham surgery, 5

value: HSA-GFP

value: 72 hours Sham


title: 10_Parental_Dox_monoculture_run1

description: Library name: 10_Parental_Dox_monoculture_run1

value: stem-cell derived pancreatic duct-like organoid


title: Young Sham6

description:
Library name: YSH6
Young adult mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload sham surgery, 6


title: Young Sham4

description:
Library name: YSH4
Young adult mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload sham surgery, 4


title: 7_KRAS_DoxInfliximab_monoculture_run1

description: Library name: 7_KRAS_DoxInfliximab_monoculture_run1


title: 6_KRAS_Dox_biStellate_run1

description: Library name: 6_KRAS_Dox_biStellate_run1


title: Young Sham3

description:
Library name: YSH3
Young adult mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload sham surgery, 3


title: Young Sham2

description:
Library name: YSH2
Young adult mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload sham surgery, 2


title: 5_KRAS_Dox_biTcells_run1

description: Library name: 5_KRAS_Dox_biTcells_run1


title: 8_KRAS_DoxInfliximab_biTcells_run1

description: Library name: 8_KRAS_DoxInfliximab_biTcells_run1


title: 3_KRAS_noDox_biStellate_run1

description: Library name: 3_KRAS_noDox_biStellate_run1

value: stem-cell derived pancreatic duct-like organoid + pancreatic stellate cells


title: 4_KRAS_Dox_monoculture_run1

description: Library name: 4_KRAS_Dox_monoculture_run1


title: Young MOV6

description:
Library name: YOV6
Young adult mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload surgery, 6

value: 72 hours MOV


title: 2_KRAS_noDox_biTcells_run1

description: Library name: 2_KRAS_noDox_biTcells_run1


title: Young MOV5

description:
Library name: YOV5
Young adult mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload surgery, 5


title: 1_KRAS_noDox_monoculture_run1

description: Library name: 1_KRAS_noDox_monoculture_run1


title: Young MOV4

description:
Library name: YOV4
Young adult mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload surgery, 4


title: DDX53 cells, rep2

city: Poznan

first: IHG PAS

last: Bioinfo Team

state: Greater Poland

address: Strzeszynska 32

department: Bioinformatics Team

country: Poland

institute: Institute of Human Genetics, Polish Academy of Sciences

description: Library name: DDX53_III

data_processing:
The pre-processing was performed by removing low-quality reads (Q<30) and sequencing adapters using Trim Galore (v0.6.10).
Differential expression analysis: The pre-processed RNA-seq reads were mapped to the human reference genome (GRCh38/hg38, Gencode v44) using STAR (v2.7.11a). Read counts were then normalized by DESeq2 R package. Low expressed genes (with less than 0.1 mean CPM in each condition i.e. DDX53, GFP or WT) were excluded from further analysis. Next, we performed the differential expression analysis comparing the DDX53 vs. GFP and the DDX53 vs. WT conditions using DESeq2. The set of significant differentially expressed genes (DEGs) was determined based on adjusted p-value (FDR) < 0.05 and |log2FC|≥1. As the final list of genes we intersected the significant DEGs of the two comparisons (DDX53 vs. GFP, DDX53 vs. WT), and we retrieved only those genes with the same trend (upregulation or downregulation) in both comparisons.
Differential splicing analysis: To quantify transcripts expression (TPM) in each condition (DDX53, GFP and WT) we employed the Salmon tool (v1.10.2) and aligned the pre-processed RNA-seq reads to the reference transcriptome (Gencode v44). The alternative splicing analysis was then performed using the SUPPA2 tool (v2.3).
Assembly: GRCh38/hg38, Gencode v44
Supplementary files format and content: tab-separated file with TPM values for each sample
Supplementary files format and content: tab-separated file with normalized counts (CPM) for each sample

growth_protocol: TCam-2 cells were cultured at 37 °C and 5% CO2 in Roswell Park Memorial Institute 1640 Medium (RPMI 1640 Medium, GlutaMAX™ Supplement Thermo Fisher Scientific, 61870044) supplemented with 10% heat-inactivated Fetal Bovine Serum (Cytiva, HYCLSV30160.03) and 1% Antibiotic-Antimycotic solution (100X) (Thermo Fisher Scientific, 15240062).

extract_protocol:
RNA was isolated with RNeasy Plus Mini Kit (Qiagen, 74136) and residual DNA was removed by TURBO DNA-free™ kit (Thermo Fisher Scientific, AM1907) treatment according to the manufacturer’s protocol.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LT kit (Illumina).

value: human testicular cancer cell line

value: DDX53 overexpression


title: Young MOV2

description:
Library name: YOV2
Young adult mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload surgery, 2


title: DDX53 cells, rep1

description: Library name: DDX53_I


title: Young MOV3

description:
Library name: YOV3
Young adult mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload surgery, 3


title: Young MOV1

description:
Library name: YOV1
Young adult mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload surgery, 1


title: PDTF, Everolimus

city: Ghent

first: sandor

last: Dedeyne

address: C. Heymanslaan 10

country: Belgium

institute: University Ghent

description: Library name: PDTF_Everolimus

data_processing:
Data pre-processing, including demultiplexing and alignment, was performed using Cell Ranger multi (version 7.2.0, 10x Genomics). Processing after quality control was performed using R version 4.5.0. The raw gene expression matrix from the CellRanger pipeline was filtered, normalized and clustered by using the Seurat (v5.3.0) pipeline. Filtering was performed on the raw gene expression matrix of all individual samples. Cells expressing less than 200 genes were initially removed, followed by outlier detection based on the median absolute deviation (MAD). Outlier cells were identified based on 3 metrics: UMI count, number of expressed genes and mitochondrial proportion. Cells were tagged as outliers when they were 5 MADs away from the median value of each metric across all cells and 15 MADs for the mitochonrial proportion. These low quality cells were removed from the analysis.
Assembly: GRCh38-2024-A
Supplementary files format and content: Tab separated value files and matrices

source_name: peritoneal metastasis lesion from colorectal adenocarcinoma

extract_protocol:
PDTFs (n=192 per condition) were dissociated through enzymatic dissociation as described previously (Blondeel et al., Nat Protocols, 2025). The resulting filtered single cell suspensions were processed using the GEM-X Flex Sample Preparation v2 Kit (#PN-1000781, 10X Genomics) following manufacturer’s instructions. Based on DAPI staining, cells were separated using the from debris by Fluorescence-Activated Cell Sorting (FACS) using the BD FACS symphony S6 and BD FACS symphony S8.
Fixed cells were multiplexed prior to gel beads-in-emulsion (GEM) generation, barcoding, and library preparation according to the 10X Genomics User Guide (Document CG000787), using the Chromium GEM-X Flex Hybridization & Wash Kit (PN-1000789) and GEM-X FLEX GEM & Library Kit (PN-1000782, 10x Genomics).

value: Day 5

value: Everolimus


title: PDTF, Trametinib

description: Library name: PDTF_Trametinib

value: peritoneal metastasis lesion from colorectal adenocarcinoma

value: Trametinib


title: Old Sham7

description:
Library name: OSH7
Aged mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload sham surgery, 7

value: Skeletal Muscle, Plantaris


title: PDTF, DMSO

description: Library name: PDTF_DMSO

value: DMSO


title: Old Sham6

description:
Library name: OSH6
Aged mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload sham surgery, 6


title: Old Sham4

description:
Library name: OSH4
Aged mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload sham surgery, 4


title: CT5.3hTERT,Uprosertib,24h_replicate3

description:
Library name: Sample12
Column name in raw_counts.txt:Uprosertib_replicate3

data_processing:
Reads were mapped to the human genome using Tophat, and gene expression counts were generated with HTSeq.
Assembly: hg38
Supplementary files format and content: output from Htseq

source_name: cell line

growth_protocol: CT5.3hTERT cancer associated fibroblasts were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 10% CO2 at 37℃.

extract_protocol:
RNA was extracted using the miRNeasy Micro Kit (Qiagen), and 27.5 ng of RNA per sample was treated with Heat-Labile Double-Strand-Specific DNase (Arcticzymes) to remove DNA contamination.
Library construction was performed using the QuantSeq-Pool Sample-Barcoded 3′ mRNA-Seq Kit (Lexogen) according to the manufacturer’s protocol.

treatment_protocol: Spheroids derived from CT5.3hTERT were treated with Everolimus(1 μM), Omipalisib(100 nM), and Uprosertib(1 μM) for 24 hours

value: cell line

value: cancer associated fibroblasts

value: WT

value: Uprosertib


title: Old Sham5

description:
Library name: OSH5
Aged mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload sham surgery, 5

value: HSA-GFP


title: CT5.3hTERT,Uprosertib,24h_replicate1

description:
Library name: Sample10
Column name in raw_counts.txt:Uprosertib_replicate1


title: CT5.3hTERT,Uprosertib,24h_replicate2

description:
Library name: Sample11
Column name in raw_counts.txt:Uprosertib_replicate2


title: AS, Erastin, rep3

city: Göteborg

first: Ganesh

last: Umapathy

address: Medicinaregatan 9 a-b

department: Sahlgrenska University Hospital

country: Sweden

institute: University of Gothenburg

description: Library name: Sample 6

data_processing:
Sequence reads were trimmed for adaptor/low-quality sequences using FASTX and Trimmomatic.
Trimmed reads were mapped to the human genome (GRCh38) and quantified per gene using HTSeq.
Differential gene expression analysis was performed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: RNA-seq data are provided in merged comma-separated text files (CSV) for Kelly and AS
Supplementary files format and content: csv files include total counts for each Sample

source_name: SK-N-AS

growth_protocol: Kelly and SK-N-AS cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics at 37C with 5% CO2.

