title: WI38_OSIS_3

description:
Library name: Sample 181
Cells were treated with 0.75 mM H2O2 for 2 hours and cultured for 8 days - replicate 3

value: Lung fibroblasts

value: WT


title: WDR343_4

status: Public on Jun 15 2026

type: SRA

city: Freiburg im Breisgau

first: Sebastian

last: Arnold

address: Albertstraße 25

department: Institute of Experimental and Clinical Pharmacology and Toxicology

country: Germany

institute: University Freiburg

library_source: transcriptomic

data_processing:
Untrimmed fastq rawdata files were mapped to the genome using Rsubread v1.28.1 package in R v3.4.4.
Gene counting was performed applying Rsubread::featureCount function with the iGenomes reference genome gtf file for annotation
(archive-2015-07-17-32-40 and archive-2015-07-17-33-26 for GRCm38).
For differential expression analysis, DESeq2 v1.18.1 was used. First, the counts were normalized by library size (DESeq2::estimateSizeFactors) and by gene-wise dispersion (gene-wise geometric mean over the samples; DESeq2::estimateDispersions), then, the differential expression analysis was performed applying negative vinomial generalized linear model fitting and Wald statistics on the normalized count data (DESeq2::DESeq2).
Subsequently, the results were filtered for adjusted p < 0.05 and the log2FC values, as indicated in the figures.
Assembly: GRCm38/mm10 (iGenomes, Illumina;chromosomes 1-19, X, Y, M; archive-2015-07-17-32-40 and archive-2015-07-17-33-26 for GRCM38)
Supplementary files format and content: TSV, containing count matrices of samples with gene name

molecule: total RNA

organism: Mus musculus

source_name: kidney

growth_protocol: IMCD3 standard DMEM medium with 10% FBS

extract_protocol: RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3ug of total RNA was used for the construction of sequencing libraries.RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: CRISPR base editing

tag: tissue

value: kidney

tag: cell line

tag: cell type

value: immortilised

tag: genotype

value: homoz mutant

tag: treatment

value: CRISPR

tag: cell subtype

value: ciliated cells


title: IgG mEPC control  sample 1 (Cut & Run)

city: Kansas City

first: Soumen

last: Paul

state: KS

address: Hemenway Building 3901 Rainbow Boulevard

department: Department of Pathology & Laboratory Medicine

country: USA

institute: University of Kansas Medical Center

description: Library name: mEPC_IgG_1

library_source: genomic

data_processing:
nf-core chipseq pipeline
Assembly: hg38(human), mm10(mouse)
Supplementary files format and content: peaks file in bed format
Supplementary files format and content: Coverage in bigwig file
Library strategy: CUT&Run

molecule: genomic DNA

source_name: Ectoplacental cone

growth_protocol: Cell culture protocol was published earlier (Okae H, Toh H, Sato T, Hiura H, Takahashi S, Shirane K, Kabayama Y, Suyama M, Sasaki H, Arima T. Derivation of Human Trophoblast Stem Cells. Cell Stem Cell. 2018 Jan 4;22(1):50-63.e6. doi: 10.1016/j.stem.2017.11.004. Epub 2017 Dec 14. PMID: 29249463)

extract_protocol:
Cut&Run experiments was performed according to the published protocol (1, 2). hTSC were cultured in the stem condition following published protocol (3). When cells reached about 70% confluency, cells were washed with room temperature PBS and trypsinized to get single cell suspension. 1000,000 hTSC cells were used per condition. Briefly 100,000 hTSC cells were washed, and CUT & RUN assay was performed using CUT & RUN Assay kit from Cell Signaling technology (#86652). For our experiment primary antibodies against PRMT1 (Cell signaling technology #2449), H4R3Me2a (Active motif #39705)and RNA-Polymerase II (Rbp1 CTD, Cell Signaling Technology #2629S) or IgG (Cell Signaling Technology #66362S). Finally, DNA fragments were purified and used directly for library preparation using the Illumina TruSeq ChIP. (1. Skene PJ, Henikoff JG, Henikoff S. Targeted in situ genome-wide profiling with high efficiency for low cell numbers. Nat Protoc. 2018 May;13 (5):1006-1019. doi: 10.1038/nprot.2018.015. Epub 2018 Apr 12. PMID: 29651053. 2. Meers MP, Bryson TD, Henikoff JG, Henikoff S. Improved CUT&RUN chromatin profiling tools. Elife. 2019 Jun 24;8:e46314. doi: 10.7554/eLife.46314. PMID: 31232687; PMCID: PMC6598765. 3. Okae H, Toh H, Sato T, Hiura H, Takahashi S, Shirane K, Kabayama Y, Suyama M, Sasaki H, Arima T. Derivation of Human Trophoblast Stem Cells. Cell Stem Cell. 2018 Jan 4;22 (1):50-63.e6. doi: 10.1016/j.stem.2017.11.004. Epub 2017 Dec 14. PMID: 29249463.)
For library preparation TruSeq RNA Library Prep Kit v2 was used. Finally, deep sequencing was performed using the Illumine NovaSeq 6000 sequencing system at the University of Kansas Genome Sequencing Facility to generate pair-end reads with read length 101 bp.

treatment_protocol: No

value: Ectoplacental cone

value: Primary trophoblast progenitors

value: mouse EPC


title: WTRv_w_o_SO4_1.fastq

city: seattle

first: Ashutosh

middle: P

last: Tripathi

state: Washington

address: 1900 9th Ave

department: Center for Global Infectious Disease Research

institute: Seattle Children's Research Institute

description: Library name: WTRv_w_o_SO4_1.fastq

data_processing:
Read alignment was performed using the Bowtie 2 custom processing pipeline (https://github.com/robertdouglasmorrison/DuffyNGS, https://github.com/robertdouglasmorrison/DuffyTools), as previously described (PMID: 25784701)
The pipeline consists of 2 stages: 1) a pre-alignment filtering step to remove unwanted transcripts such as rRNA, and 2) a genomic alignment step using Bowtie2 with the command line option 'very-sensitive.'
BAM files from step 2 are combined into read depth wiggle tracks that record both uniquely mapped and multiply mapped reads from each of the forward and reverse strangs of the genome. Multiply mapped reads are prorated over all highest-quality aligned locations. Transcript abundance is quantified by summing total reads landing inside annotated gene boundaries, expressed by RPKM.
Assembly: MT_H37Rv_V3
Supplementary files format and content: Transcript abundance is quantified by summing total reads landing inside annotated gene boundaries, expressed by RPKM.

organism: Mycobacterium tuberculosis

source_name: M. tuberculosis culture

growth_protocol: Wild-type (WT) Mycobacterium tuberculosis H37Rv was cultured in Middlebrook 7H9 medium supplemented with 10% OADC, 0.5% glycerol, 0.05% tyloxapol, and 100 µM sodium propionate until an OD₆₀₀ of 0.8 was reached. Cells were then harvested by centrifugation, washed three times with phosphate-buffered saline (PBS), and resuspended in sulfate-free HdB medium. Cultures were incubated for an additional 48 h in the presence or absence of 100 µM sodium sulfate

extract_protocol:
The bacteria were harvested at the indicated timepoint and resuspended in Trizol, and lysed by bead beating for 30 seconds at 6 m/s for 3 cycles, with intermittent cooling on ice. Cell debris was pelleted at 20,000 g for 1 minute, and the supernatant was transferred to a heavy phase-lock gel tube containing 300 μL of chloroform. The tubes were inverted for 2 minutes and centrifuged at 20,000 g for 5 minutes. RNA in the aqueous phase was precipitated with 300 μL of isopropanol and 300 μL of high-salt solution (0.8 M sodium citrate, 1.2 M sodium chloride). RNA was purified using the QIAGEN RNeasy kit, and ribosomal RNA was depleted using a previously published protocol [Culviner, P. H. et al doi:10.1128/mBio.00010-20 (2020)]. Briefly, a biotinylated oligo mixture of 23S, 16S, and 5S was incubated with RNA to anneal to rRNA, followed by incubation with streptavidin beads. mRNA was purified from the supernatant using Ampure XP beads.
The cDNA library was generated using the NEBNext Ultra II RNA Library Prep Kit and each replicate was barcoded in the DNA library using the NEBNext Multiplex Oligos for Illumina. Libraries were quantified using the KAPA qPCR quantification kit, pooled, and the WT H37RV with and without 100 µM SO4 samples were sequenced at the University of Washington Northwest Genomics Center with the Illumina NextSeq 500 High Output v2 Kit while the WT H37RV and pe22/ppe36 KO in sulphate deplete and 10 mM replete condition samples were sequenced at Fred Hutch with Illumina NovoSeqX+.

treatment_protocol: With and without 100 µM SO4 in HdB media. In SO4 repletion experiment with and without 10 mM SO4 after 48 h of starvation in sulphate free modified Sauton's media.

tag: strain

value: M. tuberculosis culture

value: Starved for SO4 in modified Sauton's for 72 h


title: WI38_OSIS_2

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description:
Library name: Sample 180
Cells were treated with 0.75 mM H2O2 for 2 hours and cultured for 8 days - replicate 2

data_processing:
BCL files were de-multiplexed and converted to FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed BBDuk from BBTools (v38.76)
Trimmed FASTQ files were aligned to human reference genome hg38 (Ensembl v104) using STAR software (v2.7.0f_0328).
featureCounts in R package Subread (v2.10.5) was used to generate gene counts
Assembly: hg38 (Ensembl v104)
Supplementary files format and content: text files containing counts

organism: Homo sapiens

extract_protocol:
Total RNA was extracted using TriPure™ Isolation Reagent (Sigma-Aldrich), following the manufacturer's instructions with phenol-chloroform extraction.
Libraries were constructed using theTruSeq Stranded Total RNA Library prep kit according to manufacturer’s protocol (Illumina).

value: Oxidative stress-induced senescence (8 days 0.75 mM H2O2)


title: H.vulgare, Chromatin_Bound(CB) RNA-seq, Morex, replicate2

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

country: China

institute: Fudan University

description: Library name: CB_RNA-seq_barley_Morex_rep2

library_source: other

data_processing:
CB RNA-seq data were cleaned using fastp (version 0.20.1).
SortMeRNA (version 2.1b) was used to remove reads originating from chloroplasts, mitochondria and rRNA.
The remaining clean reads were mapped to the corresponding genome sequences using hisat2 (v2.1.0)
Reads with a mapping quality score < 20 or mapping to multiple positions were eliminated using SAMtools (v1.16.1).
For each species, all CB RNA samples were subsampled to match the read count of each sample with the lowest number of reads. The subsampled data were then merged in each species for further analysis. Peak calling were conducted using MACS2 as described for ChIP-seq data processing.
Assembly: Triticum urartu (AA, IGDB version 1.0), Aegilops tauschii (DD, Aet_v4.0), Triticum aestivum (AABBDD, IWGSC version 1.0), Hordeum vulgare (HH, IBSC_v2), Secale cereale (Weining.v1.0) , Zea mays (B73_RefGen_v4) and Oryza sativa (MSU7.0)
Supplementary files format and content: bw files

molecule: other

organism: Hordeum vulgare

source_name: 9-day-old seedling

growth_protocol: Seedlings (above-ground) of common wheat (Triticum aestivum cultivars ‘Chinesespring’‘AK58’ and ‘Fielder’), barley (Hordeum vulgare cultivar ‘Morex’), rye (Secale cereale cultivar ‘Weining’), maize (Zea mays cultivar ‘B73’) and rice (Oryza sativa cultivars ‘ZH11’ and ‘Jap’) were harvested after 9-day growth. The roots, leaf and embryos of three wheat species (Triticum aestivum cultivar ‘Chinese Spring’, Triticum urartu cultivar ‘G1812’ and Aegilops tauschii cultivar ‘AL8-78’) were collected as follows: roots in the Hoagland solution were harvested after 9-day growth; the fresh immature embryos were isolated 14 days post anthesis; leaf were were harvested after 9-day growth.

