title: 1mM_NaVA_4h_after_HS_rep2

description: Gene expression data from 14-day-old seedlings transferred for additional 72 h onto medium supplemented with 1 mM NaVA, treated with 43.5°C for 4 h and collected immediately after.

source_name: 14-day-old Arabidopsis seedlings kept for additional 72h on medium with 1 mM NaVA before 4 h of heat shock at 43.5°C


title: ATRi+Aph06 rep1 S6/G2/M

status: Public on Mar 16 2026

type: SRA

city: Paris

first: Chun-Long

last: CHEN

state: Ile-de-France

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description:
Library name: Sample 18
Enrichement of BrdU labelled DNA (Replicate 1)
Consensus.bw
ATRi-Aph06_G1-S1_average.bw

library_source: genomic

data_processing:
Demultiplexing: bcl2fastq2 (v2.15.0, v2.18.12).
Adapter trimming: Cutadapt (v1.3-v1.9), read length ≥ 10 nt.
Mapping: bwa-mem2 (v2.2.1).
PCR duplicates were removed with Picard (http://broadinstitute.github.io/picard, v3.3).
Only proper paired-end reads with MAPQ ≥ 6 were kept.
The read densities for each sample were computed within 10 kb non-overlapping windows using R package bamsignals v1.30, and normalized to the sample with the lowest number of reads with custom scripts.
Peak calling: local maxima were identified by convoluting the normalized Repli-seq signal with a first derivative of a Gaussian (sigma 3 over ± 90 kb). The points of inflection were identified by convoluting the normalized Repli-seq signal with a kernel containing the second derivative of a Gaussian (sigma 3 over ± 90 kb). Peaks were called as a local maximum between two inflection points with opposite inclination. The peaks identified on the “consensus” sample (called consensus peaks) with a mean replication timing value (S50) less than 0.4 are named ATRAP peaks.
Differential analysis: to define the early constitutive origins with increased G1/S Repli-seq signal in ATR-depleted cells treated with Aph, a genome-wide differential analysis has been performed on the raw read density of each 10 kb adjacent window between non-treated (n=4) and ATRAP-seq samples (n=6) with the R package DESeq2 v.1.36 (fitType = local).
Over-activated early constitutive origins are defined as ATRAP peaks overlapping with windows significantly enriched in ATRAP-seq samples compared to NT (Wald test p < 0.05, log2(FC) > 0.45). The same differential analysis has been performed using different control samples i.e., 4 APH vs. 6 ATRAP and 3 ATRi vs. 6 ATRAP
Assembly: hg19
Supplementary files format and content: BigWigs files were obtained from raw counts with MAPQ ≥ 6 in 1kb non-overlapping windows, normalized to 15 million total read counts and smoothed with a rolling mean (+/- 25 kb, 1 kb step).
Supplementary files format and content: The "Consensus" bigwig file represent the average read densities of the 6 ATRAP-seq samples (3 replicates with Aph 0.3 µM and 3 with Aph 0.6 µM).
Supplementary files format and content: Bigwig files indicated with "average" correspond to the average read densities of the G1-S1 fractions of the corresponding conditions. The average for untreated cells (NT) is the average of the bigwig deposited here as well as 3 other NT samples available under GEO IDs: GSM3963958, GSM3963964 and GSM5610009
Library strategy: Repli-seq

molecule: genomic DNA

organism: Homo sapiens

source_name: JEFF cells

growth_protocol: Lymphoblasts were grown in RPMI 1640 + GlutaMAX-I medium (61870-010, ThermoFisher scientific) supplemented with 10% foetal calf serum (CVFSVF00-0T, Eurobio) and 100 µg/mL of penicillin and streptomycin (151140-122, ThermoFisher scientific) at 37°C in a humid atmosphere containing 5% CO2.

extract_protocol:
Cells were incubated overnight in lysis buffer (50 mM Tris-HCl pH8, 10 mM EDTA, 0.1% SDS, 50 ug/mL RNAse A, 100 ug/mL Proteinase K). DNA was purified from the lysates by phenol extraction.
Four µg of genomic DNA was fragmented to a mean size of 500 bp on a Covaris S220 intrument (peak power: 140, duty factor: 10%, cycle/burst: 200, time: 80 seconds). Fragmented DNA was treated with the End-Repair module (New England BioLabs, E6050) and the A-Tailing module (New England BioLabs, E6053), according to the manufacturer recommendations. Illumina Truseq indexed adapters were ligated on the resulting fragments, using the Quick Ligation module (New England BioLabs, E6056), according to the manufacturer recommendations. Following heat denaturation, BrdU-DNA was isolated by immunoprecipitation using an anti-BrdU monoclonal antibody (BD Biosciences, 347580). Immunoprecipitated fragments were amplified for 10 cycles using the KAPA Hifi DNA polymerase (KAPABiosystems, KK2502) and the resulting libraries were purified with AMPure XP beads (Beckman Coulter, A63881). Illumina libraries were pooled and sequenced on a NextSeq500 instrument on Paired-end 2x43 bp runs, using a NextSeq 500/550 High Output Kit v2 (75 cycles) kit.