extract_protocol:
RNA was harvested using ReliaPrep RNA Miniprep system (Promega #6111).
Purified RNA was sent to Novogene UK for library preparation and sequencing

treatment_protocol: KELLY and SK-N-AS neuroblastoma cell lines treated with 1 μM and 2 μM Erastin for 24 hours, respectively

value: SK-N-AS

value: neuroblast

value: Erastin (Era)

tag: time

value: 24 hours


title: CT5.3hTERT,Omipalisib,24h_replicate3

description:
Library name: Sample9
Column name in raw_counts.txt:Omipalisib_replicate3

value: Omipalisib


title: Old Sham3

description:
Library name: OSH3
Aged mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload sham surgery, 3

value: 72 hours Sham


title: Old Sham1

description:
Library name: OSH1
Aged mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload sham surgery, 1


title: Old Sham2

description:
Library name: OSH2
Aged mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload sham surgery, 2


title: Old MOV7

description:
Library name: OOV7
Aged mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload surgery, 7

value: 72 hours MOV


title: peripheral blood 31

description: Case

value: Whole Blood

value: M


title: CT5.3hTERT,Omipalisib,24h_replicate1

description:
Library name: Sample7
Column name in raw_counts:Omipalisib_replicate1


title: CT5.3hTERT,Everolimus,24h_replicate3

description:
Library name: Sample6
Column name in raw_counts.txt:Everolimus_replicate3

value: Everolimus


title: Old MOV6

description:
Library name: OOV6
Aged mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload surgery, 6

value: Skeletal Muscle, Plantaris


title: CT5.3hTERT,Everolimus,24h_replicate2

description:
Library name: Sample5
Column name in raw_counts.txt:Everolimus_replicate2


title: AS, Control, rep3

description: Library name: Sample 3

value: DMSO


title: peripheral blood 33

description: Case


title: Old MOV5

description:
Library name: OOV5
Aged mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload surgery, 5


title: Old MOV4

description:
Library name: OOV4
Aged mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload surgery, 4


title: CT5.3hTERT,DMSO,24h_replicate3

description:
Library name: Sample3
Column name in raw_counts:DMSO_replicate3

value: cell line


title: CT5.3hTERT,DMSO,24h_replicate1

description:
Library name: Sample1
Column name in raw_counts.txt:DMSO_replicate1

value: cancer associated fibroblasts


title: Old MOV3

description:
Library name: OOV3
Aged mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload surgery, 3


title: Old MOV1

description:
Library name: OOV1
Aged mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload surgery, 1


title: NOD-iβSTX4-3

city: Duarte

first: Debbie

middle: C.

last: Thurmond

state: California

address: 1500 E Duarte Rd

institute: City of Hope

description: Library name: 36044

data_processing:
Raw sequencing data sets were aligned back to the mouse genome (mm10 v.1.2.0), using the cellranger count (v.3.1.0) tool (10x Genomics) to produce expression data at a single-cell resolution. The R package Seurat (v.3.2.3) (23) was used for gene and cell filtration, normalization, variable gene finding, and clustering analysis as well as for principal component analysis (PCA) and uniform manifold approximation and projection dimension reduction. Data were then merged using standard integration and log-normalized for subsequent analysis. PCA was performed for dimension reduction, and the first 21 principal components were used for clustering analysis. Clusters were visualized with t-distributed stochastic neighbor embedding using Seurat.
Assembly: mm10
Supplementary files format and content: Seurat object in R RDS format containing normalized counts, cell type annotations and UMAP coordinates

source_name: Pancreatic islet

extract_protocol:
Islets were isolated from female NOD-Ctrl or NOD-iβSTX4 transgenic mice and dispersed into single cells with TrypLE (Invitrogen, Carlsbad, CA). Cell numbers and viability were measured using a TC20 Automated Cell Counter (Bio-Rad); only samples showing at least 70% viability were used. Cells were then loaded onto a chromium controller (10x Genomics, Pleasanton, CA) to generate single-cell Gel Bead-In Emulsions (GEMs) captured in droplets at a targeted cell recovery of 3,000 cells. GEM reverse transcriptions were performed in a Veriti 96-Well Thermal Cycler (Thermo Fisher Scientific).
The Chromium Single Cell 3' Reagent Kit V2 (10x Genomics) was used to process samples into single-cell RNA sequencing (scRNA-seq) libraries according to the manufacturer’s protocol. The libraries were sequenced with the paired-end setting of 28 cycles of read 1, 101 cycles of read 2, and 8 cycles of the index read on the Illumina NovaSeq 6000 platform at the Translational Genomics Research Institute (TGen) (Phoenix, AZ).

value: Pancreatic islet


title: Old MOV2

description:
Library name: OOV2
Aged mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload surgery, 2


title: VSMCs_AngII H4K16LA rep1

first: Liwei

address: 180 Fenglin Road

department: Department of Cardiology,Zhongshan Hospital

institute: Shanghai Institute of Cardiovascular Diseases,Fudan University

description: Library name: VSMCs_AngII1

library_source: genomic

data_processing:
Reads were first quality-trimmed using trim-galore v0.6.10 with the following parameters :’--phred33 --stringency 3 --length 20 --paired’
Sequence alignment was then performed with bowtie2 v2.2.9. Reads were mapped to the Homo_sapiens_assembly38.fasta assembly (ENCODE) . All  results are given for the build 38 assembly. Read filtering was performed with SAMtools v1.10 retaining only uniquely mapped reads with a mapping quality >=10. PCR duplicates were removed with Picard.  peak
Peak calling was performed with MACS2 v2.1.0 using the callpeaks function with the arguments –nomodel, shift = −100, and extsize = 200.
BigWig files were generated using the bamCoverage function from deeptools. Signals were normalised using RPKM.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: human aortic vascular smooth muscle cells

extract_protocol:
The frozen tissues were first washed with pre-cooled 1X PBS, then thawed on ice, cut into pieces. Next, added appropriate amount of tissue lysate, and grinded them to homogenate. 2 ul from the homogenate was be used to observe the morphology and number of nuclei under microscope. After conforming the quality of nuclei, then strained the homogenate through 40 um/35 um cell sieve. Counted the nuclei from the filtered grinding solution. Finally, about 500,000 nuclei needed to be precipitated by centrifugation at 4 ℃ temperatures.
After mixing the antibody I and Antibody Buffer in proportion, added it into the precipitate obtained in the above step, and incubated at room-temperature for 2h after mixing. The antibody II was added and incubated for 1 h at room-temperature. After centrifugation, the mixture of Dig Buffer and CUT&Tag-Tn5 enzyme was added and mixed, and incubated at room-temperature for 1 h.Purified the above products using DNA Purification Kit (MN，740609). To determine PCR cycle number, take a small amount of the purified product and do a pre_x0002_amplification.After the pre-amplified bands were correct, then done formal amplification. After determining the yield and the band type, purified and constructed the library.

value: VSMCs

value: angiotensin II

value: H4K16LA(PTM bio,#PTM-1417RM)


title: VSMCs_AngII H4K16LA rep2

description: Library name: VSMCs_AngII2

value: human aortic vascular smooth muscle cells


title: VSMCs_CON H4K16LA rep2

description: Library name: VSMCs_CON2


title: NOD-iβSTX4-2

description: Library name: 36043


title: VSMCs_CON H4K16LA rep1

description: Library name: VSMCs_CON1


title: NOD-Ctrl-2

description: Library name: 36045

value: NOD-Ctrl


title: ST-3

city: Wuhan

first: Yu

last: Fang

state: Hubei

address: Wuhan University of Science and Technology

description:
Library name: sample6
ST3

data_processing:
Clean reads were aligned to the mouse mm10 genome (HISAT2), andgene expression (FPKM) was quantified with StringTie. The identification of differentially expressed genes (|log2FC| ≥ 1, padj < 0.05) was facilitated by DESeq2, with subsequent GO/KEGG enrichment analyses being conducted
Assembly: mm39
Supplementary files format and content: xls files include FPKM values for each Sample

source_name: testis

extract_protocol:
Total RNA was extracted from mouse testicular tissues (n = 3 biological replicates per group) using Trizol reagent (Invitrogen, Carlsbad, CA, USA). The purity of the RNA was verified by NanoDrop 2000 (A260/A280: 1.8–2.1) and its integrity was assessed via Agilent 2100 Bioanalyzer (RIN ≥ 8.0). Ribosomal RNA was depleted using the Ribo-Zero™ kit (Illumina, San Diego, CA, USA), followed by the construction of the cDNA library (fragmentation, reverse transcription, adapter ligation, and PCR amplification). Qualified libraries (insert size: 200–300 bp; concentration ≥ 2 nM) were subjected to sequencing on the Illumina NovaSeq 6000 platform (PE150, ≥ 10 Gb per sample)
Total RNA was extracted from mouse testicular tissues (n = 3 biological replicates per group) using Trizol reagent (Invitrogen, Carlsbad, CA, USA). The purity of the RNA was verified by NanoDrop 2000 (A260/A280: 1.8–2.1) and its integrity was assessed via Agilent 2100 Bioanalyzer (RIN ≥ 8.0). Ribosomal RNA was depleted using the Ribo-Zero™ kit (Illumina, San Diego, CA, USA), followed by the construction of the cDNA library (fragmentation, reverse transcription, adapter ligation, and PCR amplification). Qualified libraries (insert size: 200–300 bp; concentration ≥ 2 nM) were subjected to sequencing on the Illumina NovaSeq 6000 platform (PE150, ≥ 10 Gb per sample)