extract_protocol:
Nuclei were isolated from 1 mL tissue powder solubilized in 20 mL ice-cold Honda buffer (0.44 M sucrose, 1.25% Ficoll, 2.5% Dextron T40, 20 mM HEPES, pH7.4, 10 mM MgCl2, 0.75% Triton X-100, 0.5 mM EDTA, 1 mM DTT, 8 mM β-mercaptoethanol, 2 µg/mL pepstatin A, 2 µg/mL aprotinin, 2 mM PMSF). The mixture was incubated on ice for 5 min, then filtered through 110 µm nylon mesh and a 40 µm cell strainer. The crude nuclei were spun down at 3,500 g for 5 min at 4°C, followed by washes with 150 µL of resuspension buffer (50% Glycerol, 0.5 mM EDTA, 25 mM Tris-HCl, pH 7.5, 100 mM NaCl, 1 mM DTT, 8 mM β-mercaptoethanol, 2 µg/mL pepstatin A, 2 µg/mL aprotinin, 2 mM PMSF, 0.4 U/µL RNase inhibitor) and 300 µL of wash buffer (25 mM Tris-HCl, pH 7.5, 300 mM NaCl, 1 M urea, 0.5 mM EDTA, 1% Tween 20, 1 mM DTT, 8 mM β-mercaptoethanol, 2 µg/mL pepstatin A, 2 µg/mL aprotinin, 2 mM PMSF, 0.4 U/µL RNase inhibitor). Again, the obtained nuclei were washed with another 150 µL of resuspension buffer and 150 µL of wash buffer. CB RNA was extracted from washed nuclei using TRIzol reagent and subjected to genomic DNA removal by TURBOTM DNase (Life Technologies). After purification with RNA Clean & ConcentratorTM-5 kit (Zymo Research, R1013), ~1 µg CB RNA was subjected to rRNA depletion by a riboPOOL kit (siTOOLs Biotech, PanPlant-10 nmol) and polyA RNA removal by oligo (dT) beads (NEB, S1419). PolyA RNA was enriched from total RNA by oligo(dT) beads. Purified CB RNA and PolyA RNA were transformed into cDNA libraries using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7765) and sequenced on an Illumina NovaSeq platform.
Chromatin-bound(CB) RNA-seq

value: 9-day-old seedling


title: WDR343_3


title: PRMT1 sample in mEPC sample 2 (Cut & Run)

description: Library name: mEPC_PRMT1_2


title: Gpihbp1-/-,NO4

city: Dalian

first: rui

last: fan

address: No. 193, Lianhe Road, Dalian City

institute: Dalian Medical University

description: Library name: Sample8

data_processing:
Raw sequencing reads were generated on the BGISEQ platform (PE150). Raw reads containing adaptor contamination, excessive N bases, and low-quality sequences were removed to obtain clean reads.
Clean reads were aligned to the Mus musculus reference genome (GRCm39, GCF_000001635.27) using HISAT. Clean reads were also aligned to the reference gene set using Bowtie2.
Gene expression levels were quantified and normalized as FPKM (Fragments Per Kilobase of transcript per Million mapped reads). Differentially expressed genes between WT and KO groups were identified for downstream analyses.
Assembly: GRCm39 (GCF_000001635.27)
Supplementary files format and content: Processed data files: Gene expression matrix (FPKM values) and differential expression results.

source_name: heart

extract_protocol:
Total RNA was extracted from cardiac tissue using TRIzol reagent (15596026CN, Thermo Fisher Scientific, USA), and RNA integrity was assessed using the Agilent 2100 Bioanalyzer system (Agilent Technologies, USA). Strand-specific RNA libraries were prepared according to the standard protocol for the DNBSEQ-T7 platform (BGI Genomics, Shenzhen, China).
Total RNA was isolated from rat cardiac tissues using TRIzol reagent according to the manufacturer's instructions. RNA integrity was assessed before library preparation. Poly(A)+ mRNA was enriched using oligo(dT)-attached magnetic beads and fragmented into short fragments. First-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis with dUTP replacing dTTP. After end repair, A-tailing, and adapter ligation, the uracil-containing second strand was digested with UDG to retain strand specificity. The resulting libraries were PCR amplified, quality controlled, circularized, and converted into DNA nanoballs (DNBs) through rolling circle amplification. Sequencing was performed on the DNBSEQ platform using paired-end reads.

treatment_protocol: Only male mice were included in the study. All mice were housed in individually ventilated cages with a 12-hour light/dark cycle and ad libitum access to food and sterilized water. standard rodent chow diet was used in the study

value: heart


title: WI38_OSIS_1

description:
Library name: Sample 179
Cells were treated with 0.75 mM H2O2 for 2 hours and cultured for 8 days - replicate 1


title: WDR343_2


title: PRMT1 sample in mEPC sample 1 (Cut & Run)

description: Library name: mEPC_PRMT1_1


title: Gpihbp1-/-,NO3

description: Library name: Sample7


title: WDR343_1


title: H4R3 sample in mEPC  sample 2 (Cut & Run)

description: Library name: mEPC_H4R3Me2a_2


title: WI38_IRIS_4

description:
Library name: Sample 178
Cells were treated with 15 Gy IR and cultured for 8 days - replicate 4

value: Ionizing radiation-induced senescence (8 days 15 Gy)


title: WI38_IRIS_3

description:
Library name: Sample 177
Cells were treated with 15 Gy IR and cultured for 8 days - replicate 3


title: WDR341_4


title: H4R3 sample in mEPC  sample 1 (Cut & Run)

description: Library name: mEPC_H4R3Me2a_1


title: DOX4X bio rep 3 female

city: Toronto

first: Soheil

last: Jahangiri

state: Ontario

address: 610 University Ave

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

description: Library name: S2_D1

data_processing:
Short-read quality control and trimming were performed using FastQC v0.11.5, MultiQC v1.7, and TrimGalore v0.6.6, respectively. Reads were aligned to GENCODE mouse genome vM27 using STAR v.2.7.9a, and low-quality alignments (mapq score < 15) were filtered with samtools v1.17. Next, featureCounts v2.0.1 was used to quantify the gene expression from BAM files.
Assembly: GRCm39
Supplementary files format and content: gene count matrix

molecule: polyA RNA

source_name: bone

extract_protocol:
Bone marrow were flushed with centrifugation. The remaining bone tissue were cutted into bone chips and enzymetically digested at 37°C for 25 min. Osteoblasts were sorted based on GFP expression into Buffer RLT Plus with 1% beta-mercaptoethanol.
Total RNA was extracted with RNeasy Plus Micro Kit (QIAGEN, Cat. # 74034). The cDNA libraries were prepared using SMART-Seq v4 Plus Kit (Takara, Cat. # R400752) following manufacturer’s protocol.

treatment_protocol: Young adult (8-10 week-old) mice were treated with 4 doses of doxorubucin (5 mg/kg, intravenous) or PBS, one week interval between each injection. Animals were euthanized at 8w post treatment.

value: bone

value: osteoblast

value: 4X doxorubicin IV 5 mg/kg

tag: batch


title: Gpihbp1-/-,NO2

description: Library name: Sample6


title: Gpihbp1-/-,NO1

description: Library name: Sample5


title: WI38_IRIS_2

description:
Library name: Sample 176
Cells were treated with 15 Gy IR and cultured for 8 days - replicate 2

value: Lung fibroblasts

value: WT


title: WI38_OIS_3

description:
Library name: Sample 189
Cells were transduced with a RasV12 lentivirus (MOI: 3) and cultured for 8 days - replicate 3

value: RasV12 (MOI:3)


title: WDR341_3

value: kidney

value: immortilised

value: homoz mutant

value: CRISPR


title: AAC5_12_M12_doxo_ABT

description:
Library name: Sample 9
Lung cells pooled from two Doxorucicin and ABT treated mice - replicate 3

library_source: transcriptomic single cell

data_processing:
Pre-processing of sequencing results and generation of count matrices was performed using the Cell Ranger version 6.1.1 (10x Genomics) with prebuilt annotation platform mm10-2020-A.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix including barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files

source_name: Lung

extract_protocol:
Before tissue extraction, lungs were perfused by injecting 1 ml PBS through the right ventricle. The extracted pieces were dissociated together in 2 ml of RPMI media with 0.2 mg/ml Liberase TL and 0.1 mg/ml elastase. The mixture was processed using the Gentlemacs Octodissociator (Miltenyi) at 37°C (20 min, 50 rpm; 30 s, 2,000 rpm clockwise and counterclockwise). Cells were passed through a MACS SmartStrainer (70 µm), centrifuged, and resuspended in RPMI + 20% FBS. After dissociation, cells were incubated with 5 μL of mouse TruStain FcX Fc blocking reagent for 5 min, followed by a 15-min incubation with anti-mouse Ter119-Pacific Blue at 25°C. Cells were washed and resuspended in DMEM with 15% FBS, 2 μg/ml propidium iodide, and 5 mM EDTA. FACS sorting was performed using FACS Aria FUSION (BD Biosciences) to sort 25,000 cells.
The single-cell libraries were prepared with Chromium Next GEM Single Cell 3' Kit v3 (10x Genomics) with Chromium Next GEM Chip G Single Cell Kit (10x Genomics) according to manufacturer’s protocol with Chromium Controller (10x Genomics).

tag: age

value: 3 months old

tag: Sex

value: male

value: Lung

value: Lung cells

value: Doxo + ABT


title: WI38_IRIS_1

description:
Library name: Sample 175
Cells were treated with 15 Gy IR and cultured for 8 days - replicate 1


title: WDR341_2

value: ciliated cells


title: AAC5_11_M11_doxo_ABT

description:
Library name: Sample 8
Lung cells pooled from two Doxorucicin and ABT treated mice - replicate 2


title: wildtype,NO5

description: Library name: Sample3

value: heart


title: wildtype,NO6

description: Library name: Sample4


title: WI38_ETIS_4

description:
Library name: Sample 174
Cells were cultured for 8 days in 50 µM etoposide-containing media - replicate 4

value: Etoposide-induced senescence (8 days 50 µM)


title: WDR341_1


title: wildtype,NO4

description: Library name: Sample2


title: AAC5_10_M10_doxo_ABT

description:
Library name: Sample 7
Lung cells pooled from two Doxorucicin and ABT treated mice - replicate 1


title: WI38_ETIS_3

description:
Library name: Sample 173
Cells were cultured for 8 days in 50 µM etoposide-containing media - replicate 3


title: BE_Co3_R4

value: control

value: nonciliated cells


title: AAC5_6_M6_doxo

description:
Library name: Sample 6
Lung cells pooled from two Doxorubicin treated mice - replicate 3

value: Doxo


title: wildtype,NO2

description: Library name: Sample1

value: WT


title: BE_Co3_R3


title: WI38_ETIS_2

description:
Library name: Sample 172
Cells were cultured for 8 days in 50 µM etoposide-containing media - replicate 2

value: Lung fibroblasts


title: AAC5_5_M5_doxo

description:
Library name: Sample 5
Lung cells pooled from two Doxorubicin treated mice - replicate 2


title: WI38_ETIS_1

description:
Library name: Sample 171
Cells were cultured for 8 days in 50 µM etoposide-containing media - replicate 1


title: ileum, A358, OEA

city: Hong Kong

first: Shujun

last: Xu

address: 7 Baptist University Road

department: Chinese Medicine

country: Hong Kong

institute: Hong Kong Baptist University

description: Library name: A358

data_processing:
Raw sequencing data were processed to filter cells based on gene count, mitochondrial gene proportion, and other quality control metrics. Doublets were identified and removed using DoubletFinder to ensure data reliability and accuracy.
Low-quality cells and doublets were removed using Seurat
Cell type annotation was based on marker gene expression
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files (gene expression matrix), cell annotation files, and clustering result files

source_name: ileum

extract_protocol:
After 19 days of OEA treatment, fresh ileum samples from control, TNBS-treated, and OEA-treated mice were collected, preserved in MACS® Tissue Storage Solution, and analyzed by single-cell RNA sequencing
Ileum samples were collected from mice in control, TNBS-treated, and OEA-treated groups (n=4 per group). Immediately after dissection, tissues were preserved in MACS® Tissue Storage Solution at 4°C. Single-cell suspensions were prepared from each sample following enzymatic digestion and filtration. Cell viability and concentration were assessed prior to library construction. Single-cell encapsulation, mRNA capture, and barcoding were performed using the DNBelab C4 microfluidic platform according to the manufacturer's protocol. Reverse transcription and cDNA amplification were completed in droplets. Sequencing libraries were constructed and subjected to high-throughput sequencing on a DNBSEQ platform.

value: ileum

value: OEA 50 mg/kg


title: AAC5_4_M4_doxo

description:
Library name: Sample 4
Lung cells pooled from two Doxorubicin treated mice - replicate 1


title: BE_Co3_R2

value: kidney

value: immortilised


title: WI38_P_4

description:
Library name: Sample 170
Cells were cultured for 8 days in DMSO-containing media - replicate 4

value: Control proliferating cells


title: Patient10 12weeks treatment

status: Public on Jun 16 2026

type: protein

city: Shimamoto-cho, Mishima-gun

first: Keiichi

last: Minami

state: OSAKA

address: 3-1-1 Sakurai

department: Minase Research Institute

country: Japan

institute: Ono Pharmaceutical

hyb_protocol: In this study, SOMAscan was used, and the measurements were outsourced. (SomaLogic Operating Co., Inc.)