treatment_protocol: Exponentially growing lymphoblastoid cells (~200x106), were pulse-labelled with 50 µM BrdU (Merck, B-5002) prior to recovery. Untreated cells were pulse labeled for 1 h, while all the other conditions were labeled for the last 3 h. Cells were then fixed in 70% ethanol and incubated overnight at 4°C in the presence of 15 µg/ml Hoescht 33342 (ThermoFisher Scientific, H3570). Cells were re-suspended in 1X PBS and sorted in six fractions at a time by flow cytometry based on their DNA content using a BD Biosciences INFLUX cell sorter. The first fraction contains cells in the second half of the G1 phase plus very early S (called G1/S1); the rest of the S phase was divided into four fractions (S2 to S5); and the last fraction contains cells in very late S, G2 and M phases (S6/G2/M). Aphidicolin (A0781) was obtained from Sigma-Aldrich.

tag: cell line

value: JEFF cells

tag: cell type

value: Epstein-Barr-virus-immortalized human B lymphocytes

tag: treatment

value: ATRi 100nM 16h + Aph 600nM 4h

tag: batch


title: Clec3b-tdT⁺ cells, Lenti-Klf4, rep3

city: Changchun

first: Chenchen

last: Zhao

state: Jilin Province

address: 5333 Xi’an Road

department: College of Veterinary Medicine

country: China

institute: Jilin University

description: Library name: B3

library_source: transcriptomic

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups. The genes with the parameter of false discovery rate (FDR) below 0.01 and absolute fold change ≥ 2.5 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm39/mm39
Supplementary files format and content: tab-delimited text files include raw counts and FPKM values for each Sample
Supplementary files format and content: tab-delimited text files include results of gene differential expression analysis performed using DESeq2 software

molecule: total RNA

organism: Mus musculus

source_name: Primary hepatic portal fibroblasts

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: Primary hepatic portal fibroblasts


title: Clec3b-tdT⁺ cells, Lenti-Klf4, rep2

description: Library name: B2


title: 1mM_NaVA_28h_after_HS_rep1

type: RNA

city: Warsaw

first: Olaf

last: Geyderowicz

state: Masovian Voivodeship

address: Ilji Miecznikowa 1

department: Faculty of Biology

country: Poland

institute: University of Warsaw

description: Gene expression data from 14-day-old seedlings transferred for additional 72 h onto medium supplemented with 1 mM NaVA, treated with 43.5°C for 4 h and collected 24 h after the end of the temperature treatment.

hyb_protocol: Samples were hybridized with GeneChip® Arabidopsis Gene 1.1 ST Array Strips

scan_protocol: Arrays were scanned in Gene Atlas Imaging Station (Affymetrix)

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) v4.0.3 with default settings

label: biotin

organism: Arabidopsis thaliana

source_name: 14-day-old Arabidopsis seedlings kept for additional 72h on medium with 1 mM NaVA before 4 h of heat shock at 43.5°C. Sampling 24 after the end of HS.

label_protocol: Total RNA was treated according to manufacturers protocol for GeneChip™ WT PLUS Reagent Kit (ThermoFisher Scientific, Waltham, MA, USA)

growth_protocol: Surface-sterilised Arabidopsis thaliana Col-0 seeds were sown on half-strenght and germinated for 14 days under 200 µmol/m2/s under 16 h photoperiod at 22°C.

extract_protocol: RNA was isolated using E.Z.N.A® Plant RNA Kit (Omega Bio-tek)

treatment_protocol: 14-day-old A.thaliana Col-0  seedlings grown on half-strength MS media were transferred onto fresh media with  1 mM sodium valerate (NaVA) or devoid of the inhibitor as control (C). After 72 h of growth on the new media, the plates with plants were transferred to an incubator set at 43.5°C for 4 h (HS). Immediately after the end of heat shock, the plants were returned to the growth chamber for regeneration. Plants were sampled at timepoints indicated in the SAMPLES section. In each case, 3 plantlets were pooled for each sample.

tag: sampling point


title: control_4h_after_HS_rep2

description: Gene expression data from 14-day-old seedlings transferred for additional 72 h onto control medium, treated with 43.5°C for 4 h and collected immediately after.

source_name: 14-day-old Arabidopsis seedlings kept for additional 72h on control medium before 4 h of heat shock at 43.5°C


title: ORG-0097_IO360_20211019 histologically normal breast tissue

status: Public on Mar 17 2026

city: Jacksonville

first: Derek

middle: Charles

last: Radisky

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

country: USA

institute: Mayo Clinic

description: Original RCC file: 20211019_Radisky IO360 run 2_ORG-97_02.RCC; Selected renamed RCC file: ORG-0097_IO360_20211019.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20211019; Cartridge: Radisky IO360 run 2; Lane: 2; MD5: e68802144721a39817128c2cf812a889

hyb_protocol: RNA was hybridized for 18 h at 65°C to the NanoString BC360 or IO360 CodeSet. Cartridges were processed on the nCounter Prep Station.

scan_protocol: Cartridges were scanned at 555 fields of view on the nCounter Digital Analyzer. All samples passed manufacturer QC thresholds used in the manuscript: imaging QC score > 0.85, binding density 0.1–2.25 spots/µm², and positive-control linearity R² > 0.95.

data_processing: The IO360_Raw_Matrix.xlsx values are complete raw NanoString counts extracted directly from the selected IO360 RCC files. This IO360 matrix contains 784 probes/features across 74 specimens (750 endogenous genes, 20 housekeeping probes, 8 negative controls, 6 positive controls). Raw RCC files were matched to specimens by exact specimen ID; when multiple candidate raw RCC files existed for the same specimen and panel, the latest RCC date was selected. The processed workbook sample ORG-0098 was matched to raw IO360 specimen ORG-0098 R per submitter instruction. Supplementary file IO360_processed_matrix.tsv retains the analyzed normalized values supplied in Combined IO360 and BC360.xlsx.