value: testis


title: Donor 6, Thoracic spinal cord, snRNA sample 1

city: Madison

first: Abbas

middle: Haider

last: Rizvi

state: WI

address: 1500 Highland Ave, Room 715 Room 715

department: Neuroscience

institute: University of Wisconsin-Madison

description: Library name: Donor6_Thoracic_Sample1_GEX

data_processing:
Cell Ranger ARC 2.0.2
Assembly: GRCh38
Supplementary files format and content: Donors2-6_GEX_barcodes.tsv.gz nuclei demultiplexing file for each sample
Supplementary files format and content: Donors2-6_GEX_matrix.mtx.gz counts-by-nucleus file for each sample
Supplementary files format and content: Donors2-6_GEX_features.tsv.gz feature annotation file for each sample

molecule: nuclear RNA

source_name: spinal cord

extract_protocol:
Spinal cord tissue was surgically resected from Donors 2-6 organ donors during organ donation. Individual nuclei were isolated through homogenization and gradient centrifugation.
snRNA-seq libraries were generated using 10x Chromium Single Cell Multiome ATAC+Gene Expression, following manufacturer's guidelines.

value: spinal cord


title: ST-2

institute: Wuhan University of Science and Technology

description:
Library name: sample5
ST2


title: Donor 6, Thoracic spinal cord, snRNA sample 2

description: Library name: Donor6_Thoracic_Sample2_GEX


title: NOD-Ctrl-1

description: Library name: 35728


title: ST-1

description:
Library name: sample4
ST1


title: NOD-iβSTX4-1

description: Library name: 35729


title: CT-3

description:
Library name: sample3
CT3


title: Donor 6, Lumbar spinal cord, snRNA sample 2

description: Library name: Donor6_Lumbar_Sample2_GEX


title: Donor 5, Thoracic spinal cord, snRNA sample 1

description: Library name: Donor5_Thoracic_Sample1_GEX


title: Donor 6, Lumbar spinal cord, snRNA sample 1

description: Library name: Donor6_Lumbar_Sample1_GEX


title: Donor 5, Lumbar spinal cord, snRNA sample 2

description: Library name: Donor5_Lumbar_Sample2_GEX


title: Donor 5, Thoracic spinal cord, snRNA sample 2

description: Library name: Donor5_Thoracic_Sample2_GEX


title: CT-1

description:
Library name: sample1
CT1


title: Donor 5, Lumbar spinal cord, snRNA sample 1

description: Library name: Donor5_Lumbar_Sample1_GEX


title: Donor 4, Thoracic spinal cord, snRNA sample 2

description: Library name: Donor4_Thoracic_Sample2_GEX


title: Donor 4, Thoracic spinal cord, snRNA sample 1

description: Library name: Donor4_Thoracic_Sample1_GEX


title: Nerve_MEF_2

city: Portland

first: Sebnem

middle: Ece

last: Eksi

state: Oregon

address: 2730 S Moody Ave.

institute: Oregon Health & Science University

description: Library name: RNA230928DM_Nerve_MEF_2

data_processing:
Sequencing data alignment and quantification were performed with STAR (v.2.7.10b). FASTQ files containing sequencing reads for each sample were aligned to the mouse genome assembly GRCm. STAR alignment options were set to standard ENCODE parameters as detailed in the STAR manual. Gene-level quantification was performed by setting STAR quantification mode to “GeneCounts” and used the GENCODE primary assembly basic genome annotation (M33). Stranded reads for each gene were collected into separate counts matrices representing PSC and nerve samples. One sample representing nerves treated with PSC media was excluded from further analysis due to being the only RNA-seq technical replicate in this work.
Assembly: GRCm39
Supplementary files format and content: Processed data files are tab-delimited, normalized gene expression counts matrices for PSC samples and nerve samples. These matrices were generated in R (v.4.2.2) using the standard DESeq2 (v.1.38.3) workflow to normalize expression values. Two versions of processed files are provided: "AllFeatures" includes all annotated features, while "FilteredFeatures" includes only genes that passed the minimum count threshold (minimum 10 cumulative counts across samples).

source_name: Neural

extract_protocol:
Total RNA was purified using the RNeasy Kit (Qiagen; 74004). Beta-mercaptoethanol (ß-ME) was used as the reducing agent, and the RNA extraction was performed as described by the Qiagen procedure. The RNA concentration and integrity were verified with a bioanalyzer, and 50 million read-pairs per library were prepared and sequenced by the Massively Parallel Sequencing Shared Resource at OHSU.
RNA quality was assessed using the Agilent 2100 Bioanalyzer. Libraries were prepared using the TruSeq Stranded mRNA kit (Illumina). Briefly, 200ng of total RNA was converted to cDNA using random hexamers. Synthesis of the second strand was done with the addition of dUTP, which enforced the stranded orientation of the libraries by blocking amplification off the second strand during the first round of PCR. Amplified libraries were profiled on the 4200 TapeStation (Agilent). Libraries were quantified for sequencing using an NGS Library Quantification Kit (Roche/Kapa Biosystems) on a StepOnePlus Real Time PCR Workstation (Thermo/ABI). Sequencing was done on a NovaSeq 6000 (Illumina). Base calling was done by RTA v3.4.4. Fastq files were assembled using bcl2fastq v2.20.0.422 (Illumina).

value: Neural

value: Sympathetic


title: Nerve_MEF_1

description: Library name: RNA230928DM_Nerve_MEF_1


title: Donor 4, Lumbar spinal cord, snRNA sample 2

description: Library name: Donor4_Lumbar_Sample2_GEX


title: Donor 4, Lumbar spinal cord, snRNA sample 1

description: Library name: Donor4_Lumbar_Sample1_GEX


title: CT-2

description:
Library name: sample2
CT2


title: Nerve_PSC_4

description: Library name: RNA230928DM_Nerve_PSC_4


title: Nerve_MEF_3

description: Library name: RNA230928DM_Nerve_MEF_3


title: Nerve_PSC_3

description: Library name: RNA230928DM_Nerve_PSC_3


title: Donor 6, Thoracic spinal cord, snATAC sample 2

description: Library name: Donor6_Thoracic_Sample2_ATAC

library_source: genomic single cell

data_processing:
Cell Ranger ARC 2.0.2
Assembly: GRCh38
Supplementary files format and content: Donors2-6_ATAC_fragments.tsv.gz cell-by-peak counts matrix  for each sample
Supplementary files format and content: Donors2-6_ATAC_peak_annotation.tsv fragment file  for each sample
Supplementary files format and content: .bed annotations file for each sample

extract_protocol:
Spinal cord tissue was surgically resected from organ donors during organ donation. Individual nuclei were isolated through homogenization and gradient centrifugation.
snATAC-seq libraries were generated using 10x Chromium Single Cell Multiome ATAC+Gene Expression, following manufacturer's guidelines.


title: Nerve_PSC_2

description: Library name: RNA230928DM_Nerve_PSC_2


title: Donor 6, Thoracic spinal cord, snATAC sample 1

description: Library name: Donor6_Thoracic_Sample1_ATAC


title: Young Sham1

description:
Library name: YSH1
Young adult mice treated with doxycyline in drinking water for 7 days, followed by 7-13 day washout period, then 72 hours of ambulation after synergist ablation mechanical overload sham surgery, 1

value: HSA-GFP

value: 72 hours Sham


title: Donor 6, Lumbar spinal cord, snATAC sample 1

description: Library name: Donor6_Lumbar_Sample1_ATAC


title: Nerve_3

description: Library name: RNA230928DM_Nerve_3


title: Donor 6, Lumbar spinal cord, snATAC sample 2

description: Library name: Donor6_Lumbar_Sample2_ATAC


title: Nerve_PSC_1

description: Library name: RNA230928DM_Nerve_PSC_1


title: Donor 5, Thoracic spinal cord, snATAC sample 2

description: Library name: Donor5_Thoracic_Sample2_ATAC


title: Nerve_2

description: Library name: RNA230928DM_Nerve_2


title: Nerve_1

description: Library name: RNA230928DM_Nerve_1


title: Donor 5, Thoracic spinal cord, snATAC sample 1

description: Library name: Donor5_Thoracic_Sample1_ATAC


title: PSC_N_3

description: Library name: RNA230928DM_PSC_N_3

source_name: pancreas

value: pancreas

value: Fibroblast


title: PSC_N_2

description: Library name: RNA230928DM_PSC_N_2


title: Donor 5, Lumbar spinal cord, snATAC sample 2

description: Library name: Donor5_Lumbar_Sample2_ATAC


title: Donor 5, Lumbar spinal cord, snATAC sample 1

description: Library name: Donor5_Lumbar_Sample1_ATAC


title: Donor 4, Thoracic spinal cord, snATAC sample 2

description: Library name: Donor4_Thoracic_Sample2_ATAC


title: PSC_3

description: Library name: RNA230928DM_PSC_3


title: Donor 4, Thoracic spinal cord, snATAC sample 1

description: Library name: Donor4_Thoracic_Sample1_ATAC


title: Donor 4, Lumbar spinal cord, snATAC sample 1

description: Library name: Donor4_Lumbar_Sample1_ATAC


title: Donor 4, Lumbar spinal cord, snATAC sample 2

description: Library name: Donor4_Lumbar_Sample2_ATAC


title: PSC_N_1

description: Library name: RNA230928DM_PSC_N_1


title: PSC_2

description: Library name: RNA230928DM_PSC_2


title: HFD-CDAA plive-Tet1-4

city: Nanjing

first: junjie

last: yu

address: Address: #639 Longmian Avenue, Jiangning District, Nanjing, China, 211198

institute: China Pharmaceutical University

description:
Library name: sample 8
Column name in all.fpkm_anno.xlsx :A7LV10

data_processing:
Quality control:In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N:0.1) to be high quality clean data. Alignment:Clean data were aligned to the reference genome using Hisat2 (v2.2.1). Expression analysis：Gene and isoform expression levels were estimated from the paired-end clean data using HTSeq (v0.6.1).
Assembly: GRCm39
Supplementary files format and content: xlsx files include counts and FPKM values for each Sample

source_name: Liver

growth_protocol: Six‑week‑old C57BL/6J mice were fed with high‑fat diet‑choline‑deficient amino acid‑defined (HFD‑CDAA) diet for 4 weeks.