label: SOMAmer

molecule: protein

source_name: non-CIPN

growth_protocol: Patient-derived samples were used in this study.

value: Plasma


title: ileum, A361, OEA

description: Library name: A361


title: BE_Co3_R1

value: CRISPR


title: AAC5_3_M3_DMSO

description:
Library name: Sample 3
Lung cells pooled from two DMSO treated mice - replicate 3

value: 3 months old

value: male

value: Lung

value: Lung cells

value: DMSO


title: ileum, A98, OEA

description: Library name: A98


title: WI38_P_3

description:
Library name: Sample 169
Cells were cultured for 8 days in DMSO-containing media - replicate 3


title: BE_Co2_R4

value: control


title: AAC5_2_M2_DMSO

description:
Library name: Sample 2
Lung cells pooled from two DMSO treated mice - replicate 2


title: ileum, A353, OEA

description: Library name: A353


title: BE_Co2_R3

value: nonciliated cells


title: WI38_P_2

description:
Library name: Sample 168
Cells were cultured for 8 days in DMSO-containing media - replicate 2


title: AAC5_1_M1_DMSO

description:
Library name: Sample 1
Lung cells pooled from two DMSO treated mice - replicate 1


title: WI38_P_1

description:
Library name: Sample 167
Cells were cultured for 8 days in DMSO-containing media - replicate 1


title: ileum, A366, Model

description: Library name: A366

value: PBS


title: BE_Co2_R2


title: ileum, A355, Model

description: Library name: A355


title: LND

city: Hangzhou

first: Yicheng

last: Xie

address: 3333 Binsheng Rd

institute: Children’s Hospital Zhejiang University School of Medicine

description:
Library name: LND
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: barcodes.tsv; genes.tsv; matrix.mtx.

source_name: nasal mucosal

extract_protocol:
All mice from Control group, ECRS  and LND  group were sampled and mixed for detection.  The nasal mucosal from a consistent area of the mice was rapidly removed, positioned in a container with cold PBS, and cut into small fragments.  These pieces were then washed thrice before being immersed in a digestive mixture containing collagenase I, collagenase II, and Dispase® (all from Sigma, USA).  After digestion, the cell suspension was strained through a 70 µm sieve (Miltenyi, GER).  Subsequently, the pellet was washed and resuspended proportionate to its volume.  Single cells were then isolated using the 10x Genomics Chromium Single Cell 3′ Solution (10x Genomics, USA).  Single-cell RNA-seq data were analyzed using R (v4.2.3, MathSoft, USA) with the Seurat package (v4.3.0).
scRNA-seq, RNA: 3' transcriptome sequencing, cDNA fragmentation, end filling, adding A, connection connector, Index PCR.

value: nasal mucosal

value: papain and LND


title: prAD_IRIS_4

description:
Library name: Sample 166
Cells were treated with 15 Gy IR and cultured for 8 days - replicate 4

source_name: prAD

value: prAD

value: PreAdipocytes

value: WT

value: Ionizing radiation-induced senescence (8 days 15 Gy)


title: BE_Co2_R1

value: kidney

value: immortilised


title: Model

description:
Library name: Fibroblast
10x Genomics

value: papain


title: ileum, A325, Model

description: Library name: A325

value: ileum


title: Control

description:
Library name: Control
10x Genomics


title: BE_Co1_R4

value: CRISPR


title: ileum, A339, Model

description: Library name: A339


title: prAD_IRIS_3

description:
Library name: Sample 165
Cells were treated with 15 Gy IR and cultured for 8 days - replicate 3


title: prAD_IRIS_2

description:
Library name: Sample 164
Cells were treated with 15 Gy IR and cultured for 8 days - replicate 2


title: BE_Co1_R3


title: WT4-Ovary, Day 8

city: Chapel Hill

first: Silvia

middle: B

last: Ramos

state: NC

address: 133 Medical Drive

department: Biochemistry and Biophysics

institute: UNC-Chapel Hill

description: Library name: WT4-ZC256

data_processing:
Reads were aligned to mm10 reference genome using STAR aligner standard workflow
Subreads R package used to produce raw count files from the outputs of STAR
Differential Expression analysis conducted with DESeq2 R package standard workflow
Assembly: mm10
Supplementary files format and content: Tab-deliminated .txt file containing raw counts for each sample

source_name: Ovary

extract_protocol:
RNA Quigen Mini Kit,  All 40 samples had passed the QC with a RIN>6 and DV200>70. The average RIN value of our 46 samples was 9.2 and standard deviation of 1.02
RNA libraries were prepared using NEBNext Ultra II RNA Library Prep Kit following manufacturer's protocols
RNA-seq, the RNA/DNAse treated samples were used to prepare a library using a PolyA selection

value: Ovary

value: mixture of primary cells


title: ileum, A364, CTR

description: Library name: A364


title: BE_Co1_R2


title: prAD_IRIS_1

description:
Library name: Sample 163
Cells were treated with 15 Gy IR and cultured for 8 days - replicate 1


title: WT3-Ovary, Day 8

description: Library name: WT3-ZC210


title: ileum, A362, CTR

description: Library name: A362


title: prAD_ETIS_4

description:
Library name: Sample 162
Cells were cultured for 8 days in 25 µM etoposide-containing media - replicate 4

value: Etoposide-induced senescence (8 days 25 µM)


title: BE_Co1_R1

value: control


title: WT1-Ovary, Day 9

description: Library name: WT1-ZC150


title: ileum, A351, CTR

description: Library name: A351


title: prAD_ETIS_3

description:
Library name: Sample 161
Cells were cultured for 8 days in 25 µM etoposide-containing media - replicate 3


title: AB_Co_R4

value: nonciliated cells


title: prAD_ETIS_2

description:
Library name: Sample 160
Cells were cultured for 8 days in 25 µM etoposide-containing media - replicate 2


title: KO4-Ovary, Day 8

description: Library name: KO4-ZC257

value: KO


title: dbm5, IP

city: Zhengzhou

first: Mingyang

last: Hu

state: Henan

address: jinshui

institute: Department of Nephrology, First Affiliated Hospital of Zhengzhou University

description: Library name: dbm5, IP

data_processing:
Raw reads were filtered to remove adapter sequences and low-quality reads. Clean reads were aligned to the mouse reference genome (GRCm38). Gene expression levels were quantified, and differentially expressed genes between db/m and db/db mice were identified
Assembly: GRCm38
Supplementary files format and content: xls files include all identified ac4C peaks and their annotations

source_name: KIDNEY

extract_protocol:
Total RNA was extracted from mouse kidney tissues using TRIzol reagent according to the manufacturer’s instructions. RNA quality and integrity were assessed prior to library preparation.
RNA-seq libraries were prepared from total RNA according to the manufacturer’s standard protocol and sequenced on the DNBSEQ-T7 platform using paired-end 150 bp reads.

value: KIDNEY


title: AB_Co_R3


title: dbm4, IP

description: Library name: dbm4, IP


title: KO2-Ovary, Day 6

description: Library name: KO2-ZC205


title: prAD_ETIS_1

description:
Library name: Sample 159
Cells were cultured for 8 days in 25 µM etoposide-containing media - replicate 1


title: KO1-Ovary, Day 9

description: Library name: KO1-ZC151


title: AB_Co_R2


title: dbm3, IP

description: Library name: dbm3, IP


title: prAD_P_4

description:
Library name: Sample 158
Cells were cultured for 8 days in DMSO-containing media - replicate 4

value: Control proliferating cells


title: AB_Co_R1


title: E12.5 mouse placenta

description: embryonic day 12.5

data_processing:
The data was analyzed using the 10x Genomics Chromium Single Cell software suite (cellranger-3.0.2).
The demultiplexing and conversion of Illumina base call files (BCL) to raw FASTQ files was done using "cellranger mkfastq" with default parameters.
The sequencing reads were aligned to the mouse reference mm10 and analyzed using "cellranger count".
Downstream analysis using Seurat
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: placenta

growth_protocol: Time pregnant CD1 female mice were euthanized on gestational day 7.0 -12.5  after conception and placentas were isolated and processed for single cell preparation followed by single-cell RNA sequencing.

extract_protocol:
Placenta from  embryos were isolated and pooled. They were then made into a single cell suspension as per the protocol mentioned in the publication "Trophoblast paracrine signaling regulates placental hematoendothelial niche", Home et al.(bioRxiv preprint first posted online Nov. 13, 2019)
The RT reaction to generate 10X barcoded single stranded cDNA, in the single cell containing GEMs, is performed using an Eppendorf MasterCycler Pro thermal cycler. Post GEM-RT Cleanup is conducted by breaking the GEMS with 10X Recovery Agent to separate the aqueous phase from the Recovery Agent and Partitioning oil. A cleanup of the sscDNA containing aqueous phase is completed using Dynabeads MyOne Silane beads (Life Technologies 37002D). The second strand cDNA amplification is performed using the cDNA Amplification Mix on the Eppendorf MasterCycler Pro. The 3’ gene expression library construction is initiated with fragmentation, end repair and A-tailing of the dscDNA followed by adapter ligation and a sample index PCR using the Illumina compatible indexed adapters in the Chromium i7 Multiplex kit (10X Genomics 120262). Validation of the single cell library is conducted using the Agilent Tapestation 4200 ScreenTape assay (Agilent 5067-5576).
Single Cell RNA-seq (10X Genomics Chromium Single Cell 3' v3)

treatment_protocol: no treatment

value: placenta

value: Single cells obtained from placenta


title: prAD_P_3

description:
Library name: Sample 157
Cells were cultured for 8 days in DMSO-containing media - replicate 3

value: prAD

value: PreAdipocytes

value: WT


title: BE_W60_R4

value: kidney

value: immortilised

value: homoz mutant


title: dbm2, IP

description: Library name: dbm2, IP


title: BE_W60_R3

value: CRISPR


title: E10.5 mouse placenta

description: embryonic day 10.5


title: prAD_P_2

description:
Library name: Sample 156
Cells were cultured for 8 days in DMSO-containing media - replicate 2


title: dbm1, IP

description: Library name: dbm1, IP


title: prAD_P_1

description:
Library name: Sample 155
Cells were cultured for 8 days in DMSO-containing media - replicate 1


title: dbdb6, IP

description: Library name: dbdb6, IP


title: BE_W60_R2


title: E11.5 mouse placenta

description: embryonic day 11.5


title: E8.5 mouse placenta

description: embryonic day 8.5


title: dbdb5, IP

description: Library name: dbdb5, IP


title: PBMCs_IRIS_4

description:
Library name: Sample 154
Cells were treated with 7.5 Gy IR and cultured for 6 days - replicate 4

source_name: PBMCs

value: PBMCs

value: Peripheral blood mononuclear

value: Ionizing radiation-induced senescence (6 days 7.5 Gy)


title: BE_W60_R1


title: E7.5 mouse placenta

description: embryonic day 7.5


title: dbdb4, IP

description: Library name: dbdb4, IP


title: PBMCs_IRIS_3

description:
Library name: Sample 153
Cells were treated with 7.5 Gy IR and cultured for 6 days - replicate 3


title: BE_W34_R4


title: PBMCs_IRIS_2

description:
Library name: Sample 152
Cells were treated with 7.5 Gy IR and cultured for 6 days - replicate 2


title: CT26_cl9_M8_3

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 151-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: colon

extract_protocol:
Total RNA was extracted from cells with a FastGene RNA Basic Kit (NIPPON Genetics).
RNA libraries were prepared using a TruSeq Stranded mRNA Library Prep Kit (Illumina).