label: nanostring

source_name: histologically normal breast tissue

label_protocol: NanoString nCounter direct digital counting with panel-specific reporter and capture probes according to the manufacturer protocol; no separate external labeling step was performed.

growth_protocol: Not applicable. These are human surgical FFPE specimens and were not grown or cultured before RNA extraction.

extract_protocol: From each FFPE block, three consecutive 10 µm scrolls (approximately 50 mm² total tissue area) were deparaffinized in xylene and rehydrated through graded ethanol. RNA was extracted using the Qiagen RNeasy FFPE Kit (Cat. 73504) according to the manufacturer instructions. RNA integrity was assessed by spectrophotometry (A260/280 > 1.8) and DV200 (>40% required for inclusion). One hundred nanograms of RNA were used per hybridization.

treatment_protocol: Not applicable. Tissue was collected at surgery with no experimental ex vivo treatment before NanoString profiling.

tag: tissue

value: breast

value: FFPE surgical specimen

value: not specified

tag: panel

value: NHB

value: Black

tag: ethnicity

value: unknown

value: Pre

tag: parity

value: Parous

tag: breastfed

value: No

tag: density

tag: involution

value: Partial

value: Breast Reduction

tag: diagnosis

value: no


title: Sham_2, scRNA-seq

first: Lin

last: Lei

address: 5333 Xi’an Road, Changchun, Jilin, China

department: State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, College of Veterinary Medicine

description:
Library name: Sample 2
10X Genomics

library_source: transcriptomic single cell

data_processing:
Raw base-call files were demultiplexed and converted into FASTQ format using bcl2fastq software v2.20 (Illumina). Only confidently mapped, non-PCR duplicates with valid barcodes and unique molecular identifiers were utilized in generating the gene-barcode matrix, by using the CellRanger software v7.0.0 (10X Genomics) with standard settings and aligned to mm10/GRCm38 reference genome (Ensembl 105). Subsequent analysis was performed in R v4.1.3 using the generated count matrices generated by CellRanger.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver

extract_protocol:
Mice subjected BDL and Sham operation were first anesthetized. After cannulation of the inferior vena cava, Hanks' balanced salt solution (HBSS) without Ca2+ and Mg2+ containing 1% EDTA was used to perfuse the liver in situ retrograde perfusion through the portal vein for 5 min at 37°C. Then, NCD mice received a retrograde stepwise perfusion of HBSS with Ca2+ and Mg2+ containing 0.5 mg/mL collagenase Ⅳfor 10 min at 37°C, while CDAHFD mice and BDL mice received the same perfusion solution with a higher concentration of collagenase Ⅳ at 1 mg/mL. After perfusion, the liver was rapidly collected and carefully dispersed into ice-cold HBSS without Ca2+ and Mg2+. After removing as much liver parenchyma as possible, the minced bilio-vascular tree fragments were incubated in low glucose DMEM containing 0.075 mg/mL collagenase P, 0.02 mg/mL DNase, 3% FBS, 1% Hepes and 1% Penicillin-Streptomycin at 37°C for 15 min under agitation. The bilio-vascular fragments were then filtered and collected using a 350-mesh (40 µm) cell sieve. Following centrifugation at 1,250 rpm for 5 min at 4°C, the cell pellet was resuspended and incubated with 0.05% Trypsin-EDTA containing 0.02 mg/mL DNase for 15 min at 37°C under agitation. Next, the dissociated cells were gently and repeatedly pipetted and filtered three times through a 500-mesh (25 µm) cell sieve to obtain single-cell suspensions. Finally, the dead cells were removed from single-cell suspensions with the Dead Cell Removal kit according to the manufacturer’s protocol. Cell viability (> 95%) was determined using trypan blue staining.
10X Genomics Chromium Single-Cell 3’kits (V3) were used to prepare barcoded scRNA-seq libraries according to the manufacturer’s protocol. Single-cell suspensions were loaded onto 10X Chromium Single-Cell Controller Instrument to generated single cell gel beads in emulsions (GEMs), aiming to capture a total of 2,000-4,000 cells per library for Control samples (Sham mice), and 8,000-10,000 cells per library for BDL samples. After GEMs generation, DNA amplification and library construction were performed, and the libraries were sequenced on a Novaseq 6000 (Illumina) platform (paired-end multiplexing run,150 bp).

value: Liver

value: single-cell suspension from bilio-vascular tree fragments

tag: genotype

value: C57BL/6, WT

value: Sham operation


title: MM130079

city: New Orleans

first: Hong-Wen

last: Deng

state: LA

institute: Tulane University

description:
Library name: MM130079
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

data_processing:
Sequencing reads were quality-filtered and aligned to the human reference genome using BSMAP. Methylation levels at CpG sites were calculated as the ratio of methylated reads to total reads covering each site. CpG sites overlapping known SNPs were removed. Rank-based inverse normal transformation was applied for normalization. Reads with >10% unknown bases or >10% of bases with quality scores <20 were further excluded to obtain high-quality data. The cleaned reads were aligned to the GRCh37/hg19 human reference genome using BSMAP, then converted to GRCh38/hg38 using the UCSC LiftOver tool (https://genome.ucsc.edu/cgi-bin/hgLiftOver).
Assembly: GRCh38/hg38
Supplementary files format and content: Processed data files contain tab-delimited matrices of CpG-level DNA methylation beta values. Rows represent CpG loci with genomic coordinates, and columns represent individual samples. Chromosome-specific methylation matrices are provided in compressed format.