extract_protocol:
Total RNA was extracted from liver using TRlzol® Reagent according the manufacturer's instructions.
1 µg total RNA was used for library preparation. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

treatment_protocol: Mice received hydrodynamic tail vein injection of plive‑Tet1 overexpression plasmid, and plive‑Con was used as the control.

value: Liver

tag: strain

value: WT

value: plive-Tet4 injection + HFD-CDAA diet


title: HFD-CDAA plive-Tet1-3

description:
Library name: sample 7
Column name in all.fpkm_anno.xlsx :A7LV9

value: plive-Tet3 injection + HFD-CDAA diet


title: fastGRO Q901, TPT rep2

city: Nam-gu, Pohang-si

first: Hyerim

last: Jung

state: Gyeongsangbuk-do

address: 47, Jigok-ro

department: Dept. of Life Sciences

country: South Korea

institute: Pohang University of Science & Technology (POSTECH)

description: Library name: Q901-2h-TPT-6h-rep2

data_processing:
fastGRO data were trimmed with fastp (0.23.4) and rRNA was removed. The trimmed reads were aligned to hg38 using Bowtie2 and deduplicated with UMI-tools (1.1.4). The bigWig files were generated by deepTools[46] bamCoverage (3.5.1) and visualized with UCSC genome browser. The expression level except promoter regions (+300~TES, >350bp) was calculated with HOMER analyzeRepeats.pl and DESeq2.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: GRO-Seq

growth_protocol: MCF-7 was maintained in DMEM (Thermo Fisher Scientific, Waltham, MA, USA, Gibco™, 31053028) with 10% FBS (Invitrogen, Carlsbad, CA, USA, 10091148), GlutaMAX (Thermo Fisher Scientific, Gibco™, 35050061) and Penicillin-Streptomycin (Welgene, Gyeongsansi, South Korea, LS202-02) ), and for short-term treatment, DMEM (Gibco™, 31053028) with 10% charcoal stripped FBS (Gibco™, A3382101), and GlutaMAX (Gibco™, 35050061) was used.

extract_protocol:
For fastGRO, nuclei were isolated with ice cold swelling buffer (10mM Tris-HCl pH 7.5, 2mM MgCl2, 3mM CaCl2, 2U/ml SUPERase-In RNase inhibitor (Invitrogen, AM2696)), swelling buffer with glycerol (10mM Tris-HCl pH 7.5, 2mM MgCl2, 3mM CaCl2, 10% glycerol, 2U/ml SUPERase-In RNase inhibitor), and lysis buffer (10mM Tris-HCl pH 7.5, 2mM MgCl2, 3mM CaCl2, 10% glycerol, 1% NP-40, 2U/ml SUPERase-In RNase inhibitor). Nuclei were stored in freeze buffer (50mM Tri-HCl pH 8.0, 40% glycerol, 5mM MgCl2, 0.1mM EDTA pH 8.0, 2U/ml SUPERase-In RNase inhibitor) at -80℃.
fastGRO library preparation was performed following the PRO-seq protocol. Following the ligation of the 3' adapter, samples were treated with RppH (NEB, M0356S) and PNK (NEB, M0201S), and 5' adapter was ligated. RNA was purified using streptavidin-coupled magnetic beads and washed between incubation steps with high-salt buffer (50 mM Tris-HCl pH 7.4, 2 M NaCl, 0.5% Triton X-100, 1 mM EDTA pH 8.0, 40 U/10 mL SUPERase-In RNase inhibitor) and low-salt buffer (50 mM Tris-HCl pH 7.4, 0.1% Triton X-100, 1 mM EDTA pH 8.0, 40 U/10 mL SUPERase-In RNase inhibitor). The biotinylated RNA was converted to DNA with reverse-transcription step (Maxima H-reverse transcriptase, Thermo Fisher Scientific, EP0751) and amplified (Q5 High-Fidelity DNA Polymerase, NEB, M0491L) for sequencing.

treatment_protocol: For fastGRO, cells were treated with 100 nM Q901 for 2 h followed by 1 μM TPT for 6 h.

value: Q901 1h, TPT 1h


title: HFD-CDAA plive-Tet1-2

description:
Library name: sample 6
Column name in all.fpkm_anno.xlsx :A7LV5

value: plive-Tet2 injection + HFD-CDAA diet


title: fastGRO Q901 rep2

description: Library name: Q901-2h-Ct-6h-rep2


title: fastGRO TPT rep2

description: Library name: Ct-2h-TPT-6h-rep2

value: TPT 1h


title: HFD-CDAA plive-Con-4

description:
Library name: sample 4
Column name in all.fpkm_anno.xlsx :A7LV15

value: plive-Con injection + HFD-CDAA diet


title: fastGRO DMSO rep2

description: Library name: Ct-2h-Ct-6h-rep2

value: DMSO


title: fastGRO Q901, TPT rep1

description: Library name: Q901-2h-TPT-6h-rep1


title: HFD-CDAA plive-Con-3

description:
Library name: sample 3
Column name in all.fpkm_anno.xlsx :A7LV6


title: HFD-CDAA plive-Tet1-1

description:
Library name: sample 5
Column name in all.fpkm_anno.xlsx :A7LV4

value: plive-Tet1 injection + HFD-CDAA diet


title: HFD-CDAA plive-Con-2

description:
Library name: sample 2
Column name in all.fpkm_anno.xlsx :A7LV2


title: fastGRO TPT rep1

description: Library name: Ct-2h-TPT-6h-rep1


title: fastGRO Q901 rep1

description: Library name: Q901-2h-Ct-6h-rep1


title: fastGRO DMSO rep1

description: Library name: Ct-2h-Ct-6h-rep1


title: day 7 control

description: Library name: day7 noDox

data_processing:
CellRanger pipeline (v3.1.0, 10x Genomics) was used for demultiplexing, alignment, barcode and UMI counting, as well as filtering and correction.
Assembly: GRCh38
Supplementary files format and content: tab-separated barcodes and features files, and matrix files

extract_protocol:
Samples were collected on days 1, 3, 5, and 7 following the initiation of Dox treatment. Single cells were cryopreserved in DMEM (Gibco) supplemented with 10% heat-inactivated FBS and 10% DMSO. Prior to sequencing, the cells were thawed, and dead cells were removed using the Dead Cell Removal Kit (Miltenyi Biotec).
An RNA library was generated using the 10x Genomics Chromium Single Cell 3’ Library and Gel Bead Kit v3.1, and the amplified cDNA was sequenced on an Illumina NovaSeq 6000 S2 flow cell.

treatment_protocol: Doxycycline treatment to induce KRASG12D expression

value: stem-cell derived pancreatic duct-like organoid

value: wildtype

value: no treatment


title: TCF1_KO2

city: Beijing

first: Qi

last: Xing

address: 30 Shuangqing Road

institute: Tsinghua University

description: Library name: Sample 20

data_processing:
Low quality reads and adaptor sequences were removed by Trim Galore v0.4.4.
Clean reads were aligned to Mus musculus genome (mm10) by Bowtie2 with default parameter. Uniquely mapped reads were counted by featureCounts (from Subread package).
FPKM (Fragments Per Kilobase of exon model per Million mapped reads) were calculated using RSEM
Differentially expressed genes (DEGs) were identified by DESeq2 with cut-off thresholds of 1.5-fold change and FDR adjusted p-value<0.05 (for Bcl6RFP and BLIMP1-WT/cKO comparisons) or 1.25-fold change and p-value<0.05 (for BCL6-WT/cKO and TCF1-WT/cKO comparisons).
Assembly: mm10
Supplementary files format and content: txt files include FPKM values for each sample

source_name: small intestine

extract_protocol:
Total RNA was extracted from sorted cells using MagZol  (Magen, cat#R4801-02) according to the manufacturer’s protocol.
RNA-seq library was constructed for deep sequencing by BGI Genomics or Novogene.