value: colon

value: MR1-overexpressing mutant


title: dbdb3, IP

description: Library name: dbdb3, IP


title: BE_W34_R3

value: nonciliated cells


title: CT26_cl9_M8_2


title: dbdb2, IP

description: Library name: dbdb2, IP

value: KIDNEY


title: CT26_cl9_M8_1


title: PBMCs_IRIS_1

description:
Library name: Sample 151
Cells were treated with 7.5 Gy IR and cultured for 6 days - replicate 1


title: BE_W34_R2


title: dbdb1, IP

description: Library name: dbdb1, IP


title: PBMCs_ETIS_4

description:
Library name: Sample 150
Cells were cultured for 6 days in 20 µM etoposide-containing media - replicate 4

value: Etoposide-induced senescence (6 days 20 µM)


title: BE_W34_R1


title: dbm5

description: Library name: dbm5


title: CT26_cl9_3


title: PBMCs_ETIS_3

description:
Library name: Sample 149
Cells were cultured for 6 days in 20 µM etoposide-containing media - replicate 3


title: PC 12 cell, Erastin + PQR NPs, C3

city: Jinzhong City, Shanxi Province

first: Chen-Long

last: Li

address: No. 98, University Street, Yuci District, Jinzhong City, Shanxi Province

institute: Shanxi Medical University

description:
Library name: Sample 9
rat-derived PC12 cells

data_processing:
Fastp (v0.23.4) is used to further filter the raw data. The standards for data filtering mainly include: filtering reads with sequencing adapters; Calculate the average quality threshold using a 4-base sliding window, and if it falls below this threshold, it will be excised, default value is Q20; Filter reads with N (uncertain bases) exceeding 5 bases; Reads smaller than the set length will be discarded or deleted, default is 15; After filtering, clean data was obtained.
The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 (v2.2.1).
Based on the alignment results of HISAT2, reconstruct the transcript using StringTie2 (v2.1.4) and calculate the expression levels of all genes in each sample.
In order to ensure comparability of gene expression levels between different genes and samples, FPKM was used to standardize expression levels.
Assembly: Rnor_6.0 (GCA_000001895.4)
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample
Supplementary files format and content: csv fles include FPKM values for each Sample

organism: Rattus norvegicus

source_name: PC 12

extract_protocol:
Total RNA was isolated and purified using the TRlzol method (lnvitrogen, CA, USA)according to the manufacturer's provided protocol.
Poly (A) RNA is purifed from lug total RNA using Dynabeads Oligo (dT) (ThermoFisher, CA, USA) using two rounds of purification, First strand cDNA was synthesized usingrandom hexamer primer and M-MuLY Reverse Transeriptase (RNase H-). Second strandcDNA synthesis was subsequently performed using DNA Polymerase l and RNase H.Remaining overhangs were converted into blunt ends via exonuelease/polymerase aetivitiesand the enzymes were removed. Afer adenylation of the 3' ends of the DNA fragments,lllumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select eDNAfragments of the preferred 300 bp in length, the library fragments were purifed using theAMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fagments with ligatedadaptor molecules on both ends were selectively enriched using lllumina PCR Primer Cocktailin a 15 cycle PCR reaction. Products were purifed (AMPure XP system) and quantified usingthe Agilent high sensitivity DNA assay on 5400 Fragment Analyzer system(AgilentTechnologies, CA, USA), The libraries were seguenced on llumina Novaseg 6000 and 150bp paired-end reads were generated.

value: PC 12

value: neuronal-like rat-derived cell line

value: Erastin+PQR NPs


title: CT26_cl9_2


title: PBMCs_ETIS_2

description:
Library name: Sample 148
Cells were cultured for 6 days in 20 µM etoposide-containing media - replicate 2


title: dbm4

description: Library name: dbm4


title: PBMCs_ETIS_1

description:
Library name: Sample 147
Cells were cultured for 6 days in 20 µM etoposide-containing media - replicate 1


title: PC 12 cell, Erastin + PQR NPs, C2

description:
Library name: Sample 8
rat-derived PC12 cells


title: CT26_cl9_1


title: PC 12 cell, Erastin + PQR NPs, C1

description:
Library name: Sample 7
rat-derived PC12 cells


title: dbm3

description: Library name: dbm3


title: dbm2

description: Library name: dbm2


title: Post-processed sheep cortical nuclei

city: Bryan

first: Manshi

last: Patel

state: Texas

address: 8447 John Sharp Pkwy

department: Neuroscience & Experimental Sciences

institute: Texas A&M University Health Science Center

description: Library name: Post-processed sheep cortical nuclei

data_processing:
DRAGEN secondary analysis
Reference Genome - Custome made through Illumina Reference Builder
Gene-barcode matrices were filtered to remove barcodes with low UMI counts and high mitochondrial read fraction prior to downstream analysis.
Assembly: Ovis aries ARS-UI_Ramb_v2.0
Supplementary files format and content: Gene-barcode matrices are provided in Matrix Market format (matrix.mtx.gz) with accompanying barcodes.tsv.gz and features.tsv.gz files
Supplementary files format and content: Processed files contain UMI counts per gene per nucleus for pre-processed and post-processed cortical nuclei samples.

molecule: nuclear RNA

organism: Ovis aries

source_name: Cerebral cortex

growth_protocol: Adult Rambouillet sheep (female, 18–36 months)

extract_protocol:
Cerebral cortex was rapidly dissected post-mortem, minced on ice, and homogenized in nuclei isolation buffer. Nuclei were filtered, counted, and processed according to the manufacturer’s recommendations for single-nucleus RNA sequencing.
Illumina T2 Kit - snRNA seq

treatment_protocol: No in vivo treatment was applied prior to tissue collection

value: Cerebral cortex

value: Mixed neural cells (neurons, oligodendrocytes, astrocytes, microglia)

value: Wildtype

value: Post-processed (no debris/RBC removal)


title: PC 12 cell, Erastin, B3

description:
Library name: Sample 6
rat-derived PC12 cells

value: WT

value: Erastin


title: PBMCs_P_4

description:
Library name: Sample 146
Cells were cultured for 6 days in DMSO-containing media - replicate 4

value: PBMCs

value: Control proliferating cells


title: PBMCs_P_3

description:
Library name: Sample 145
Cells were cultured for 6 days in DMSO-containing media - replicate 3

value: Peripheral blood mononuclear


title: Pre-processed sheep cortical nuclei

description: Library name: Pre-processed sheep cortical nuclei

value: Pre-processed (no debris/RBC removal)


title: PC 12 cell, Erastin, B2

description:
Library name: Sample 5
rat-derived PC12 cells


title: dbm1

description: Library name: dbm1


title: Mock_rep3

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

country: Belgium

institute: VIB

description:
Library name: Mock_rep3
10X Genomics 3' v4

data_processing:
Read alignment + counting; STAR (CellRanger v8.0.1)
Assembly: Solanum lycopersicum ITAG4.0
Supplementary files format and content: raw count matrix in .h5 format
Supplementary files format and content: filtered count matrix in .h5 format

organism: Solanum lycopersicum

source_name: Root

growth_protocol: At four weeks post transformation, composite plants were individually transferred to 50 ml falcons containing a sand-vermiculite mixture (1:1). The composite tomato plants were grown under greenhouse conditions (22h light, 6h dark) at 24°C until 6 weeks post inoculation (wpi). The plants were watered twice weekly with modified Hoagland solution, containing 20 µM KH2PO4 until harvest (Hoagland and Arnon, 1950).

extract_protocol:
AMF- and mock-inoculated composite tomato cv. Moneymaker plants with roots co-expressing pRolD::mCherry and pSlPT4::GFP were harvested for nuclei extraction at 6 wpi. Per repeat, root sections of a total of 10-12 plants were pooled, in order to obtain a total of approximately 200 mg root material. Harvested root material was placed in the lid of a glass petri dish and chopped intensively in 1 ml of nuclei extraction buffer (NEB; 10 mM MES-KOH pH 7, 10 mM NaCl, 10 mM KCl, 2 mM EDTA, 250 mM mannitol, 0.1 mM spermine, 0.5 mM spermidine, 0.4 u/µl RNase inhibitor - 50:50 mix of Invitrogen SUPERase-InTM and Promega RNAsin Plus) using a razor blade for 1 min on ice, followed by 1 min of incubation. The chopped root material was strained through a 40 µm strainer (pluriSelect), together with 1 additional ml of NEB to collect remaining debris on the petri dish. Nuclei were stained using 40 µl of propidium iodide (PI), and sorted using the BD Biosciences FACSDiscover™ S8 Cell Sorter.
Nuclei were centrifuged at 4°C for 10 minutes at 700 g using a swinging bucket rotor, resuspended in nuclei buffer and around 30k nuclei were loaded on a Chromium X Single Cell Instrument (10x Genomics). In the first replicate, the Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 (10x Genomics) was used, while in the other two replicates the Chromium GEM-X Single Cell 3’ Kit v4 was used, both according to the manufacturer’s instructions.

treatment_protocol: AMF-inoculated plants were supplemented with R. irregularis DAOM197198 (approx. 250 spores per plant, Symplanta, Germany).

value: Root

value: Mock

tag: replicate


title: PBMCs_P_2

description:
Library name: Sample 144
Cells were cultured for 6 days in DMSO-containing media - replicate 2


title: dbdb6

description: Library name: dbdb6

value: KIDNEY


title: AMF_rep3

description:
Library name: AMF_rep3
10X Genomics 3' v4

value: AMF


title: dbdb5

description: Library name: dbdb5


title: PBMCs_P_1

description:
Library name: Sample 143
Cells were cultured for 6 days in DMSO-containing media - replicate 1


title: PC 12 cell, Erastin, B1

description:
Library name: Sample 4
rat-derived PC12 cells

value: PC 12


title: PC 12 cell, Control, A3

description:
Library name: Sample 3
rat-derived PC12 cells

value: neuronal-like rat-derived cell line

value: untreat


title: dbdb4

description: Library name: dbdb4


title: Mock_rep2

description:
Library name: Mock_rep2
10X Genomics 3' v4


title: NHO_IRIS_4

description:
Library name: Sample 142
Cells were treated with 10 Gy IR and cultured for 8 days - replicate 4

source_name: NHO

value: NHO

value: Osteoblasts

value: Ionizing radiation-induced senescence (8 days 10 Gy)


title: PC 12 cell, Control, A2

description:
Library name: Sample 2
rat-derived PC12 cells


title: AMF_rep2

description:
Library name: AMF_rep2
10X Genomics 3' v4


title: dbdb2

description: Library name: dbdb2


title: NHO_IRIS_3

description:
Library name: Sample 141
Cells were treated with 10 Gy IR and cultured for 8 days - replicate 3


title: Mock_rep1

description:
Library name: Mock_rep1
10X Genomics 3' v3.1


title: dbdb3

description: Library name: dbdb3


title: NHO_IRIS_1

description:
Library name: Sample 139
Cells were treated with 10 Gy IR and cultured for 8 days - replicate 1


title: PC 12 cell, Control, A1

description:
Library name: Sample 1
rat-derived PC12 cells


title: dbdb1

description: Library name: dbdb1


title: Untreat_D3_sg2

city: San Francisco

first: Qi

last: Liu

state: California

address: HSW RM 901A, 513 Parnassus Avenue

institute: UCSF Health, San Francisco , California, US

description: Library name: Sample30

data_processing:
Raw sequencing reads were quality-checked using FastQC and trimmed using fastp to remove adapter sequences and low-quality bases. Clean reads were aligned to the human reference genome (GRCh38) using STAR. Gene-level counts were generated using featureCounts, and differential gene expression analysis was performed using DESeq2 in R.
Assembly: GRCh38
Supplementary files format and content: Processed data files include normalized gene expression values (FPKM+1) derived from RNA-seq data. Rows correspond to genes and columns correspond to individual samples, with the first row indicating sample identifiers and the first column indicating gene names. The file "RNAseq_fpkm.xlsx" contains FPKM+1 values for each sample.

source_name: human primary T cell

growth_protocol: Human peripheral blood leukopaks from anonymous healthy donors were obtained from Stemcell Technologies (catalog no. 200-0092) under Institutional Review Board–approved protocols. CD3⁺ primary human T cells were isolated using the EasySep™ Human T Cell Isolation Kit (catalog no. 17951) following the manufacturer’s instructions. Immediately after isolation, T cells were either cryopreserved or used directly in downstream experiments. Freshly isolated T cells were seeded at 1 × 10⁶ cells/mL in appropriate culture vessels and activated using CST Dynabeads (Thermo Fisher Scientific, 40203D) at a 1:1 bead-to-cell ratio. Cells were cultured in cX-VIVO medium: X-VIVO™ 15 (Lonza Bioscience, 04-418Q) supplemented with 5% fetal bovine serum (Fisher Scientific), 50 µM 2-mercaptoethanol (Thermo Fisher Scientific, 21985023), and 10 mM N-acetyl-L-cysteine (Neta Scientific, SIAL-A7250-50G) in the presence of 50U human IL-2 from R&D systems ( 202-GMP-01M) or 30U human IL-2 from NIH (BULK Ro 23-6019). Where indicated, GPCR agonists were added at the following concentrations: 1 μg/mL prostaglandin E₂ (Thomas Scientific, C956T61), 10 μM dobutamine hydrochloride (Tocris, 0515), 20 μM CGS-21680 hydrochloride (Tocris, 1063), and 10 mM HCl (adjusted to pH 6.6 in the final medium).