source_name: peripheral blood

extract_protocol:
Genomic DNA was extracted from purified peripheral blood monocytes using the QIAamp DNA Mini Kit (Qiagen) following the manufacturer’s protocol. DNA concentration and purity were evaluated using NanoDrop spectrophotometry and agarose gel electrophoresis.
Monocytes were isolated from peripheral blood mononuclear cells using negative selection. Genomic DNA was extracted and fragmented. Libraries were prepared following bisulfite conversion using the EZ DNA Methylation-Gold kit and sequenced on the Illumina HiSeq 4000 platform.

value: peripheral blood

value: monocytes

tag: population

value: European American

tag: Sex

value: male

tag: age

tag: bmi

tag: smoke

tag: alcohol drinking


title: APH06 rep1 S3

description:
Library name: Sample 9
Enrichement of BrdU labelled DNA (Replicate 1)
Aph_G1-S1_average.bw

tag: cell line

value: JEFF cells

tag: cell type

value: Epstein-Barr-virus-immortalized human B lymphocytes

tag: treatment

value: APH 600nM 4h

tag: batch


title: MM130031

description:
Library name: MM130031
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz

tag: tissue

value: African American


title: MM130074

description:
Library name: MM130074
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130029

description:
Library name: MM130029
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: APH06 rep1 G1/S1

description:
Library name: Sample 7
Enrichement of BrdU labelled DNA (Replicate 1)
Aph_G1-S1_average.bw


title: Sham_1, scRNA-seq

description:
Library name: Sample 1
10X Genomics


title: Clec3b-tdT⁺ cells, KLF4 (ChIP)

description: Library name: Clec3b-tdT⁺ cells, ChIP

data_processing:
The libraries were sequenced on an Illumina NovaSeq™ 6000 platform (Illumina), generating 150 bp paired-end reads. Base calling was performed using bcl2fastq (v2.17) for Novaseq output.
Raw sequencing data of FASTQ format were processed using fastp (v0.24.0) to obtain high-quality clean reads by removing adapter sequences, reads containing poly-N, and low-quality reads.
Clean reads were aligned to the mouse reference genome (mm39/GRCm39) using bowtie2 (v2.4.2), and the resulting alignments were stored in BAM files. Only uniquely mapped and non-duplicate reads were retained for downstream analyses.
For visualization, BAM files were merged (if applicable) and converted to bigWig format using the bamCoverage function from deepTools (v3.4.1).
Peak calling was performed using MACS2 (v2.2.7.1) with default parameters (-q 0.05) on uniquely mapped reads, using input DNA as background. The identified peaks were further subjected to gene annotation analysis and visualization using the Chipseeker R package (v1.44.0) and IGV software.
Assembly: mm39/GRCm39
Supplementary files format and content: PF_Input_mm39.bigwig: this file is in bigWig format, which stores genome-wide coverage data of mapped reads from the Input sample (control). The bigWig format allows efficient visualization of read density over the genome, commonly used in genome browsers (e.g., IGV, UCSC). Coverage values are normalized to reads per million (RPM) and represent the background signal.
Supplementary files format and content: PF_IP_mm39.bigwig: this file is also in bigWig format and contains genome-wide coverage data of mapped reads from the ChIP (IP) sample. It represents the signal enrichment (including both specific binding and background) after ChIP for a specific protein or histone mark. Like the Input file, coverage is normalized (RPM) and visualizable in genome browsers.
Supplementary files format and content: PF_peak_annotation.xls: this is a tab-delimited text file containing the annotation results of ChIP-seq peaks, generated using the ChIPseeker R package. The file includes detailed information about the genomic features associated with each identified peak, such as gene IDs, gene symbols, genomic locations, distances to transcription start sites (TSS), and the functional elements (e.g., promoter, exon, intron, intergenic) where the peaks are located. The annotations provide insights into the potential regulatory roles of the ChIP-seq peaks.

extract_protocol:
Clec3b-tdT⁺ cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and the reaction was quenched by the addition of glycine. Cells were washed twice with ice-cold PBS and harvested by scraping. Chromatin was fragmented by sonication in SDS lysis buffer using a Bioruptor (Scientz-IID, Scientz) to generate DNA fragments of approximately 100–500 bp. After preclearing with protein G agarose beads, the lysates were incubated overnight at 4 °C with either 2 µg of control IgG (CST, 2729S) or 2 µg of anti-KLF4 antibody (abcam, ab214666) for immunoprecipitation. Immune complexes were captured with protein G agarose beads, and cross-links were reversed by incubation at 65°C overnight.
The sequencing libraries of immunoprecipitated chromatin DNA were generated with varied index label by NEBNext® UltraTM DNA Library Prep Kit for Illumina (NEB, USA, cat. E7645L). Add End Repair Reaction Buffer (10X) and End Prep Enzyme Mix for end repair by the following condition: 20°C for 30min, 65°C for 30min. And then NEBNext Adaptor and Blunt/TA Ligase Master Mix was added to ligate adaptor at 20°C for 15min. USER Enzyme was added to remove base U of adaptor at 37°C for 5min. After purification with beads, products are amplified with PCR by the following conditions: initial denaturation at 98℃ for 10 sec; denaturation at 98℃ for 10 sec, annealing at 65℃ for 30 sec, and extension at 72℃ for 30 sec. The library size was selected and then purified with AMPure XP Beads. Qubit was used for library quantification and High-sensitivity DNA chip was used for test of library insert size.