value: small intestine

value: Tcf7fl/fl Cd8cre


title: day 7 Dox treatment

description: Library name: day 7 Dox

value: 3µg/ml Doxycycline


title: TCF1_KO1

description: Library name: Sample 19


title: TCF1_WT2

description: Library name: Sample 18


title: day 5 Dox treatment

description: Library name: day 5 Dox


title: Prdm1_KO2

description: Library name: Sample 16

value: Prdm1fl/fl Cd8cre


title: TCF1_WT1

description: Library name: Sample 17


title: HFD-CDAA plive-Con-1

description:
Library name: sample 1
Column name in all.fpkm_anno.xlsx : A7LV1

value: Liver


title: day 3 Dox treatment

description: Library name: day 3 Dox


title: day 1 Dox treatment

description: Library name: day 1 Dox


title: day 7 untreated 3

description: Library name: day7_control_3

data_processing:
Data quality control was performed using the fastp tool, and reads were aligned to the GRCh38 reference genome using Bowtie2. Peak calling was carried out with MACS2.
Assembly: GRCh38
Supplementary files format and content: narrowPeak files

extract_protocol:
Organoids were collected on days 3, 5, and 7 following the initiation of Dox treatment, along with matched controls that were not treated with Dox. For each sample, 50,000 cells were lysed and fragmented using 2x TD Tagment DNA Buffer containing TDE1 Tagment DNA Enzyme (Illumina), Digitonin (Promega), and Protease Inhibitor Cocktail (Roche). After a 30-minute incubation at 37°C, samples were purified using the MinElute Kit (Qiagen).
The libraries were sequenced on a NovaSeq 6000 instrument (Illumina) following a 50-base-pair, paired-end recipe.

value: day 7


title: Prdm1_WT2

description: Library name: Sample 14


title: Prdm1_KO1

description: Library name: Sample 15


title: day 7 untreated 2

description: Library name: day7_control_2


title: SI_RFP_N3

description: Library name: Sample 8


title: Prdm1_WT1

description: Library name: Sample 13


title: day 7 untreated 1

description: Library name: day7_control_1


title: day 7 Dox treatment 1

description: Library name: day7_Dox_1


title: day 7 Dox treatment 3

description: Library name: day7_Dox_3


title: SI_RFP_N2

description: Library name: Sample 7


title: day 7 Dox treatment 2

description: Library name: day7_Dox_2


title: day 5 untreated 3

description: Library name: day 5_control_3

value: day 5


title: SI_RFP_N1

description: Library name: Sample 6


title: SI_RFP_P3

description: Library name: Sample 5


title: day 5 untreated 1

description: Library name: day 5_control_1


title: SI_RFP_P1

description: Library name: Sample 3


title: LI_1

description: Library name: Sample 1


title: day 5 Dox treatment 3

description: Library name: day5_Dox_3


title: LI_2

description: Library name: Sample 2


title: SI_RFP_P2

description: Library name: Sample 4


title: day 5 Dox treatment 2

description: Library name: day5_Dox_2


title: day 5 untreated 2

description: Library name: day 5_control_2


title: Isolated injured cardiac tissue from Abcc6 KO mice

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

description: Library name: KO

data_processing:
Raw reads were processed using the Cell Ranger Pipeline (10x Genomics). The Cellranger output expression matrices were merged for each sample. The R package Seurat (v4.3.0) was used to cluster the cells in the merged matrix. Cells with less than 100 genes or more than 10% of mitochondrial expression were first filtered out as low-quality cells. The NormalizeData function was used to normalize the expression level for each cell with default parameters. The FindVariableFeatures function was used to select variable genes with default parameters. The ScaleData function was used to scale and center the counts in the dataset. Principal component analysis (PCA) was performed on the variable genes. The RunHarmony function from the Harmony package was applied to remove potential batch effects among samples processed in different batches. Uniform Manifold Approximation and Projection (UMAP) dimensional reduction was performed using the RunUMAP function. The clusters were obtained using the FindNeighbors and FindClusters functions with the resolution set to 0.5. The cluster marker genes were found using the FindAllMarkers function. The cell types were annotated by overlapping the cluster markers with the published marker genes. The dot plot was plotted using the DotPlot function. Differential expression analysis between two groups of cells was conducted using the FindMarkers function. Genes with adjusted p-value smaller than 0.05 were considered significantly differentially expressed.
Assembly: mm10
Supplementary files format and content: rds file contains the raw expression matrix

source_name: cardiac tissue

extract_protocol:
3 days post cryo injury WT and ABCC6 KO mice scar regions of the heart were harvested and digested by 0.1 µg/mL liberase TH (Sigma, 5401151001). After digestion, cells were incubated with 10 µM Calcein AM (Abcam, ab141420) and live cells were collected by flow cytometry
Single-cell gene expression libraries were created using Chromium Next GEM Single Cell 3' (v3.1 Chemistry) (10x Genomics), Chromium Next GEM Chip G Single Cell Kit (10x Genomics), and Single Index Kit T Set A (10x Genomics) according to the manufacturer’s instructions. Briefly, samples were loaded to target 10,000 cells to form GEMs and barcode individual cells. GEMs were then cleaned cDNA and libraries were also created according to the manufacturer’s instructions. Library quality was assessed using the 4200 TapeStation System and D1000 ScreenTape (Agilent) and Qubit 2.0 (Invitrogen) for concentration and size distribution. Samples were sequenced using Novaseq 6000 (Illumina) using 100 cycles. 200 M reads were targeted for each sample, targeting 20,000 reads per cell. Raw reads were processed using the Cell Ranger Pipeline (10x Genomics)

treatment_protocol: Mice were anesthetized and intubated using a volume-cycled ventilator. A left thoracotomy was performed at the level of the second intercostal space. The exposed beating heart was subjected to cryoinjury by applying a 1 mm steel rod pre-cooled in dry ice for 10 seconds

value: cardiac tissue

value: Abcc6 KO

value: cryo injury


title: day 5 Dox treatment 1

description: Library name: day5_Dox_1


title: Isolated injured cardiac tissue from WT mice

description: Library name: WT

value: WT


title: day 3 untreated 3

description: Library name: day3_control_3

value: day 3


title: day 3 untreated 1

description: Library name: day3_control_1


title: Adult mouse cardiomyocytes, MI, AAV9-Control

first: Zhenzhen

last: Zhan

address: Jimo Road 150

department: Research Center for Translational Medicine

institute: Shanghai East Hospital, Tongji University School of Medicine,

description: Library name: Control_AMCMs

data_processing:
ATAC-seq reads were trimmed from 3' end until the final base had a quality score > 20, using Fastx  (version:0.0.13), discarding reads left with < 20 bp.
ATAC-seq reads were aligned to the  reference  mm10 genome using Bowtie (version:0.12.8). MACS (version 2.2.7.1) was applied to call peaks.
To create ATAC-seq coverage plots, the locations of the mapped ATAC-seq reads were renormalized (to reads per million, rpkm) and reformatted in the bigWig file format.
The bam file and R package DiffBind were used to analyze the differences between the peaks of the specified two samples. The default parameters were set as  P value < 0.05. The differences between the obtained peaks were annotated.
The annotation program was the same as the above peak annotation program, including different peak location and annotation information, etc.
Assembly: mm10
Supplementary files format and content: bigWig files

source_name: adult mouse heart

extract_protocol:
Adult hearts from the indicated treatments were dissected, cannulated, and dissociated into a single-cell suspension via collagenase digestion (Collagenase type II, Worthington) using a Langendorff apparatus. AMCM yields and the percentage of viable rod-shaped cells were quantified using a hemocytometer.
For the ATAC-seq library preparation, 50,000 viable cells were used and collected. The samples were prepared using the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme) following the manufacturer’s protocol. Briefly, the cell pellets were resuspended in the kit-provided cold lysis buffer and incubated on ice for 5 min. Then, the cells were collected and resuspended with 50 μl transposition mixtures according to ATAC Kit instructions. Mixtures were incubated for the PCR reaction. Mixtures were purified with VAHTS DNA Clean Beads (Vazyme) and amplified for 15 cycles using TruePrep Index Kit V2 for Illumina (Vazyme). Amplification products were further purified with VAHTS DNA Clean Beads.

treatment_protocol: Adult mice underwent permanent ligation of the left anterior descending (LAD) coronary artery and were immediately followed by an intramyocardial injection of AAV9-cTnT-GFP (control viral vector) or AAV9-cTnT-Rbm22-GFP at the infarct border zone. Cardiac tissues were collected post-MI for the isolation of adult mouse cardiomyocytes (AMCMs).

value: adult mouse heart

tag: disease state

value: myocardial infarction

value: adult mouse cardiomyocytes

value: AAV9-cTnT-GFP (control viral vector) intramyocardial injection


title: day 3 Dox treatment 3

description: Library name: day3_Dox_3

value: stem-cell derived pancreatic duct-like organoid


title: PSC_1

description: Library name: RNA230928DM_PSC_1

value: pancreas

value: Fibroblast


title: day 3 Dox treatment 2

description: Library name: day3_Dox_2

value: 3µg/ml Doxycycline


title: day 0 untreated 3

description: Library name: day0_control_3

value: wildtype

value: no treatment

value: day 0


title: day 0 untreated 2

description: Library name: day0_control_2


title: day 3 Dox treatment 1

description: Library name: day3_Dox_1


title: day 3 untreated 2

description: Library name: day3_control_2


title: Liver, Y665H_female_rep2

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

description: Library name: Sample 33

data_processing:
The fastq files were subjected to QC analyses using the FastQC tool (version 0.11.9). Quality filtering and alignment of the raw reads was done using Trimmomatic (version 0.36) and subsequently aligned to the reference genome mm10 applying STAR RNA-seq aligner (version 2.7.11b), Samtools (version 1.9) and Picard (version 2.9.2). Htseq (version 0.9.1) was applied to calculate raw read counts.
Assembly: mm10
Supplementary files format and content: raw read counts from RNA-seq samples

growth_protocol: Total RNA-seq was done for the liver tissue of wild-type and mutant mice carrying a point mutation in Stat5-Y665.