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA quality and quantity were assessed prior to library preparation by Novogene. More than 100 ng of total RNA was used for library construction.
mRNA libraries were prepared using poly(A) enrichment and constructed following standard protocols by Novogene. Libraries were sequenced on an Illumina NovaSeq X Plus platform with paired-end 150 bp reads (PE150) by Novogene.

value: human primary T cell


title: AMF_rep1

description:
Library name: AMF_rep1
10X Genomics 3' v3.1


title: NHO_IRIS_2

description:
Library name: Sample 140
Cells were treated with 10 Gy IR and cultured for 8 days - replicate 2

value: WT


title: T.aestivum, ChIP-seq, H3K4me3, Chinese Spring, panicle

description: Library name: CS_panicle_H3K4me3_rep1

data_processing:
The sequencing reads were trimmed with fastp (0.22.0).
The clean reads were aligned with bwa program (version 0.7.17-r1188).
Peaks were called using MACS (v2.1.0.20150731).
Assembly: Aegilops tauschii (DD, Aet_v4.0), Secale cereale (Weining.v1.0)
Supplementary files format and content: peak files

organism: Triticum aestivum

source_name: panicle

growth_protocol: Seeds were surface-sterilized via a 10-min incubation in 30% H2O2 and then thoroughly washed five times with distilled water. The seeds were germinated in water for 3 days at 22 °C.The germinated seeds with residual endosperm were transferred to soil  and grown under 16 h light/ 8 h dark condition at 22 °C in greenhouse.

extract_protocol:
The 9-day-old seedlings (above-ground parts) were harvested and directly vacuum-infiltrated with a formaldehyde cross-linking solution for ChIP-seq. More than 10 ng of ChIP DNA extracted from each sample was used to prepare the sequencing samples.
ChIP-seq

value: panicle

tag: chip antibody

value: H3 trimethyl-Lys 4 (Abcam)


title: NHO_ETIS_4

description:
Library name: Sample 138
Cells were cultured for 8 days in 20 µM etoposide-containing media - replicate 4

value: Etoposide-induced senescence (8 days 20 µM)


title: Untreat_D3_AAVS1

description: Library name: Sample28


title: N5723

city: Shanghai

first: Zejie

last: Lin

address: 280 South Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

description: Library name: sample3

data_processing:
Raw sequencing data were processed using Cell Ranger v8.0.1 (10x Genomics). Reads were aligned to a custom mouse reference genome based on GRCm39 with default settings. The genes of EGFP and mCherry were manually added to enable detection of SuM-projecting mPFC extinction neurons or ZI-projecting mPFC extinction neurons respectively. Downstream analysis was conducted on R server (v4.2.2). Filtered feature-barcode matrices from Cell Ranger were imported into Seurat (v5.1.0) and converted into Seurat objects. To avoid potential technical noise, poor-quality cells were removed according to the number of detected genes, the ratio of genes to UMIs and the proportion of mitochondrial transcripts in total counts. (nFeature > 200, log10(genes/UMIs) > 0.8 & percent.mt < 5%). Data were normalized using the LogNormalize method, and ~2,000 highly variable genes were identified. ScaleData function was applied to scale the expression across each matrix. Potential doublets were estimated and filtered out via DoubletFinder (v2.0.4) with sample-specific pK values determined by parameter sweeping and expected doublet rates estimated from the number of captured nuclei. After doublet removal, all datasets were merged into an individual Seurat object and scaled again. Dimension reducing methods including PCA, UMAP and tSNE were then conducted to observe the distribution of cells from each sample, where top 20 variable dimensions were included. Batch effects across samples were minimal, therefore no additional integration methods (e.g., Harmony) were applied to maintain the potential alterations between neurons. Cell clusters were identified by specific marker genes from FindAllClusters function. The appropriate resolution (resolution = 0.5) was determined using Clustree (v0.5.1), in which all non-neuronal cell types could be separated.
Assembly: GRCm39
Supplementary files format and content: Processed data files include a gene expression matrix in Matrix Market format (matrix.mtx.gz), along with accompanying gene annotation (features.tsv.gz) and cell barcode (barcodes.tsv.gz) files for each sample.

source_name: medial prefrontal cortex

extract_protocol:
The mice were anesthetized and were performed a trans-cardiac perfusion with ice-cold N-methyl-D-glucamine-artificial cerebrospinal fluid (NMDG-ACSF) containing the following components (in mM): 93 N-methyl-D-glucamine, 2.5 KCl, 1.2 NaH2PO4, 30 NaHCO3, 20 HEPES, 25 D-glucose, 5 sodium ascorbate, 2 Thiourea, 3 Sodium pyruvate, 10 MgSO4, 11.9 N-acetyl-L-cysteine, 1 CaCl2, and 6 ml HCl (pH 7.35–7.45), continually bubbled with O2 and CO2 (95% O2/5% CO2, v/v). Coronal brain slices (400 μm thick) containing regions of the mPFC were cut using a vibratome (Leica VT1000S, Germany), then promptly transferred to ice-cold NMDG-ACSF and incubated for 15 min. TTX (1 μM), CNQX (20 μM; Sigma-Aldrich, Catalog no. C239) and D-APV (100 μM; Sigma-Aldrich, Catalog no. A8054) were added in this step. The micro-dissected tissues were promptly frozen in liquid nitrogen and then stored at -80 ℃ until use. Frozen tissues were softened in the A buffer, and sieved through a 70 μm cell strainer. Triton X-100 was added to the sample homogenate to achieve a final concentration of 0.1%. The sample was on ice for 5 min incubated inutes, and then large impurities were removed using a 40 μm cell strainer. After centrifugation, 1 mL of C Buffer was added to the precipitate, and the cell nuclei precipitate was gently resuspended. Then, 500 μL of G2 buffer was slowly added to the bottom of the LoBind Tube, and 500 μL of G1 buffer was slowly and gently added to the upper layer of the G2 buffer without disturbing the boundary liquid surface. Resuspended cell nuclei were slowly added to the G1 buffer surface. After centrifugation, the cell nuclei aggregated at the bottom of the tube. The cell nuclei were resuspended in an appropriate amount of 1 × PBS with 0.5% BSA. Then, dissociated single nuclei were stained with AO/PI for quantity and agglomeration rate assessment using Countstar Fluorescence Cell Analyzer. The concentrations of the nuclei were adjusted to approximately 1,000 nuclei/μL for snRNA-seq.
The snRNA-seq libraries were generated using the 10×Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V3 Reagent Kits (10×Genomics, Pleasanton, CA). Briefly, nuclei were concentrated to approximately 1000 nuclei/µL and loaded into each channel to generate single-cell Gel Bead-In-Emulsions (GEMs). After the RT step, GEMs were broken and barcoded-cDNA was purified and amplified. The amplified barcoded cDNA was fragmented, A-tailed, ligated with adaptors and index PCR amplified. The final libraries were quantified using the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific) and the size distribution of the libraries were determined using a High Sensitivity DNA chip on a Bioanalyzer 2200 (Agilent). All libraries were sequenced by DNBSEQ-T7 on a 150 bp paired-end run.

value: medial prefrontal cortex

value: nucleus

value: Fos 2A-iCreER


title: Untreat_D3_sg1

description: Library name: Sample29


title: T.aestivum, ChIP-seq, H3K27me3, Chinese Spring, panicle

description: Library name: CS_panicle_H3K27me3_rep1

value: H3 trimethyl-Lys 27 (ABclonal, A2363)


title: N5721

description: Library name: sample2


title: NHO_ETIS_3

description:
Library name: Sample 137
Cells were cultured for 8 days in 20 µM etoposide-containing media - replicate 3

data_processing:
BCL files were de-multiplexed and converted to FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed BBDuk from BBTools (v38.76)
Trimmed FASTQ files were aligned to human reference genome hg38 (Ensembl v104) using STAR software (v2.7.0f_0328).
featureCounts in R package Subread (v2.10.5) was used to generate gene counts
Assembly: hg38 (Ensembl v104)
Supplementary files format and content: text files containing counts

extract_protocol:
Total RNA was extracted using TriPure™ Isolation Reagent (Sigma-Aldrich), following the manufacturer's instructions with phenol-chloroform extraction.
Libraries were constructed using theTruSeq Stranded Total RNA Library prep kit according to manufacturer’s protocol (Illumina).


title: Untreat_D2_sg2

description: Library name: Sample27


title: V-C2b_rep4

city: Cambridge

first: Anders

last: Hansen

state: MA

address: 32 Vassar St, Building 56-722

institute: Massachusetts Institute of Technolo

description: Library name: Sample30

data_processing:
RCMC data analysis was done using a Snakemake pipeline modified from Hong et al., bioRxiv, 2025. Reads mapped to the 128x MS2 arrays were multiply mapped due to the presence of four copies of A repeats and four copies of B repeats within the arrays, and were rescued and uniformly redistributed among the four copies of the repeats after the initial alignment step.
A two-pass empirical redistribution algorithm resolved multi-mapped reads from a 1632 bp heterozygously duplicated fragment. First-pass baseline pairtools alignments generated a virtual 4C profile from 5 kb flanking sequences. The second pass reassigned reads using a probabilistic model, applying an assignment weight of 0.5 to the heterozygous upstream copy and 1.0 to the homozygous downstream copy.
Biological replicates and conditions processed across multiple sequencing runs were aggregated into pooled datasets. To remove unligated background artifacts prior to normalization, inward-facing read pairs were subtracted from the aggregated contact matrices using the remove-inward function of the neighbor-balance toolkit (Paggi et al., bioRxiv, 2025).
The filtered contact data was compiled into multi-resolution matrices from a base 400 bp resolution using cooler zoomify (Abdennur et al., Bioinformatics, 2020). Matrices were normalized using iterative correction and eigenvector decomposition (ICE), and then re-normalized against local interaction patterns using the neighbor-balance algorithm to restore true variations in physical density (Paggi et al., bioRxiv, 2025).
Assembly: mm39
Supplementary files format and content: mcool files are multi-resolution cooler files containing balance-normalized count matrices

growth_protocol: Mouse embryonic stem cells (JM8.N4 mESCs) were cultured on plates pre-coated with 0.1% sterile gelatin solution (Sigma-Aldrich, G1890-100G) under feeder free conditions in a base medium consisting of KnockOut DMEM (Thermofisher, 10829-018) with 15% FBS (HyClone, SH30396.03, Lot. No. AE28209315) and 1000U/mL LIF (home-made), 1 mM MEM Non-Essential Amino Acid Solution (Thermofisher, 11140-050), 2 mM GlutaMAX (Thermofisher, 35050-061), 100 ug/ml Penicillin-Streptomycin (Thermofisher, 15140-122), 100 ug/ml Primocin (Fisher Scientific, NC9392943) and 0.1 mM 2-mercapoethanol (Sigma, M-3148) supplemented with 2i, 10 uM MEK inhibitor (Tocris, PD0325901) and 3 uM GSK inhibitor (Sigma, SML1046-25MG), as well as 2 uM GSK-3484862 (TargetMol, T11469). mESCs were fed daily by replacing half the medium and passaged every two days using TrypLE Express Enzyme (1X, Thermo Fisher Scientific, 12605028) for dissociation.

extract_protocol:
Region Capture Micro-C (RCMC) was performed as previously described (Huseyin et al., Nature Protocols, 2026).
RCMC

treatment_protocol: For conditions with RAD21 or CTCF depletion, cells were treated with 100 µM 5ph-IAA or 500 nM dTAG-13 respectively for three hours before harvest. During harvest, the same concentration of drugs was maintained in PBS to prevent the reversal of protein degradation.