value: Primary hepatic portal fibroblasts

value: Klf4 overexpression

tag: chip antibody


title: MM130066

description:
Library name: MM130066
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: control_28h_after_HS_rep2

description: Gene expression data from 14-day-old seedlings transferred for additional 72 h onto control medium, treated with 43.5°C for 4 h and collected 24 h after the end of the temperature treatment.

source_name: 14-day-old Arabidopsis seedlings kept for additional 72h on control medium before 4 h of heat shock at 43.5°C. Sampling 24 after the end of HS.

tag: sampling point


title: ATRi+Aph06 rep1 S4

description:
Library name: Sample 16
Enrichement of BrdU labelled DNA (Replicate 1)
Consensus.bw
ATRi-Aph06_G1-S1_average.bw

value: ATRi 100nM 16h + Aph 600nM 4h


title: control_28h_after_HS_rep1


title: control_28h_after_HS_rep3


title: ATRi rep1 S5

description:
Library name: Sample 5
Enrichement of BrdU labelled DNA (Replicate 1)
ATRi_G1-S1_average.bw

value: ATRi 100nM 16h


title: Clec3b-tdT⁺ cells (Input)

description: Library name: Clec3b-tdT⁺ cells, INPUT


title: ATRi+Aph06 rep1 S2

description:
Library name: Sample 14
Enrichement of BrdU labelled DNA (Replicate 1)
Consensus.bw
ATRi-Aph06_G1-S1_average.bw


title: APH06 rep1 S6/G2/M

description:
Library name: Sample 12
Enrichement of BrdU labelled DNA (Replicate 1)
Aph_G1-S1_average.bw


title: 1mM_NaVA_4h_after_HS_rep1

description: Gene expression data from 14-day-old seedlings transferred for additional 72 h onto medium supplemented with 1 mM NaVA, treated with 43.5°C for 4 h and collected immediately after.


title: 1mM_NaVA_4h_after_HS_rep3


title: Clec3b-tdT⁺ cells, Lenti-Klf4, rep4

description: Library name: B4


title: MM130048

description:
Library name: MM130048
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130057

description:
Library name: MM130057
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz


title: MM130020

description:
Library name: MM130020
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130042

description:
Library name: MM130042
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz


title: Clec3b-tdT⁺ cells, Lenti-Klf4, rep1

description: Library name: B1


title: MM130019

description:
Library name: MM130019
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: MM130034

description:
Library name: MM130034
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: 1mM_NaVA_24h_rep3

description: Gene expression data from 14-day-old seedlings transferred for additional 24 h onto medium supplemented with 1 mM NaVA

source_name: 14-day-old Arabidopsis seedlings 24 h after transfer to medium with 1 mM NaVA


title: APH06 rep1 S5

description:
Library name: Sample 11
Enrichement of BrdU labelled DNA (Replicate 1)
Aph_G1-S1_average.bw


title: APH06 rep1 S4

description:
Library name: Sample 10
Enrichement of BrdU labelled DNA (Replicate 1)
Aph_G1-S1_average.bw


title: 1mM_NaVA_72h_rep3

description: Gene expression data from 14-day-old seedlings transferred for additional 72 h onto medium supplemented with 1 mM NaVA

source_name: 14-day-old Arabidopsis seedlings 72 h after transfer to medium with 1 mM NaVA


title: control_4h_after_HS_rep3

description: Gene expression data from 14-day-old seedlings transferred for additional 72 h onto control medium, treated with 43.5°C for 4 h and collected immediately after.


title: MM130032

description:
Library name: MM130032
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: Clec3b-tdT⁺ cells, Lenti-Ctrl, rep2

description: Library name: A2


title: CYP12h group, female

city: Fuzhou

first: Guixuan

last: Zhou

state: Fujian

address: No.2 Xueyuan Road,Minhou

institute: Fuzhou University

data_processing:
The RNA sequencing data were mapped to the mouse genome assembly GRCm39 using the HISAT2 program.
Assembly: GRCm39
Supplementary files format and content: Shh GFP CYP gene_name_counts.txt

source_name: back skin

extract_protocol:
Total RNAs of the Shh-GFP cells were isolated using a RNA isolater Reagent (Vazyme, Nanjing, China), and quality was monitored by Agilent 2100 analysis.mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer.
First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified.

treatment_protocol: Hairs in the back skin of 7-8 weeks-old mice were removed by wax to induce anagen. CYP was intraperitoneally injected in mice 9 days after depilation at 150mg/kg to cause hair loss. Shh-expressing cells were isolated from hair follicles in mice before or 12 and 24 hours post CYP treatment using flow cytometry.

value: back skin

value: female


title: MM130028

description:
Library name: MM130028
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: APH06 rep1 S2

description:
Library name: Sample 8
Enrichement of BrdU labelled DNA (Replicate 1)
Aph_G1-S1_average.bw


title: lung, PVC100 treated, 2 months,rep1

city: Shanghai

first: manyi

last: pan

address: Manufacturing Bureau Road, Shanghai

department: Department of Respiratory and Critical Care Medicine

institute: Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

description: Library name: PVC100

data_processing:
Raw reads were processed using FastQC (version 0.11.4) for quality control. Low-quality reads were removed using fastp. Poly-A tails and adapter sequences were trimmed with Cutadapt (version 1.18). Reads were aligned to the GRCm38 (mm10) reference genome using STAR (version 2.5.3a) with default parameters. Gene counts were generated using featureCounts (version 1.6.2), with a UMI threshold of 30,000.
Assembly: GRCm38 mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

extract_protocol:
Lung tissues were dissociated into single-cell suspensions using sCelLive™ Tissue Preservation Solution, Singleron Python™ Automated Tissue Separator, and sCelLive™ Tissue Isolation Mix according to the manufacturer's instructions
Raw reads were processed using FastQC (version 0.11.4) for quality control. Low-quality reads were removed using fastp. Poly-A tails and adapter sequences were trimmed with Cutadapt (version 1.18). Reads were aligned to the GRCm38 (mm10) reference genome using STAR (version 2.5.3a) with default parameters. Gene counts were generated using featureCounts (version 1.6.2), with a UMI threshold of 30,000.