extract_protocol:
Total RNA was extracted from the frozen tissue from mice and purified with RNeasy Plus Mini Kit (Invitrogen, 12183018A). Ribosomal RNA was removed from 1ug of total RNAs and cDNA was synthesized using SuperScript III (Invitrogen). Libraries for sequencing were prepared according to the manufacturer’s instructions with TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina, RS-122-2301) and paired-end sequencing was done with a Novaseq 6000 instrument (Illumina).
Libraries for sequencing were prepared using standard New England Biolabs's protocols.

value: liver

tag: Stage

value: 2-month-old age

value: female


title: Liver, Y665H_female_rep3

description: Library name: Sample 34


title: Liver, Y665H_female_rep1

description: Library name: Sample 32


title: Liver, Y665H_female_rep4

description: Library name: Sample 35


title: Liver, Y665H_female_rep5

description: Library name: Sample 36


title: day 0 untreated 1

first: Alexander

address: Albert-Einstein-Allee 23, 89071 Ulm

institute: University Hospital Ulm

description: Library name: day0_control_1


title: Adult mouse cardiomyocytes, MI, AAV9-Rbm22

description: Library name: RBM22_AMCMs

value: AAV9-cTnT-Rbm22-GFP viral vector intramyocardial injection


title: Liver, Y665F_female_rep6

description: Library name: Sample 31


title: Liver, Y665F_female_rep4

description: Library name: Sample 29


title: Adult blood donor 9 0HR

city: San Francisco

first: Laura

middle: R

last: Dwyer

address: 513 Parnassus Ave

institute: UCSF

description:
Library name: AB9_0HR
AB9_0HR

data_processing:
Read alignment done with kallisto (v. 0.46.2) using Ensembl reference genome GRCh38 (109)
Assembly: hg38
Supplementary files format and content: Abundance tsv files for individual samples

source_name: Adult blood

extract_protocol:
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. Sequencer Used: Novaseq 6000, S4 Flowcell, Paired-End 150 cycles
After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or DTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina Novaseq 6000, S4 Flowcell, Paired-End 150 cycles. Samples that passed QC were advanced to RNA sequencing and included in data analysis. Six samples for each age and time point were submitted, but only those that passed RNA quality control were advanced to sequencing and analysis.

value: Adult blood

value: PBMC

value: naive CD4+ T cells

tag: time point


title: Adult blood donor 8 3HR

description:
Library name: AB8_3HR
AB8_3HR


title: Liver, Y665F_female_rep5

description: Library name: Sample 30

source_name: liver


title: Adult blood donor 9 3HR

description:
Library name: AB9_3HR
AB9_3HR


title: Adult blood donor 8 0HR

description:
Library name: AB8_0HR
AB8_0HR


title: Liver, Y665F_female_rep2

description: Library name: Sample 27


title: Liver, Y665H_female_rep6

description: Library name: Sample 37


title: Liver, Y665F_female_rep1

description: Library name: Sample 26


title: Adult blood donor 6 48HR

description:
Library name: AB6_48HR
AB6_48HR


title: Liver, WT_female_rep5

description: Library name: Sample 24

value: WT


title: Adult blood donor 7 0HR

description:
Library name: AB7_0HR
AB7_0HR


title: Liver, WT_female_rep6

description: Library name: Sample 25


title: Liver, WT_female_rep4

description: Library name: Sample 23


title: IWAT, H3K27ac CUT&Tag, replicate 2

city: Guangzhou

last: He

state: Guangdong

address: No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China

department: Department of Basic Research

institute: Guangzhou National Laboratory

description: Library name: Tissue_H3K27ac_rep2

data_processing:
Raw sequencing reads were processed by fastp with parameter "-q 20 --detect_adapter_for_pe --trim_poly_g" to trim the adapter and poly G end. Then reads were mapped to mouse reference genome (mm39) by bowtie2 with default parameter. Properly mapped high MAPQ reads were remained by samtools view "-f 2 -q 20". Then PCR duplicates were removed by picard tools. Finally, we use macs2 with "-q 0.05 -B --nomodel -f BAMPE --keep-dup all" to call peaks.
Assembly: mm39
Supplementary files format and content: narrowPeak
Library strategy: CUT&Tag

source_name: White adipose

extract_protocol:
For ChIP-seq, brown preadipocytes or brown adipocytes were fixed with 1% formaldehyde for 10min and the reaction was quenched by 0.125M glycine. Cells were then washed with PBS for two times. Cells were lysed in ChIP buffer (1% SDS, 50 mM Tris-HCl, pH 8.0, 10 mM EDTA, and protease inhibitor cocktail) for 30 min at 4°C. The DNA was fragmented to 200-500bp by sonication and centrifuged at 12,000 g for 5min. The supernatant was diluted with ChIP IP buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl and protease inhibitor cocktail). For the CUT&Tag assay was performed using the NovoNGS® CUT &Tag 2.0 A High-Sensitivity Kit (for Illuina®) (Cat# N259-YH01-01A, Novoprotein Scientific, Inc.,) following the manufacturer's protocol.
The ChIP DNA library was constructed with VAHTS Turbo DNA Library Prep Kit for Illumina (Vazyme Biotech) according to the manufacturer’s instructions. For the CUT&Tag assay was performed using the NovoNGS® CUT &Tag 2.0 A High-Sensitivity Kit (for Illuina®) (Cat# N259-YH01-01A, Novoprotein Scientific, Inc.,) following the manufacturer's protocol.

value: White adipose

tag: chip antibody


title: Liver, WT_female_rep2

description: Library name: Sample 21


title: Adult blood donor 7 3HR

description:
Library name: AB7_3HR
AB7_3HR


title: Adult blood donor 5 24HR

description:
Library name: AB5_24HR
AB5_24HR


title: Adult blood donor 5 48HR

description:
Library name: AB5_48HR
AB5_48HR


title: Liver, WT_female_rep3

description: Library name: Sample 22


title: Liver, WT_female_rep1

description: Library name: Sample 20


title: Liver, Y665H_male_rep4

description: Library name: Sample 19

value: male


title: Adult blood donor 6 24HR

description:
Library name: AB6_24HR
AB6_24HR


title: Adult blood donor 4 48HR

description:
Library name: AB4_48HR
AB4_48HR


title: Adult blood donor 4 24HR

description:
Library name: AB4_24HR
AB4_24HR


title: Liver, Y665H_male_rep3

description: Library name: Sample 18


title: Adult blood donor 4 0HR

description:
Library name: AB4_0HR
AB4_0HR


title: Liver, Y665H_male_rep2

description: Library name: Sample 17


title: Liver, Y665F_female_rep3

description: Library name: Sample 28


title: Adult blood donor 3 24HR

description:
Library name: AB3_24HR
AB3_24HR


title: Liver, Y665H_male_rep1

description: Library name: Sample 16


title: Adult blood donor 2 24HR

description:
Library name: AB2_24HR
AB2_24HR


title: Liver, Y665F_male_rep8

description: Library name: Sample 14


title: Adult blood donor 4 3HR

description:
Library name: AB4_3HR
AB4_3HR


title: Adult blood donor 2 48HR

description:
Library name: AB2_48HR
AB2_48HR


title: Liver, Y665F_male_rep9

description: Library name: Sample 15


title: Adult blood donor 2 3HR

description:
Library name: AB2_3HR
AB2_3HR


title: Adult blood donor 1 48HR

description:
Library name: AB1_48HR
AB1_48HR


title: Cord blood donor 7 3HR

description:
Library name: CB7_3HR
CB7_3HR

source_name: Cord blood

value: Cord blood


title: Liver, Y665F_male_rep5

description: Library name: Sample 11


title: Liver, Y665F_male_rep6

description: Library name: Sample 12


title: Adult blood donor 2 0HR

description:
Library name: AB2_0HR
AB2_0HR


title: Liver, Y665F_male_rep7

description: Library name: Sample 13


title: Cord blood donor 7 0HR

description:
Library name: CB7_0HR
CB7_0HR


title: Liver, Y665F_male_rep4

description: Library name: Sample 10


title: NK 4-1007 B

city: Brno

first: Ioanna

last: Papatheodorou

address: Studentska

department: Center for Translational Medicine

country: Czech Republic

institute: International Clinical Research Center (ICRC), St.Anne’s Hospital

description: Library name: 1007_B_c366

data_processing:
Sequences were trimmed for adaptors/low quality sequences using Trim galore with default parameters.
Trimmed sequences were mapped to GRCh38-p10 (human genome) with HISAT2 using the default parameteres.
Read counts were determined with Htseq -count.
Raw gene counts were normalized following VST transformation by use of the package DESeq2 in the R v4.3.3. environment.
Differentially expressed genes were determined with DESeq2 in the R v4.3.3. enviroment.
Assembly: GRCh38-p10
Supplementary files format and content: The txt delimited file named NK_dataset_raw_counts_outliers_removed.txt contains all the raw HTseq derived counts.
Supplementary files format and content: The txt delimited file named NK_cells_norm_counts_outlier_removed.txt contains all the normalized counts following VST transformation.