value: ESC

value: Untreated


title: N5422

description: Library name: sample1


title: NHO_ETIS_2

description:
Library name: Sample 136
Cells were cultured for 8 days in 20 µM etoposide-containing media - replicate 2


title: Untreat_D2_sg1

description: Library name: Sample26


title: WT5-Liver, Day 8

description: Library name: WT5-ZC1153 liver

source_name: Liver

value: Liver

value: mixture of primary cells


title: NHO_ETIS_1

description:
Library name: Sample 135
Cells were cultured for 8 days in 20 µM etoposide-containing media - replicate 1


title: S-G5H7_rep3

description: Library name: Sample28


title: V-C2b_rep3

description: Library name: Sample29


title: Untreat_D1_sg2

description: Library name: Sample24


title: WT4-Liver, Day 7

description: Library name: WT4-ZC1190 liver


title: S-G5H7_rep2

description: Library name: Sample27


title: Untreat_D2_AAVS1

description: Library name: Sample25


title: WT3-Liver, Day 8

description: Library name: WT3-ZC1184 liver


title: NHO_P_3

description:
Library name: Sample 133
Cells were cultured for 8 days in DMSO-containing media - replicate 3

value: Control proliferating cells


title: Untreat_D1_sg1

description: Library name: Sample23


title: S_V-A6B8-dRAD21_rep2

description: Library name: Sample26

value: 100 uM 5ph-IAA for 3hr


title: WT2-Liver, Day 6

description: Library name: WT2-ZC1131 liver


title: NHO_P_2

description:
Library name: Sample 132
Cells were cultured for 8 days in DMSO-containing media - replicate 2

value: NHO

value: Osteoblasts


title: S_V-A6B8-dRAD21_rep1

description: Library name: Sample25


title: WT1-Liver, Day 8

description: Library name: WT1-ZC1122 liver


title: Untreat_D1_AAVS1

description: Library name: Sample22

value: human primary T cell


title: Treat_D3_sg2

description: Library name: Sample21


title: Treat_D3_sg1

description: Library name: Sample20


title: NHA_IRIS_4

description:
Library name: Sample 130
Cells were treated with 10 Gy IR and cultured for 8 days - replicate 4

source_name: NHA

value: NHA

value: Astrocytes

value: WT

value: Ionizing radiation-induced senescence (8 days 10 Gy)


title: KO5-Liver, Day 8

description: Library name: K05-ZC1152 liver

value: KO


title: S_V-A6B8_rep2

description: Library name: Sample23


title: NHO_P_1

description:
Library name: Sample 131
Cells were cultured for 8 days in DMSO-containing media - replicate 1


title: S_V-A6B8_rep3

description: Library name: Sample24


title: KO4-Liver, Day 8

description: Library name: K04-ZC1175 liver


title: Treat_D3_AAVS1

description: Library name: Sample19


title: G2_UT_rep2

description: Library name: Sample22


title: KO3-Liver, Day 7

description: Library name: K03-ZC1189 liver


title: NHA_IRIS_2

description:
Library name: Sample 128
Cells were treated with 10 Gy IR and cultured for 8 days - replicate 2


title: G2_UT_rep1

description: Library name: Sample21


title: NHA_IRIS_1

description:
Library name: Sample 127
Cells were treated with 10 Gy IR and cultured for 8 days - replicate 1


title: KO2-Liver, Day 6

description: Library name: K02-ZC1130 liver


title: G2_dRAD21_rep4

description: Library name: Sample20


title: KO1-Liver, Day 8

description: Library name: K01-ZC1124 liver


title: NHA_ETIS_4

description:
Library name: Sample 126
Cells were cultured for 8 days in 20 µM etoposide-containing media - replicate 4

value: Etoposide-induced senescence (8 days 20 µM)


title: G2_dRAD21_rep3

description: Library name: Sample19


title: WT4-Kidney, Day 8

description: Library name: WT4-ZC1139 kidney

source_name: Kidney

value: Kidney


title: NHA_ETIS_3

description:
Library name: Sample 125
Cells were cultured for 8 days in 20 µM etoposide-containing media - replicate 3


title: Treat_D1_sg2

description: Library name: Sample15


title: G2_dCTCF_rep6

description: Library name: Sample18

value: 500nM dTag-13 for 3hr


title: WT3-Kidney, Day 8

description: Library name: WT3-ZC1137 kidney


title: Treat_D1_sg1

description: Library name: Sample14


title: NHA_ETIS_2

description:
Library name: Sample 124
Cells were cultured for 8 days in 20 µM etoposide-containing media - replicate 2


title: WT2-Kidney, Day 6

description: Library name: WT2-ZC1131 kidney


title: NHA_ETIS_1

description:
Library name: Sample 123
Cells were cultured for 8 days in 20 µM etoposide-containing media - replicate 1


title: Treat_D1_AAVS1

description: Library name: Sample13


title: G2_dCTCF_rep2

description: Library name: Sample16

value: ESC


title: KO5-Kidney, Day 8

description: Library name: K05-ZC1152 kidney


title: G2_dCTCF_rep1

description: Library name: Sample15


title: Donor3_KO_ivv

description: Library name: Sample12


title: NHA_P_4

description:
Library name: Sample 122
Cells were cultured for 8 days in DMSO-containing media - replicate 4


title: NHA_P_3

description:
Library name: Sample 121
Cells were cultured for 8 days in DMSO-containing media - replicate 3


title: G2_dCTCF_dRAD21_rep4

description: Library name: Sample14

value: 100 uM 5ph-IAA and 500nM dTag-13 for 3hr


title: KO4-Kidney, Day 8

description: Library name: K04-ZC1138 kidney


title: Donor3_AAVS1_2_ivv

description: Library name: Sample11


title: KO3-Kidney, Day 8

description: Library name: K03-ZC1135 kidney


title: Donor3_AAVS1_1_ivv

description: Library name: Sample10


title: NHA_P_2

description:
Library name: Sample 120
Cells were cultured for 8 days in DMSO-containing media - replicate 2


title: G2_dCTCF_dRAD21_rep3

description: Library name: Sample13


title: NHO_P_4

description:
Library name: Sample 134
Cells were cultured for 8 days in DMSO-containing media - replicate 4


title: NHA_P_1

description:
Library name: Sample 119
Cells were cultured for 8 days in DMSO-containing media - replicate 1


title: WT5-Lung, Day 8

description: Library name: WT5-ZC1153 lung

source_name: Lung

value: Lung


title: Donor2_KO_ivv

description: Library name: Sample9


title: Myoblasts_IRIS_4

description:
Library name: Sample 118
Cells were treated with 10 Gy IR and cultured for 8 days - replicate 4

source_name: Myoblasts

value: Myoblasts


title: WT4-Lung, Day 7

description: Library name: WT4-ZC1139 lung

value: mixture of primary cells


title: Donor2_AAVS1_ivv

description: Library name: Sample8


title: E11G8_rep6

description: Library name: Sample12

value: Untreated


title: E11G8_rep5

description: Library name: Sample11


title: Myoblasts_IRIS_3

description:
Library name: Sample 117
Cells were treated with 10 Gy IR and cultured for 8 days - replicate 3


title: Donor1_KO_4_ivv

description: Library name: Sample7


title: WT2-Lung, Day 6

description: Library name: WT2-ZC1131 lung


title: E11G8_rep3

description: Library name: Sample10


title: Myoblasts_IRIS_2

description:
Library name: Sample 116
Cells were treated with 10 Gy IR and cultured for 8 days - replicate 2


title: KO3-Lung, Day 8

description: Library name: K03-ZC1135 lung


title: Donor1_KO_3_ivv

description: Library name: Sample6


title: NHA_IRIS_3

description:
Library name: Sample 129
Cells were treated with 10 Gy IR and cultured for 8 days - replicate 3


title: E11G8_rep2

description: Library name: Sample9


title: KO2-Lung, Day 6

description: Library name: K02-ZC1130 lung


title: Myoblasts_IRIS_1

description:
Library name: Sample 115
Cells were treated with 10 Gy IR and cultured for 8 days - replicate 1


title: Donor1_KO_2_ivv

description: Library name: Sample5


title: KO1-Lung, Day 8

description: Library name: K01-ZC1124 lung


title: Myoblasts_ETIS_4

description:
Library name: Sample 114
Cells were cultured for 8 days in 20 µM etoposide-containing media - replicate 4


title: Dre_Vika-S_V-A6B8-E11_rep2

description: Library name: Sample8

value: Labels only control


title: Treat_D2_sg2

description: Library name: Sample18


title: Donor1_KO_1_ivv

description: Library name: Sample4


title: Dre_Vika-S_V-A6B8-E11_rep1

description: Library name: Sample7


title: Treat_D2_AAVS1

description: Library name: Sample16


title: WT5-BMcells, Day 8

description: Library name: WT5-ZC1205 BM cells

source_name: Bone Marrow

value: Bone Marrow


title: Myoblasts_ETIS_3

description:
Library name: Sample 113
Cells were cultured for 8 days in 20 µM etoposide-containing media - replicate 3


title: Donor1_AAVS1_3_ivv

description: Library name: Sample3

value: human primary T cell


title: 15C-A2_rep2

description: Library name: Sample6


title: WT4-BMcells, Day 7

description: Library name: WT4-ZC1190 BM cells


title: Treat_D2_sg1

description: Library name: Sample17


title: Myoblasts_ETIS_2

description:
Library name: Sample 112
Cells were cultured for 8 days in 20 µM etoposide-containing media - replicate 2


title: Donor1_AAVS1_2_ivv

description: Library name: Sample2


title: 15C-A2_rep1

description: Library name: Sample5


title: Myoblasts_ETIS_1

description:
Library name: Sample 111
Cells were cultured for 8 days in 20 µM etoposide-containing media - replicate 1


title: 15B_rep2

description: Library name: Sample4


title: WT3-BMcells, Day8

description: Library name: WT3-ZC1153 BM cells


title: WT2-BMcells, Day8

description: Library name: WT2-ZC1139 BM cells


title: Donor1_AAVS1_1_ivv

description: Library name: Sample1


title: Myoblasts_P_4

description:
Library name: Sample 110
Cells were cultured for 8 days in DMSO-containing media - replicate 4

value: Control proliferating cells


title: G2_dCTCF_rep5

description: Library name: Sample17


title: RWPE1_RCMC_WT_R2

city: Los Angeles

first: Suhn

middle: K

last: Rhie

state: CA

address: 1450 Biggy Street NRT 3504

department: Cancer Biology

institute: University of Southern California

description:
Library name: RWPE1 RCMC WT R2
RCMC

data_processing:
RCMC data were processed following 4DN data protal guidelines (PMID: 35501320). Briefly, we first aligned the raw sequencing reads with BWA MEM v0.7.17 (PMID: 19451168), and the aligned reads were paired, sorted, and filtered with Pairtoolsv0.3.0 (https://pairtools.readthedocs.io/en/latest) and converted into pairs files. Next, we normalized paired data to generate matrix files with Juicertools (PMID: 27467249) for Juicer (v1.5) (hic files).
Assembly: hg38
Supplementary files format and content: .hic

source_name: Prostate

growth_protocol: 22Rv1 (CRL-2505) and RWPE-1 (CRL-11609) cells were obtained from the American Type Culture Collection (ATCC). RC-77N/E and RC77T/E cells were received from Johng Sik Rhim. Cells were cultured according to the suggested protocols at 37°C with 5% CO2. 22Rv1 cells were cultured in RPMI 1640 (Corning, #10-040-CV) supplemented with 10% FBS (Avantor Seradigm, #89510-188) and 1% penicillin/streptomycin. RWPE-1, RC-77N/E, and RC77T/E cells were cultured in the Keratinocyte Serum Free Medium kit (Thermo Fisher Scientific, #17005-042).

extract_protocol:
For RCMC, cells were fixed with 3mM DSG and 1% formaldehyde. After quenching, cells were lysed on ice to obtain nuclei. Chromatin was digested in situ with MNase to fragment the DNA at nucleosome resolution. DNA was repaired with biotinylated dNTPs, and then free DNA ends were proximity ligated while unligated ends were digested. Chromatin was then reverse crosslinked and digested by Protease K. Lastly, DNA was purified by phenol chlroroform extraction and purified. 250 - 400 bp dinucleosomal DNA fragments were selected on an agarose gel and end polished. Streptavidin beads were used to pull down ligated dinucleosomal DNA fragments.
RCMC library: DNA fragments bound to streptavidin beads were made into libraries using NEBNext Ultra II DNA Library Prep Kit (NEB) nad KAPA HiFi HotStart ReadyMix (Roche)following manufacturer's instructions. Purified libraies were pooled together and made into RCMC libaries following the Twist Standard Hybridization Target Enrichment Protocol (Twist Biosciences). Briefly, the libraries were hybridized to custom probe panels for loci of interest on chromosome 6 and bound to streptavidin beads. DNA fragments on the beads were amplified using Equinox Library Amp Mix (Twist Biosciences) and purified.