value: lung

value: primary cells

value: all cell types

tag: strain


title: ATRi rep1 S6/G2/M

description:
Library name: Sample 6
Enrichement of BrdU labelled DNA (Replicate 1)
ATRi_G1-S1_average.bw


title: Clec3b-tdT⁺ cells, Lenti-Ctrl, rep1

description: Library name: A1


title: MM130010

description:
Library name: MM130010
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz

value: peripheral blood


title: 1mM_NaVA_72h_rep1


title: control_24h_rep3

description: Gene expression data from 14-day-old seedlings transferred for additional 24 h onto control medium

source_name: 14-day-old Arabidopsis seedlings 24 h after transfer to control medium


title: ATRi rep1 S4

description:
Library name: Sample 4
Enrichement of BrdU labelled DNA (Replicate 1)
ATRi_G1-S1_average.bw


title: CYP24h group, bio rep2, male


title: MM130021

description:
Library name: MM130021
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz

value: monocytes


title: control group, bio rep1, male

value: PBS


title: control_24h_rep2


title: control_4h_after_HS_rep1


title: lung, control, 2 months,rep1

description: Library name: CON


title: MM130023

description:
Library name: MM130023
DNA methylation profiling
AFA_chr1_methylation_matrix.tsv.gz, AFA_chr2_methylation_matrix.tsv.gz, AFA_chr3_methylation_matrix.tsv.gz, AFA_chr4_methylation_matrix.tsv.gz, AFA_chr5_methylation_matrix.tsv.gz, AFA_chr6_methylation_matrix.tsv.gz, AFA_chr7_methylation_matrix.tsv.gz, AFA_chr8_methylation_matrix.tsv.gz, AFA_chr9_methylation_matrix.tsv.gz, AFA_chr10_methylation_matrix.tsv.gz, AFA_chr11_methylation_matrix.tsv.gz, AFA_chr12_methylation_matrix.tsv.gz, AFA_chr13_methylation_matrix.tsv.gz, AFA_chr14_methylation_matrix.tsv.gz, AFA_chr15_methylation_matrix.tsv.gz, AFA_chr16_methylation_matrix.tsv.gz, AFA_chr17_methylation_matrix.tsv.gz, AFA_chr18_methylation_matrix.tsv.gz, AFA_chr19_methylation_matrix.tsv.gz, AFA_chr20_methylation_matrix.tsv.gz, AFA_chr21_methylation_matrix.tsv.gz, AFA_chr22_methylation_matrix.tsv.gz

value: male


title: control group, female


title: MM130002

description:
Library name: MM130002
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: European American


title: Clec3b-tdT⁺ cells, Lenti-Ctrl, rep4

description: Library name: A4


title: control_24h_rep1


title: ATRi rep1 S3

description:
Library name: Sample 3
Enrichement of BrdU labelled DNA (Replicate 1)
ATRi_G1-S1_average.bw

value: JEFF cells

value: Epstein-Barr-virus-immortalized human B lymphocytes


title: MM130006

description:
Library name: MM130006
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: ZXY-8_L2_Q0248W0071

status: Public on Mar 15 2026

city: Nanning

first: Wang

last: Xi

state: Guangxi

address: 100 University East Road, Nanning City, Guangxi

department: School of Medicine

institute: Guangxi University

description: Library name: Sample14

data_processing:
Raw FASTQ reads were trimmed with Trimmomatic (v0.39) and aligned to the mouse mm10 genome using HISAT2 (v2.2.1). Gene-level counts were quantified with featureCounts (v2.0.1) using GENCODE vM25 annotation. Genes with low expression (average count < 10) were filtered out. Differential expression analysis was performed using DESeq2 (v1.38.3), with significance defined as adjusted P < 0.05 and |log2FC| > 1. GSEA was conducted using GSEA software (v4.1.0) against MSigDB Hallmark gene sets, with FDR q < 0.25 considered significant.
Assembly: mm10
Supplementary files format and content: .gz .csv

source_name: spleen

extract_protocol:
Splenic cDC1s were sorted by FACS from WT, E2A/HEB ΔDC, and Id2 ΔDC mice as live, singlet, lineage-negative (B220⁻NK1.1⁻TCRβ⁻) CD11c⁺MHCII⁺XCR1⁺CD172a⁻ cells with post-sort purity >97%. For stimulated conditions, sorted cDC1s were cultured with heat-killed Listeria monocytogenes-OVA (HKLM-OVA) for 6 hours prior to RNA extraction.
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM II RNA Library Prep Kit for Illumina  following manufacturer's protocols.