source_name: Peripheral blood

growth_protocol: NK MACs medium with 5% human serum, 1x106/ml

extract_protocol:
Cells were lysed with TRI reagent and RNA was extracted with Quagen RNEasy mini kit
Libraries were constructed with the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD using 250 ng of RNA as input for bulk RNAseq

treatment_protocol: Magnetic isolation from PBMC (purity >90%). Overnight stimulation with IL-2 (500IU/ml)

value: Peripheral blood

value: healthy donor

value: NK cells

value: Overnight stimulation with IL-2


title: NK 4-1007 C

description: Library name: 1007_C_c367


title: NK 4-0925 B

description: Library name: 0925_B_c356


title: NK 4-0925 C

description: Library name: 0925_C_c358


title: Liver, Y665F_male_rep3

description: Library name: Sample 9


title: NK 4-0925 A

description: Library name: 0925_A_c354


title: Cord blood donor 6 3HR

description:
Library name: CB6_3HR
CB6_3HR


title: Liver, Y665F_male_rep2

description: Library name: Sample 8


title: Cord blood donor 6 0HR

description:
Library name: CB6_0HR
CB6_0HR


title: NK 4-0910 C

description: Library name: 0910_C_c346


title: NK 4-0904 C

description: Library name: 0904_C_c340


title: NK 4-0730 C

description: Library name: 0730_C_c325


title: NK 4-0910 B

description: Library name: 0910_B_c344


title: NK 4-0730 B

description: Library name: 0730_B_c323


title: Cord blood donor 5 48HR

description:
Library name: CB5_48HR
CB5_48HR


title: Nk 4-0617 C

description: Library name: 0617_C_c307


title: NK 4-0730 A

description: Library name: 0730_A_c321


title: Cord blood donor 5 24HR

description:
Library name: CB5_24HR
CB5_24HR


title: Nk 4-0617 B

description: Library name: 0617_B_c305


title: Liver, WT_male_rep5

description: Library name: Sample 5


title: Cord blood donor 4 48HR

description:
Library name: CB4_48HR
CB4_48HR


title: CT5.3hTERT,Omipalisib,24h_replicate2

address: C. Heymanslaan 10

institute: University Ghent

description:
Library name: Sample8
Column name in raw_counts.txt:Omipalisib_replicate2

data_processing:
Reads were mapped to the human genome using Tophat, and gene expression counts were generated with HTSeq.
Assembly: hg38
Supplementary files format and content: output from Htseq

source_name: cell line

extract_protocol:
RNA was extracted using the miRNeasy Micro Kit (Qiagen), and 27.5 ng of RNA per sample was treated with Heat-Labile Double-Strand-Specific DNase (Arcticzymes) to remove DNA contamination.
Library construction was performed using the QuantSeq-Pool Sample-Barcoded 3′ mRNA-Seq Kit (Lexogen) according to the manufacturer’s protocol.

value: cell line

value: cancer associated fibroblasts

value: Omipalisib


title: NK 4-0613 C

description: Library name: 0613_C_c301


title: NK 4-0613 B

description: Library name: 0613_B_c299


title: Liver, Y665F_male_rep1

description: Library name: Sample 7

value: liver

value: 2-month-old age


title: TOP1 Q901, TPT rep2

description: Library name: TOP1-Q901-TPT-rep2

data_processing:
ChIP-seq data were trimmed with Trim Galore (0.6.7)[37] and aligned to hg38 (v36) using Bowtie 2 (2.4.5)[38]. The bigWig files were generated by HOMER (v4.11)[39] makeUCSCfile and visualized with UCSC genome browser. For pan pol II, Ser5P, and Ser2P ChIP-seq, read counting was generated by HOMER analyzeRepeats.pl and DESeq2 (1.40.0)[40]. For CDK7, MYC, E2F1, and TOP1 ChIP-seq, peakcalling was performed with MACS3 (3.0.0b1)[41] and IDR (2.0.3)[42].
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
For ChIP-seq, MCF-7 cells were crosslinked for 10 (MYC, E2F1 and TOP1) or 15 (other protein) min at RT by crosslinking buffer (50mM HEPES pH 8.0, 100mM NaCl, 1mM EDTA pH 8.0, 0.5mM EGTA pH 8.0) with 1% formaldehyde (Sigma-Aldrich, F8775-4X25ML) followed by quenching with 125mM glycine (Daejung, Siheung-si, South Korea, 4068-4105) for 5 min. Cells were washed with ice cold 1X PBS and pellets were stored at -80℃.
ChIP-seq libraries were generated with NEBNext End Repair Module (NEB, E6050L), NEBNext dA-Tailing Module (NEB, E6053L), Quick Ligation Kit (NEB, M2200L), and NEBNext Multiplex Oligos for Illumina (NEB, E7335S, E7500S, E7710S) according to the manufacturer's protocol.

treatment_protocol: For the short-term condition, MCF-7 cells were treated with DMSO or 100 nM Q901 for 1 h followed by 1 h of EtOH/E2 treatment (the E2 condition was not used in this study). For long-term treatment, MCF-7 cells were treated with DMSO or 100 nM Q901 for 4, 24 h. For TPT treatment, cells were treated with 100 nM Q901 for 2 h followed by 1 μM TPT for 6 h.

value: Q901 1h, TPT 1h

value: TOP1 (Abcam, ab109374)


title: Liver, WT_male_rep3

description: Library name: Sample 3


title: Nk 4-0613 A

description: Library name: 0613_A_c297


title: CT5.3hTERT,Everolimus,24h_replicate1

description:
Library name: Sample4
Column name in raw_counts.txt:Everolimus_replicate1

value: Everolimus


title: Cord blood donor 4 24HR

description:
Library name: CB4_24HR
CB4_24HR

value: PBMC

value: naive CD4+ T cells


title: TOP1 Q901 rep2

description: Library name: TOP1-Q901-rep2


title: CT5.3hTERT,DMSO,24h_replicate2

description:
Library name: Sample2
Column name in raw_counts.txt:DMSO_replicate2

value: WT

value: DMSO


title: Liver, WT_male_rep4

description: Library name: Sample 4

value: male


title: Cord blood donor 4 0HR

description:
Library name: CB4_0HR
CB4_0HR

value: Cord blood


title: Cord blood donor 3 48HR

description:
Library name: CB3_48HR
CB3_48HR


title: TOP1 TPT rep2

description: Library name: TOP1-TPT-rep2

value: TPT 1h


title: Liver, WT_male_rep1

description: Library name: Sample 1


title: MYC TPT rep2

description: Library name: MYC-TPT-rep2

value: c-Myc/N-Myc (D3N8F) (Cell Signaling Technology, 13987)


title: MYC Q901, TPT rep2

description: Library name: MYC-Q901-TPT-rep2


title: Y665H_female_rep4

description: Library name: Sample 24

source_name: Adipose

growth_protocol: Total RNA-seq was done for the  adipose tissue of wild-type and mutant mice carrying a point mutation in Stat5-Y665.

extract_protocol:
Total RNA was extracted from the tissue from mice and purified with RNeasy Plus Mini Kit (Invitrogen, 12183018A). Ribosomal RNA was removed from 1ug of total RNAs and cDNA was synthesized using SuperScript III (Invitrogen). Libraries for sequencing were prepared according to the manufacturer’s instructions with TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina, RS-122-2301) and paired-end sequencing was done with a Novaseq 6000 instrument (Illumina).
Libraries for sequencing were prepared using standard New England Biolabs's protocols.

value: Adipose

value: female


title: Cord blood donor 4 3HR

description:
Library name: CB4_3HR
CB4_3HR


title: Liver, WT_male_rep2

description: Library name: Sample 2


title: MYC Q901 rep2

description: Library name: MYC-Q901-rep2


title: Cord blood donor 3 24HR

description:
Library name: CB3_24HR
CB3_24HR


title: MYC DMSO rep2

description: Library name: MYC-DMSO-rep2


title: Y665H_female_rep3

description: Library name: Sample 23


title: TOP1 DMSO rep2

description: Library name: TOP1-DMSO-rep2


title: MYC, TOP1 input rep2

description: Library name: MYC-TOP1-input-rep2


title: Cord blood donor 3 3HR

description:
Library name: CB3_3HR
CB3_3HR


title: TOP1 TPT rep1

description: Library name: TOP1-TPT-rep1


title: TOP1 Q901, TPT rep1

description: Library name: TOP1-Q901-TPT-rep1


title: TOP1 Q901 rep1

description: Library name: TOP1-Q901-rep1


title: Cord blood donor 3 0HR

description:
Library name: CB3_0HR
CB3_0HR


title: Y665H_female_rep1

description: Library name: Sample 21


title: MYC Q901, TPT rep1

description: Library name: MYC-Q901-TPT-rep1


title: Cord blood donor 2 48HR

description:
Library name: CB2_48HR
CB2_48HR


title: TOP1 DMSO rep1

description: Library name: TOP1-DMSO-rep1


title: MYC DMSO rep1

description: Library name: MYC-DMSO-rep1


title: Y665F_female_rep4

description: Library name: Sample 20


title: Cord blood donor 2 24HR

description:
Library name: CB2_24HR
CB2_24HR


title: Y665F_female_rep3

description: Library name: Sample 19


title: MYC, TOP1 input rep1

description: Library name: MYC-TOP1-input-rep1


title: MYC Q901 rep1

description: Library name: MYC-Q901-rep1


title: Y665F_female_rep2

description: Library name: Sample 18


title: E2F1 Q901 24h rep2

description: Library name: E2F1-Q901-24h-rep2

value: E2F1 (Cell Signaling Technology, 3742)