value: Prostate

value: prostate cells


title: WT1-BMcells, Day 8

description: Library name: WT1-ZC1137 BM cells

value: WT


title: 15B_rep1

description: Library name: Sample3


title: Myoblasts_P_3

city: Baltimore

first: Supriyo

last: De

address: 251 Bayview Blvd

institute: NIA-IRP, NIH

description:
Library name: Sample 109
Cells were cultured for 8 days in DMSO-containing media - replicate 3


title: RWPE1_RCMC_WT_R1

description:
Library name: RWPE1 RCMC WT R1
RCMC


title: KO5-BMcells, Day 8

description: Library name: K05-ZC1200 BM cells

value: KO


title: 15A_rep2

description: Library name: Sample2


title: Myoblasts_P_2

description:
Library name: Sample 108
Cells were cultured for 8 days in DMSO-containing media - replicate 2


title: KO4-BMcells, Day 7

description: Library name: K04-ZC1189 BM cells


title: 15A_rep1

description: Library name: Sample1


title: 22Rv1_RCMC_rPCE_del_R2

description:
Library name: 22Rv1 RCMC rPCE del R2
RCMC


title: Myoblasts_P_1

description:
Library name: Sample 107
Cells were cultured for 8 days in DMSO-containing media - replicate 1


title: 22Rv1_RCMC_rPCE_del_R1

description:
Library name: 22Rv1 RCMC rPCE del R1
RCMC


title: KO3-BMcells, Day 8

description: Library name: K03-ZC1152 BM cells


title: HVSMC_IRIS_4

description:
Library name: Sample 106
Cells were treated with 15 Gy IR and cultured for 8 days - replicate 4

source_name: HVSMC

value: HVSMC

value: Vascular smooth muscle cells

value: Ionizing radiation-induced senescence (8 days 15 Gy)


title: GGT_ZT20_c

city: Chongqing

first: Mengyue

last: Chen

state: Chongqing

address: No. 1, Medical College Road, Yuzhong District, Chongqing City

department: Department of Infectious Diseases

institute: the Second Affiliated Hospital，Chongqing medical university

description: Library name: sample_37

data_processing:
Compare the quality-controlled raw data, which is referred to as “clean data” (reads), with the reference genome to obtain mapped data (reads) for subsequent transcript assembly, expression quantification, and other purposes. Conduct a quality assessment of the alignment results from this transcriptome sequencing, focusing on sequencing saturation, gene coverage, the distribution of reads across different regions of the reference genome, and the distribution of reads across different chromosomes. Software used: HiSat2 (http://ccb.jhu.edu/software/hisat2/index.shtml).
The abundance of transcripts reflects the level of gene expression. The higher the abundance of transcripts, the higher the level of gene expression. In RNA-Seq analysis, the level of gene expression is calculated by counting the number of sequences (clean reads) that are localized to specific regions of the genome. The expression levels of genes and transcripts are quantitatively analyzed using software RSEM to facilitate subsequent analysis of differences in gene/transcript expression between different samples. By combining sequence functional information, the regulatory mechanisms of genes can be elucidated. Software used: RSEM (http://deweylab.github.io/RSEM/).
After obtaining the read counts for the genes, perform an analysis of gene expression differences between samples (≥ 2) to identify genes with differential expression between samples. Subsequently, study the functions of the differentially expressed genes. The software used for differential expression analysis is DESeq2 (with biological replicates) or DEGseq (without biological replicates, used by default). The default screening criteria for significantly differentially expressed genes are: FDR < 0.05 and |log2FC| ≥ 1. When a gene meets both of these conditions, it is considered a differentially expressed gene (DEG). The software used is DEGseq (https://www.rdocumentation.org/packages/DEGseq/versions/1.26.0); DESeq2 (http://bioconductor.org/packages/stats/bioc/DESeq2/).
Using the GO (Gene Ontology) database, genes can be categorized based on the biological processes (Biological Process, BP) they are involved in, the cellular components (Cellular Component, CC) they comprise, and the molecular functions (Molecular Function, MF) they perform. Differentially expressed genes can be annotated with GO terms. Using the KEGG (Kyoto Encyclopedia of Genes and Genomes) database, genes can be classified based on the pathways or functions they participate in. Differentially expressed genes can also be annotated with KEGG terms. Software used: Diamond (https://github.com/bbuchfink/diamond).
Assembly: mm10
Supplementary files format and content: gene.TPM.matrix.annot.xlsx

source_name: Kidney proximal tubules specific CD36 knockout mice, sampling at ZT20, biol rep 3

extract_protocol:
Take a suitable amount of tissue, the liquid nitrogen is fully milled and transferred to a 1.5ml centrifuge with 1ml Trizol pre-cooled. The vibration causes it to fully crack. Place it at room temperature for 5 minutes, which may be extended appropriately if difficult to extract tissue. 4C, 13000g centrifuge for 5 minutes, draw the upper liquid into another centrifuge tube, according to 0.2 ml chloroform / 1 ml trizol amount of pre-cooled chloroform, that is, 200 ul, vibrate mix and leave at room temperature for 5 minutes. 4C, 13000g centrifuge for 15 minutes, draw the upper aqueous phase (the tip of the gun does not contact the intermediate protein layer) to another centrifuge (400 ul), add an equal volume of pre-cooled isopropanol, and leave at room temperature for 10 minutes.After centrifuging 13,000 g at 4 ° C for 10 minutes, discard the liquid, there will be a small white precipitation on the bottom of the tube (perhaps not visible to the naked eye when the amount of RNA is very small). Add 1ml pre-cooled 75% ethanol to float the precipitation.At 4 ° C, 12,000 g centrifuged for 5 minutes, purified (suck purified with 1000 sets of 10uL gunheads and discarded), centrifuged the centrifuge tube for a few seconds, dumped the residue suspended on the wall of the tube, sucked out the residues with 10ul gunheads, and left it at room temperature for 3-5min. Note not to be too dry, otherwise the RNA is insoluble and may cause degradation.Add 20-50 ul (the amount added depends on the amount of RNA extracted) of sterilized 0.1% DEPC water to dissolve.
Total RNA is extracted from the tissue sample, and the concentration and purity of the extracted RNA are analyzed using the Nanodrop2000. The integrity of the RNA is assessed through agarose gel electrophoresis, and the RIN value is determined using the Agilent5300. For a single library construction, the total RNA required is 1 μg, with a concentration ≥ 30 ng/μL and an RQN > 6.5, with an OD260/280 range of 1.8 to 2.2. In eukaryotic organisms, mRNA has a polyA tail structure. Using magnetic beads coated with Oligo(dT) and polyA, A-T base pairing can be achieved, allowing mRNA to be isolated from total RNA for transcriptome analysis. The Illumina platform is designed for sequencing short sequence fragments; the enriched mRNA obtained is a complete RNA sequence with an average length of several kilobases.It needs to be subjected to random disruption. By incorporating a fragmentation buffer and selecting suitable conditions, mRNA can be randomly broken into small fragments of approximately 300 bp. Under the action of reverse transcriptase, using random primers, mRNA serves as a template to reverse-synthesize a single strand of cDNA. Subsequently, double-strand synthesis (dUTP replacing dTTP; this strand is subsequently degraded by the UDG enzyme; ultimately, the first strand representing the original RNA direction is amplified and sequenced) is performed, resulting in a stable double-stranded structure. The double-stranded cDNA structure has sticky ends; EndRepairMix is added to fill these with blunt ends, followed by the addition of an A base at the 3’ end for connecting Y-shaped adapters. UDG enzyme is used to degrade the second-strand cDNA containing dUTI, leaving only the first-strand cDNA, which is then amplified by PCR. The product after connecting the adapter is purified and fragmented, and the purified fragment is used for PCR amplification to obtain the final library. Sequencing is performed on the Nova seq X plus platform.

value: renal cortical


title: 22Rv1_RCMC_cPCE_del_R2

description:
Library name: 22Rv1 RCMC cPCE del R2
RCMC


title: GGT_ZT20_b

description: Library name: sample_36

source_name: Kidney proximal tubules specific CD36 knockout mice, sampling at ZT20, biol rep 2


title: KO2-BMcells, Day 8

description: Library name: K02-ZC1138 BM cells


title: 22Rv1_RCMC_cPCE_del_R1

description:
Library name: 22Rv1 RCMC cPCE del R1
RCMC


title: HVSMC_IRIS_3

description:
Library name: Sample 105
Cells were treated with 15 Gy IR and cultured for 8 days - replicate 3


title: KO1-BMcells, Day 8

description: Library name: K01-ZC1135 BM cells


title: GGT_ZT20_a

description: Library name: sample_35

source_name: Kidney proximal tubules specific CD36 knockout mice, sampling at ZT20, biol rep 1


title: HVSMC_IRIS_2

description:
Library name: Sample 104
Cells were treated with 15 Gy IR and cultured for 8 days - replicate 2


title: WT3-Spleen, Day 7

description:
Library name: WT3-ZC162-M
WT3 contains samples from both animals: ZC143-F and ZC162-M

source_name: Spleen

value: Spleen


title: HVSMC_IRIS_1

description:
Library name: Sample 103
Cells were treated with 15 Gy IR and cultured for 8 days - replicate 1


title: 22Rv1_RCMC_NTC_R1

description:
Library name: 22Rv1 RCMC NTC R1
RCMC


title: GGT_ZT16_c

description: Library name: sample_34

source_name: Kidney proximal tubules specific CD36 knockout mice, sampling at ZT16, biol rep 3


title: GGT_ZT16_b

description: Library name: sample_33

source_name: Kidney proximal tubules specific CD36 knockout mice, sampling at ZT16, biol rep 2


title: WT3-Spleen, Day 8

description:
Library name: WT3-ZC143-F
WT3 contains samples from both animals: ZC143-F and ZC162-M


title: 22Rv1_RCMC_NTC_R2

description:
Library name: 22Rv1 RCMC NTC R2
RCMC


title: 22Rv1_RCMC_WT_R2

description:
Library name: 22Rv1 RCMC WT R2
RCMC


title: Total_ZFC3H1_0HdTAG_rep2

city: Aarhus

first: Jerome

middle: O

last: Rouviere

address: Universitetsbyen 81

country: Denmark

institute: Aarhus University

description: Library name: Total_ZFC3H1_0HdTAG_rep2

data_processing:
The raw sequence reads received from service providers were first quality checked using FastQC (Babraham Bioinformatics group). Reads were then trimmed for adaptors and filtered using Trim Galore (Babraham Bioinformatics group). Trimmed reads were mapped to hg38, using Hisat2 in paired-end mode. Mapped files were sorted and checked for pairing using SAMtools. Reads were then deduplicated using MarkDuplicates (Picard – Broad Institute) and further filtered to keep only unique mappers by using SAMtools. Relative samples size was then estimated by generating coverage counts using htseq-count (HTSeq-counts) over the Genecode annotation and analyzing then with DEseq2 to define size factors. In the case of fractionated pA+ RNAseq, size factors were measured separately for the nuclear and cytoplasmic fractions to avoid any compensation of compartment specific phenotypes. Finally, reads were converted to bigwig (bw) files normalized to size factors, with a binning of 5, using bamCoverage (Deeptools).
Assembly: hg38
Supplementary files format and content: bigwig (bw) - normalized coverage with a binning of 5

source_name: cervix

growth_protocol: HeLa cells were cultured in standard DMEM medium supplemented with 10% FBS and penicillin-streptomycin mix.

extract_protocol:
Total RNA was extracted using TRIZOL reagent according to manufacturer’s instructions
Library construction and sequencing were paid services from the Beijing Genome Institute (BGI) in case of total pA+ RNAseq and from Lexogen for the fractionated and exogenously expressing ZFC3H1 pA+ RNAseq.

treatment_protocol: When specified, cels were treated with dTAGV-1 at a concentration of 500nM for 4H

value: cervix

value: HeLa Kyoto


title: HVSMC_DIS_4

description:
Library name: Sample 102
Cells were cultured for 8 days in 85 nM doxorubicin-containing media - replicate 4

value: Doxorubicin-induced senescence (8 days 85 nM)


title: GGT_ZT16_a

description: Library name: sample_32

source_name: Kidney proximal tubules specific CD36 knockout mice, sampling at ZT16, biol rep 1


title: WT2-Spleen, Day 7

description: Library name: WT2-ZC161-M

value: mixture of primary cells


title: HVSMC_DIS_3

description:
Library name: Sample 101
Cells were cultured for 8 days in 85 nM doxorubicin-containing media - replicate 3


title: GGT_ZT12_c

description: Library name: sample_31

source_name: Kidney proximal tubules specific CD36 knockout mice, sampling at ZT12, biol rep 3


title: 22Rv1_RCMC_WT_R1

description:
Library name: 22Rv1 RCMC WT R1
RCMC


title: HVSMC_DIS_2

description:
Library name: Sample 100
Cells were cultured for 8 days in 85 nM doxorubicin-containing media - replicate 2


title: WT1-Spleen, Day 13

description: Library name: WT1-ZC128-F


title: 22Rv1_CTCF_rPCE_del_R2

description:
Library name: 22Rv1 CTCF rPCE del R2
ChIP-seq

data_processing:
ChIP-seq data were processed following ENCODE3 guidelines (PMID: 22955616). Briefly, BWA (PMID: 19451168) was used to align the raw sequencing reads to the human reference genome (hg38). Library complexity was computed to determine the PCR bottleneck coefficients, non-redundant fraction, normalized strand cross-correlation coefficient, and relative strand cross-correlation coefficient. PCR duplicates and unaligned reads were removed using Picard (https://github.com/broadinstitute/picard) and samtools (PMID: 19505943). Uniquely mapped reads were used to call peaks using MACS2 (PMID: 18798982) (narrowPeak format).
Assembly: hg38
Supplementary files format and content: .bw

extract_protocol:
For ChIP-seq, cells were grown to 70%-90% confluence and cross-linked with 1% formaldehyde for 10 minutes and quenched with 125nM glycine for 5 minutes at RT. Nuclei were lysed in nuclei lysis buffer, and performed snap-freeze using liquid nitrogen. Chromain was sonicated to an approximate length of 200 bp - 500 bp using bioruptor sonicator.
ChIP-seq library: Libraries were prepared using the KAPA Hyper Prep Kit from KAPA Biosystems. End-Repair and A-Tailing Buffers, DNA ligase, and ligation buffer were used. Ampure beads were used for post-ligation clean up, and KAPA HiFi HotStart Ready Mix and Nextflex Primer Mix were used for amplification of adapter modified DNA fragments.