value: spleen

value: primary cell


title: A6_L3_UDI213

description: Library name: Sample13


title: EKO-HK_L2_UDI387

description: Library name: Sample9


title: A3_L1_UDI204

description: Library name: Sample12


title: control_72h_rep3

description: Gene expression data from 14-day-old seedlings transferred for additional 72 h onto control medium

source_name: 14-day-old Arabidopsis seedlings 72 h after transfer to control medium


title: ATRi rep1 S2

description:
Library name: Sample 2
Enrichement of BrdU labelled DNA (Replicate 1)
ATRi_G1-S1_average.bw


title: WTDC1HKLM9.23

description: Library name: Sample8


title: EKO-ctr_L2_UDI386

description: Library name: Sample6


title: EKODC10.5X10-6con

description: Library name: Sample5


title: EKODC10.5X10-69.13

description: Library name: Sample4


title: CYP24h group, bio rep1, female


title: WT-ctr_L2_UDI370

description: Library name: Sample3


title: CTRLPF_R1

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave. S1070

institute: Dana-Farber Cancer Institute

data_processing:
ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT samtools 1.16.1 ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS samtools 1.16.1 ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS samtools 1.16.1 ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX samtools 1.16.1 ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT samtools 1.16.1 ALIGN_BOWTIE2:BOWTIE2_TARGET_ALIGN bowtie2 2.4.4  pigz 2.6  samtools 1.16.1 AWK_EXTRACT_SUMMITS awk 1.3.4 AWK_NAME_PEAK_BED awk 1.3.4 CONSENSUS_PEAKS:AWK awk 1.3.4 CONSENSUS_PEAKS:BEDTOOLS_MERGE bedtools 2.30.0 CONSENSUS_PEAKS:SORT sort 8.3 CUSTOM_DUMPSOFTWAREVERSIONS python 3.11.0  yaml 6 DEDUPLICATE_PICARD:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT samtools 1.16.1 DEDUPLICATE_PICARD:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS samtools 1.16.1 DEDUPLICATE_PICARD:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS samtools 1.16.1 DEDUPLICATE_PICARD:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX samtools 1.16.1 DEDUPLICATE_PICARD:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT samtools 1.16.1 DEDUPLICATE_PICARD:PICARD_MARKDUPLICATES picard 2.27.4-SNAPSHOT DEEPTOOLS_COMPUTEMATRIX_GENE deeptools 3.5.1 DEEPTOOLS_COMPUTEMATRIX_PEAKS deeptools 3.5.1 DEEPTOOLS_PLOTHEATMAP_GENE deeptools 3.5.1 DEEPTOOLS_PLOTHEATMAP_PEAKS deeptools 3.5.1 DEEPTOOLS_QC:DEEPTOOLS_MULTIBAMSUMMARY deeptools 3.5.1 DEEPTOOLS_QC:DEEPTOOLS_PLOTCORRELATION deeptools 3.5.1 DEEPTOOLS_QC:DEEPTOOLS_PLOTFINGERPRINT deeptools 3.5.1 DEEPTOOLS_QC:DEEPTOOLS_PLOTPCA deeptools 3.5.1 EXTRACT_BT2_TARGET_META:AWK_SCRIPT awk 1.3.4 EXTRACT_PICARD_DUP_META:AWK awk 1.3.4 FASTQC_TRIMGALORE:FASTQC fastqc 0.11.9 FASTQC_TRIMGALORE:TRIMGALORE cutadapt 2.1  trim_galore 0.6.6 FILTER_READS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS samtools 1.16.1 FILTER_READS:SAMTOOLS_INDEX samtools 1.16.1 FILTER_READS:SAMTOOLS_SORT samtools 1.16.1 FILTER_READS:SAMTOOLS_VIEW samtools 1.15.1 FRAG_LEN_HIST numpy 1.22.3  pandas 1.4.2  python 3.9.12  seaborn 0.11.2 MARK_DUPLICATES_PICARD:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT samtools 1.16.1 MARK_DUPLICATES_PICARD:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS samtools 1.16.1 MARK_DUPLICATES_PICARD:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS samtools 1.16.1 MARK_DUPLICATES_PICARD:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX samtools 1.16.1 MARK_DUPLICATES_PICARD:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT samtools 1.16.1 MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES picard 2.27.4-SNAPSHOT PEAK_QC:BEDTOOLS_INTERSECT bedtools 2.30.0 PEAK_QC:CALCULATE_PEAK_REPROD dask 2022.04.1  numpy 1.22.3  pandas 1.4.2  python 3.9.12 PEAK_QC:CONSENSUS_PEAK_COUNTS bedtools 2.30.0 PEAK_QC:CUT_CALC_REPROD cut 8.3 PEAK_QC:PLOT_CONSENSUS_PEAKS numpy 1.22.3  pandas 1.4.2  python 3.9.12  upsetplot 0.6.0 PEAK_QC:PRIMARY_PEAK_COUNTS bedtools 2.30.0 PREPARE_GENOME:GTF2BED perl 5.26.2 PREPARE_GENOME:SAMTOOLS_FAIDX samtools 1.16.1 PREPARE_GENOME:TABIX_BGZIPTABIX tabix 1.12 PREPARE_GENOME:TARGET_CHROMSIZES getchromsizes 1.16.1 PREPARE_PEAKCALLING:BEDTOOLS_SORT bedtools 2.30.0 PREPARE_PEAKCALLING:DEEPTOOLS_BAMCOVERAGE deeptools 3.5.1 PREPARE_PEAKCALLING:UCSC_BEDCLIP ucsc 377 PREPARE_PEAKCALLING:UCSC_BEDGRAPHTOBIGWIG ucsc 377 PRESEQ_LCEXTRAP preseq 3.1.1 SAMTOOLS_CUSTOMVIEW samtools 1.16.1 SEACR_CALLPEAK_IGG bedtools 2.30.0  r-base 4.0.2  seacr 1.3
Assembly: mm10
Supplementary files format and content: bigwig files with CPM normalized signal intensities
Library strategy: Cut&Run

source_name: breast cancer

growth_protocol: Specified cells were injeccted into mammary fat pads of A/J mice and mice were treated with either DMSO or EED226.