title: E2F1 DMSO 24h rep2

description: Library name: E2F1-DMSO-24h-rep2

value: DMSO 24h


title: Y665F_female_rep1

description: Library name: Sample 17


title: Cord blood donor 1 48HR

description:
Library name: CB1_48HR
CB1_48HR


title: Cord blood donor 2 0HR

description:
Library name: CB2_0HR
CB2_0HR


title: MYC TPT rep1

description: Library name: MYC-TPT-rep1


title: MYC DMSO 24h rep2

description: Library name: MYC-DMSO-24h-rep2


title: WT_female_rep4

description: Library name: Sample 16


title: MYC, E2F1 4h, 24h input rep2

description: Library name: MYC-E2F1-input-24h-rep2


title: Liver, WT_male_rep6

description: Library name: Sample 6

value: liver


title: E2F1 DMSO 24h rep1

description: Library name: E2F1-DMSO-24h-rep1


title: Cord blood donor 1 0HR

description:
Library name: CB1_0HR
CB1_0HR


title: E2F1 Q901 24h rep1

description: Library name: E2F1-Q901-24h-rep1


title: MYC Q901 24h rep2

description: Library name: MYC-Q901-24h-rep2


title: Y665H_female_rep2

description: Library name: Sample 22

value: 2-month-old age


title: Cord blood donor 1 3HR

description:
Library name: CB1_3HR
CB1_3HR


title: MYC DMSO 24h rep1

description: Library name: MYC-DMSO-24h-rep1


title: WT_female_rep2

description: Library name: Sample 14


title: MYC, E2F1 4h, 24h input rep1

description: Library name: MYC-E2F1-input-24h-rep1


title: WT_female_rep1

description: Library name: Sample 13


title: WT_female_rep3

description: Library name: Sample 15


title: CD8 T cells, 4 stimulations hypoxia,  rep 4

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

description:
D2074H
In the processed data file, there are these columns: Geneid (ENSEMBLE ID), Chr (Chromosome where gene is anotated), Start (position of the chromosome where the gene starts), End position of the chromosome where the gene ends), Strand (DNA strand that codifies for the gene, + or -), Length (length of the gene in base pairs), the following columns are the names for each studied sample

data_processing:
Using STAR software [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/], FASTQ files were aligned to Genome data base (GRCh38) and read counts obtained for each gene
Assembly: GRCh38
Supplementary files format and content: A matrix is generated as a plain text file (*.txt) with Program featureCounts v2.0.3 (Command:"featureCounts" "-p" "--primary" "-C" "-t" "exon" "-g" "gene_id" "-a"), in which each column is a sample, each row is a gene (ensembl_ID), and in each cell indicates the number of raw counts obtained by STAR per sample and gene.

source_name: PBMC

growth_protocol: Human peripheral blood mononuclear cells (PBMCs) were isolated from buffy coats of blood donors by Ficoll-Paque Plus (Cytiva Cat. #: 17144003) density centrifugation (1200 xg for 10 min at RT) using SepMate-50 tubes (StemCell Cat. #: 85450). CD8+ T cells were isolated from PBMCs using the EasySep Human CD8+ T Cell Isolation Kit (StemCell Cat. #: 17953RF) and a RoboSep cell separator (StemCell) according to the manufacturer’s indications. Human CD8+ T cells were stimulated four times (every two days) on culture plates coated with 5 μg/mL anti-CD3 (BD Biosciences Cat. #: 567118) and soluble 1 μg/mL anti-CD28 antibodies (Invitrogen Cat. #: 16-0289-81) in RPMI 1640 GlutaMAX medium (Gibco Cat. #: 61870044) supplemented with 10% FBS (Thermo Fisher Cat. #: 10270106) and 100 IU/mL human IL-2 IS premium grade (Miltenyi Biotec Cat. #: 130-097-748). The last two stimulations were performed in a glucose-reduced medium composed of glucose-free RPMI (Gibco Cat. #: 11879020) and RPMI 1640 GlutaMAX media (1:3), under normoxia (21% O2) or hypoxia (1% O2). T cell concentration in the initial and following stimulations was 1 million cells/mL and 0.5 million/mL, respectively.

extract_protocol:
NucleoSpin RNA kit (Macherey-Nagel Cat. No.740955.250), with Dnase treatment. Total RNA was eluted in RNase-free water
Sequencing libraries were prepared following the protocol "TruSeq Stranded mRNA Sample Preparation Guide (Part#15031047 Rev.E)" with the “TruSeq® Stranded mRNA Library Prep” kit  (Illumina Inc. Cat. # 20020594) and TruSeq RNA CD Index Plate (96 Indexes, 96 Samples) (Illumina Inc. Cat. # 20019792)

treatment_protocol: CD8+ T cells were stimulated once or four times. From the third stimulacion a reduction to 66% glucose was performed and T cell were subjected to either normoxia or hypoxia

value: CD8+ T cells


title: CDK7 Q901 24h rep2

description: Library name: CDK7-QS1409-24h-rep2

value: CDK7 (Bethyl, A300-405A)


title: Y665H_male_rep4

description: Library name: Sample 12


title: CD8 T cells, 4 stimulations hypoxia,  rep 3

description:
D1994H
In the processed data file, there are these columns: Geneid (ENSEMBLE ID), Chr (Chromosome where gene is anotated), Start (position of the chromosome where the gene starts), End position of the chromosome where the gene ends), Strand (DNA strand that codifies for the gene, + or -), Length (length of the gene in base pairs), the following columns are the names for each studied sample


title: CDK7 Q901 4h rep2

description: Library name: CDK7-QS1409-4h-rep2


title: CDK7 DMSO 24h rep2

description: Library name: CDK7-DMSO-24h-rep2


title: MYC Q901 24h rep1

description: Library name: MYC-Q901-24h-rep1


title: CDK7 DMSO 4h rep2

description: Library name: CDK7-DMSO-4h-rep2

value: DMSO 4h


title: Y665H_male_rep3

description: Library name: Sample 11


title: CD8 T cells, 4 stimulations hypoxia,  rep 2

description:
D1954H
In the processed data file, there are these columns: Geneid (ENSEMBLE ID), Chr (Chromosome where gene is anotated), Start (position of the chromosome where the gene starts), End position of the chromosome where the gene ends), Strand (DNA strand that codifies for the gene, + or -), Length (length of the gene in base pairs), the following columns are the names for each studied sample

value: PBMC


title: Ser2P Q901 24h rep2

description: Library name: Ser2P-QS1409-24h-rep2

value: phospho-Rpb1 CTD Ser2 (Abcam, ab5095)


title: Ser2P DMSO 24h rep2

description: Library name: Ser2P-DMSO-24h-rep2


title: Y665H_male_rep2

description: Library name: Sample 10


title: CD8 T cells, 4 stimulations hypoxia,  rep 1

description:
D1784H
In the processed data file, there are these columns: Geneid (ENSEMBLE ID), Chr (Chromosome where gene is anotated), Start (position of the chromosome where the gene starts), End position of the chromosome where the gene ends), Strand (DNA strand that codifies for the gene, + or -), Length (length of the gene in base pairs), the following columns are the names for each studied sample


title: Ser2P Q901 4h rep2

description: Library name: Ser2P-QS1409-4h-rep2


title: Cord blood donor 1 24HR

description:
Library name: CB1_24HR
CB1_24HR

value: naive CD4+ T cells


title: Ser5P Q901 24h rep2

description: Library name: Ser5P-QS1409-24h-rep2

value: phospho-Rpb1 CTD Ser5 (Abcam, ab5408)


title: CD8 T cells, 4 stimulations normoxia,  rep 3

description:
D1994N
In the processed data file, there are these columns: Geneid (ENSEMBLE ID), Chr (Chromosome where gene is anotated), Start (position of the chromosome where the gene starts), End position of the chromosome where the gene ends), Strand (DNA strand that codifies for the gene, + or -), Length (length of the gene in base pairs), the following columns are the names for each studied sample


title: Y665F_male_rep4

description: Library name: Sample 8

value: male


title: Ser5P DMSO 24h rep2

description: Library name: Ser5P-DMSO-24h-rep2


title: Ser5P Q901 4h rep2

description: Library name: Ser5P-QS1409-4h-rep2


title: CD8 T cells, 4 stimulations normoxia,  rep 2

description:
D1954N
In the processed data file, there are these columns: Geneid (ENSEMBLE ID), Chr (Chromosome where gene is anotated), Start (position of the chromosome where the gene starts), End position of the chromosome where the gene ends), Strand (DNA strand that codifies for the gene, + or -), Length (length of the gene in base pairs), the following columns are the names for each studied sample


title: Y665F_male_rep3

description: Library name: Sample 7


title: Ser5P DMSO 4h rep2

description: Library name: Ser5P-DMSO-4h-rep2


title: Ser2P DMSO 4h rep2

description: Library name: Ser2P-DMSO-4h-rep2


title: Y665F_male_rep2

description: Library name: Sample 6


title: pan pol II Q901 24h rep2

description: Library name: pan-pol-II-QS1409-24h-rep2

value: pan Rpb1 CTD (Cell Signaling Technology, 2629)


title: Y665H_male_rep1

description: Library name: Sample 9