value: CTCF


title: GGT_ZT12_b

description: Library name: sample_30

source_name: Kidney proximal tubules specific CD36 knockout mice, sampling at ZT12, biol rep 2


title: KO4-Spleen, Day 6

description: Library name: KO4-ZC109-M


title: HVSMC_DIS_1

description:
Library name: Sample 99
Cells were cultured for 8 days in 85 nM doxorubicin-containing media - replicate 1


title: 22Rv1_CTCF_rPCE_del_R1

description:
Library name: 22Rv1 CTCF rPCE del R1
ChIP-seq


title: KO3-Spleen, Day 9

description: Library name: KO3-ZC151-F


title: GGT_ZT12_a

description: Library name: sample_29

source_name: Kidney proximal tubules specific CD36 knockout mice, sampling at ZT12, biol rep 1


title: 22Rv1_FOXA1_rPCE_del_R2

description:
Library name: 22Rv1 FOXA1 rPCE del R2
ChIP-seq


title: HVSMC_P_3

description:
Library name: Sample 97
Cells were cultured for 8 days in DMSO-containing media - replicate 3


title: KO2-Spleen, Day 7

description: Library name: KO2-ZC159-M


title: 22Rv1_FOXA1_rPCE_del_R1

description:
Library name: 22Rv1 FOXA1 rPCE del R1
ChIP-seq


title: GGT_ZT8_c

description: Library name: sample_28

source_name: Kidney proximal tubules specific CD36 knockout mice, sampling at ZT8, biol rep 3


title: GGT_ZT8_b

description: Library name: sample_27

source_name: Kidney proximal tubules specific CD36 knockout mice, sampling at ZT8, biol rep 2


title: KO1-Spleen, Day 7

description: Library name: KO1-ZC158-M


title: HVSMC_P_2

description:
Library name: Sample 96
Cells were cultured for 8 days in DMSO-containing media - replicate 2


title: 22Rv1_FOXA1_cPCE_del_R2

description:
Library name: 22Rv1 FOXA1 cPCE del R2
ChIP-seq


title: GGT_ZT8_a

description: Library name: sample_26

source_name: Kidney proximal tubules specific CD36 knockout mice, sampling at ZT8, biol rep 1


title: HVSMC_P_1

description:
Library name: Sample 95
Cells were cultured for 8 days in DMSO-containing media - replicate 1


title: GGT_ZT4_c

description: Library name: sample_25

source_name: Kidney proximal tubules specific CD36 knockout mice, sampling at ZT4, biol rep 3


title: 22Rv1_FOXA1_cPCE_del_R1

description:
Library name: 22Rv1 FOXA1 cPCE del R1
ChIP-seq

source_name: Prostate


title: LC049_VI

type: RNA

city: Lørenskog

first: Hilde

middle: Loge

last: Nilsen

address: Sykehusveien 25

country: Norway

institute: Akershus University Hospital

hyb_protocol: Amplification and labelling efficiency were controlled on the NanoDrop. The cRNA quality was assessed by measuring the RNA absorbance ratio 260nm/280nm. The specific activity of labeled cRNA (pmol Cy3 per ug cRNA) was defined to be 6 or above according to the Agilent recommendations.

scan_protocol: Standard Illumina Protocol

data_processing: Expression signals were normalized with the limma R package. Control probes were removed before processing. Background correction was done with the backgroundCorrect function, using the normexp method and offset 16. Hence the lowest possible normalized expression value is log2(16) = 4. Batch correction was done using the normalizeBetweenArrays function, using the quantile method.

source_name: Gut epithelium, NP, Rectum

label_protocol: mRNA amplification, labelling, and hybridization were done following the manufacturer’s instructions (Agilent One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling). In short, 50 ng RNA was amplified and labelled with Cy3 using the Low Input Quick Amp Labeling Kit, one-color (product number 5190-2331), and the labelled cRNA was purified using the Qiagen RNeasy Mini Kit.

extract_protocol: Total RNA was isolated using AllPrep kit (Qiagen, Hilden, Germany). The tissue biopsies were homogenized in Buffer RLT using a 5 mm steal bead in the FastPrep-24 Classic Instrument (MP Biomedicals, Irvine, CA, USA) at 6 m/s for 40 sec. The samples were centrifuged and the lysate transferred to new tubes. Further processing was according to the manufacture’s protocol. RNA concentration was measured using the QiaCubeNanoDrop ND-1000 spectrophotometer (Qiagen). The RNA quality, indicated by the RNA integrity number (RIN), was assessed with an Agilent 2100 Bioanalyser, Agilent 2100 Expert software and Agilent RNA 6000 Nano Kit (Agilent Technologies Inc., Santa Clara, CA, USA). RNA samples with RIN number below 7.0 were excluded.

value: gut epithelium

tag: status

value: Non-progressor

tag: segment

value: Rectum

tag: inflammation

value: Chronic active

tag: neoplasia


title: GGT_ZT4_b

description: Library name: sample_24

source_name: Kidney proximal tubules specific CD36 knockout mice, sampling at ZT4, biol rep 2


title: HUVEC_IRIS_4

description:
Library name: Sample 94
Cells were treated with 7.5 Gy IR and cultured for 8 days - replicate 4

source_name: HUVEC

value: HUVEC

value: Venal endothelial

value: Ionizing radiation-induced senescence (8 days 7.5 Gy)


title: 22Rv1_FOXA1_NTC_R2

description:
Library name: 22Rv1 FOXA1 NTC R2
ChIP-seq

value: Prostate

value: prostate cells


title: LC052_II

source_name: Gut epithelium, P, Ascendens

value: Progressor

value: Ascendens


title: HUVEC_IRIS_3

description:
Library name: Sample 93
Cells were treated with 7.5 Gy IR and cultured for 8 days - replicate 3

value: WT


title: 22Rv1_FOXA1_NTC_R1

description:
Library name: 22Rv1 FOXA1 NTC R1
ChIP-seq


title: HVSMC_P_4

description:
Library name: Sample 98
Cells were cultured for 8 days in DMSO-containing media - replicate 4

source_name: HVSMC

value: HVSMC

value: Vascular smooth muscle cells

value: Control proliferating cells


title: GGT_ZT4_a

description: Library name: sample_23

source_name: Kidney proximal tubules specific CD36 knockout mice, sampling at ZT4, biol rep 1

value: renal cortical


title: LC049_IV

source_name: Gut epithelium, NP, Descendens

value: Descendens


title: LC049_II

source_name: Gut epithelium, NP, Ascendens

value: gut epithelium


title: GGT_ZT0_c

description: Library name: sample_22

source_name: Kidney proximal tubules specific CD36 knockout mice, sampling at ZT0, biol rep 3


title: LC046_VI

value: Non-progressor


title: HUVEC_IRIS_1

description:
Library name: Sample 91
Cells were treated with 7.5 Gy IR and cultured for 8 days - replicate 1


title: 22Rv1_CTCF_cPCE_del_R1

description:
Library name: 22Rv1 CTCF cPCE del R1
ChIP-seq

value: CTCF


title: GGT_ZT0_b

description: Library name: sample_21

source_name: Kidney proximal tubules specific CD36 knockout mice, sampling at ZT0, biol rep 2


title: 22Rv1_CTCF_NTC_R2

description:
Library name: 22Rv1 CTCF NTC R2
ChIP-seq


title: GGT_ZT0_a

description: Library name: sample_20

source_name: Kidney proximal tubules specific CD36 knockout mice, sampling at ZT0, biol rep 1


title: HUVEC_ETIS_4

description:
Library name: Sample 90
Cells were cultured for 8 days in 50 µM etoposide-containing media - replicate 4

value: Etoposide-induced senescence (8 days 10 µM)


title: HUVEC_ETIS_3

description:
Library name: Sample 89
Cells were cultured for 8 days in 50 µM etoposide-containing media - replicate 3

value: HUVEC


title: LC046_IV

value: Chronic active


title: FLOX_ZT20_c

description: Library name: sample_19

source_name: CD36f/f mice, sampling at ZT20, biol rep 3


title: HUVEC_ETIS_2

description:
Library name: Sample 88
Cells were cultured for 8 days in 50 µM etoposide-containing media - replicate 2

value: Venal endothelial


title: LC043_VI

value: Rectum


title: 22Rv1_H3K27ac_resPCE_del_R2

description:
Library name: 22Rv1 H3K27ac resPCE del R2
ChIP-seq

value: Prostate

value: prostate cells


title: LC052_V

source_name: Gut epithelium, P, Sigmoideum

value: Progressor

value: Sigmoideum


title: 22Rv1_H3K27ac_resPCE_del_R1

description:
Library name: 22Rv1 H3K27ac resPCE del R1
ChIP-seq


title: FLOX_ZT20_a

description: Library name: sample_17

source_name: CD36f/f mice, sampling at ZT20, biol rep 1


title: HUVEC_P_4

description:
Library name: Sample 87
Cells were cultured for 8 days in DMSO-containing media - replicate 4

value: WT


title: 22Rv1_H3K27ac_rPCE_del_R2

description:
Library name: 22Rv1 H3K27ac rPCE del R2
ChIP-seq


title: FLOX_ZT16_d

description: Library name: sample_16

source_name: CD36f/f mice, sampling at ZT16, biol rep 4


title: HUVEC_P_3

description:
Library name: Sample 86
Cells were cultured for 8 days in DMSO-containing media - replicate 3


title: LC052_III_D_2

source_name: Gut epithelium, P, Transversum

value: Transversum


title: HUVEC_P_2

description:
Library name: Sample 85
Cells were cultured for 8 days in DMSO-containing media - replicate 2

value: Control proliferating cells


title: 22Rv1_H3K27ac_rPCE_del_R1

description:
Library name: 22Rv1 H3K27ac rPCE del R1
ChIP-seq

source_name: Prostate


title: FLOX_ZT16_c

description: Library name: sample_15

source_name: CD36f/f mice, sampling at ZT16, biol rep 3

value: renal cortical


title: HUVEC_P_1

description:
Library name: Sample 84
Cells were cultured for 8 days in DMSO-containing media - replicate 1


title: 22Rv1_H3K27ac_cPCE_del_R2

description:
Library name: 22Rv1 H3K27ac cPCE del R2
ChIP-seq


title: FLOX_ZT16_b

description: Library name: sample_14

source_name: CD36f/f mice, sampling at ZT16, biol rep 2


title: HSAEC_IRIS_4

description:
Library name: Sample 83
Cells were treated with 10 Gy IR and cultured for 8 days - replicate 4

source_name: HSAEC

value: HSAEC

value: Lung epithelial

value: Ionizing radiation-induced senescence (8 days 10 Gy)


title: LC054_IV

value: gut epithelium

value: Non-progressor

value: Descendens


title: FLOX_ZT16_a

description: Library name: sample_13

source_name: CD36f/f mice, sampling at ZT16, biol rep 1


title: LC053_VI

source_name: Gut epithelium, NP, Rectum


title: HSAEC_IRIS_3

description:
Library name: Sample 82
Cells were treated with 10 Gy IR and cultured for 8 days - replicate 3


title: 22Rv1_H3K27ac_NTC_R2

description:
Library name: 22Rv1 H3K27ac NTC R2
ChIP-seq


title: FLOX_ZT12_c

description: Library name: sample_12

source_name: CD36f/f mice, sampling at ZT12, biol rep 3


title: HSAEC_IRIS_2

description:
Library name: Sample 81
Cells were treated with 10 Gy IR and cultured for 8 days - replicate 2


title: 22Rv1_H3K27ac_NTC_R1

description:
Library name: 22Rv1 H3K27ac NTC R1
ChIP-seq


title: LC053_V

source_name: Gut epithelium, NP, Sigmoideum