extract_protocol:
At endpoint, tumors were collected, minced into small pieces using scalpels and digested with 2 mg/ml collagenase IV, 2mg/ml hyaluronidase and 2 mg/ml BSA in DMEM/F12 at 37C for 60 minutes. Afterwards, cells were stained with LIVE/DEAD Aqua, CD45 and Epcam antibodies and sorted for live cells, CD45-negative, Epcam-positive cells.
Cut&Run libraries were prepared using IDT xGen DNA library prep reagents on a Beckman Coulter Biomek i7 liquid handling platform from approximately 1ng of DNA with 14 cycles of PCR amplification according to manufacturer’s protocol. Finished sequencing libraries were quantified by Qubit fluorometer and Agilent TapeStation 2200. Library pooling and indexing was evaluated with shallow sequencing on an Illumina NovaSeq X Plus. Subsequently, libraries were sequenced on an Illumina NovaSeq X Plus targeting 20 million 150bp read pairs by the Molecular Biology Core facilities at Dana-Farber Cancer Institute.

value: breast cancer

value: sorted tumor cells

value: WGD- and WGD+

value: DMSO


title: CYP24h group, male

value: back skin


title: Fus_EED_R2

value: WGD+


title: Fus_EED_R3


title: DP_EED_R2

value: WGD-


title: Fus_Veh_R2


title: control_72h_rep1


title: Fus_Veh_R1


title: DP_EED_R1


title: Fus_Veh_R3


title: MM130017

description:
Library name: MM130017
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: CYP12h group, bio rep2, female

value: female


title: DP_EED_R3


title: DP_Veh_R3


title: CYP12h group, bio rep1, female


title: Adu_sds_Day21_F2

city: Xuzhou

first: Gao

last: can

state: Jiangsu

address: 209 Tongshan Road

institute: Jiangsu Province Key Laboratory of Anesthesiology Xuzhou Medical University

description: Library name: Adu_sds_Day21_F2

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Homo sapiens reference genome using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: hg38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

molecule: polyA RNA

source_name: Brain tissue

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: Brain tissue


title: Clec3b-tdT⁺ cells, Lenti-Ctrl, rep3

description: Library name: A3

value: Primary hepatic portal fibroblasts


title: Adu_sds_Day21_F1

description: Library name: Adu_sds_Day21_F1


title: Adu_sds_Day1_B4

description: Library name: Adu_sds_Day1_B4


title: DP_Veh_R2


title: control_72h_rep2


title: Adu_sds_Day21_F4

description: Library name: Adu_sds_Day21_F4


title: 1mM_NaVA_72h_rep2

description: Gene expression data from 14-day-old seedlings transferred for additional 72 h onto medium supplemented with 1 mM NaVA


title: Adu_sds_Day1_B3

description: Library name: Adu_sds_Day1_B3


title: DP_Veh_R1


title: Adu_sds_Day1_B2

description: Library name: Adu_sds_Day1_B2


title: ATRi rep1 G1/S1

description:
Library name: Sample 1
Enrichement of BrdU labelled DNA (Replicate 1)
ATRi_G1-S1_average.bw

source_name: JEFF cells

value: ATRi 100nM 16h


title: Adu_sds_Day1_B1

description: Library name: Adu_sds_Day1_B1


title: Adu_ctrl_Day21_E2

description: Library name: Adu_ctrl_Day21_E2


title: lung, PE100 treated, 2 months,rep1

description: Library name: PE100

value: lung

value: primary cells

value: all cell types


title: 1mM_NaVA_24h_rep2

description: Gene expression data from 14-day-old seedlings transferred for additional 24 h onto medium supplemented with 1 mM NaVA


title: Adu_ctrl_Day21_E3

description: Library name: Adu_ctrl_Day21_E3


title: 1mM_NaVA_24h_rep1


title: MM130011

description:
Library name: MM130011
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz

value: peripheral blood

value: monocytes

value: European American

value: male


title: lung, PVC1 treated, 2 months,rep1

description: Library name: PVC1


title: Adu_ctrl_Day21_E4

description: Library name: Adu_ctrl_Day21_E4


title: F8

type: genomic

city: torrance

first: Omid

last: Khorram

state: CA

address: 1124  w carson st

institute: The lundquist Institute at UCLA medical center

description:
MeDIP-chip two-color microarray
hg19

hyb_protocol: Labeled MeDIP DNA and input DNA were co-hybridized onto Arraystar Human ncRNA Promoter Microarrays (4×180K format, Agilent SurePrint G3 platform) according to the manufacturer’s protocol. The arrays cover approximately 27,248 lncRNA promoter regions and 622 miRNA promoter regions with ~180,000 probes tiled across promoter regions.

scan_protocol: Following hybridization and washing, arrays were scanned using an Agilent DNA Microarray Scanner (G2505C). Raw signal intensities were extracted using Agilent Feature Extraction software (version 11.0.1.1).

data_processing: Raw signal intensities were extracted using Agilent Feature Extraction software. Log2 ratios of MeDIP versus input signals were calculated for each probe. Data normalization was performed using median-centering, quantile normalization, and linear smoothing with Bioconductor packages including Ringo, limma, and MEDME. Methylation enrichment peaks were identified using a sliding-window peak-finding algorithm implemented in NimbleScan v2.5. Differential enrichment peaks between experimental groups were determined using the M′ value method.

source_name: Fibroid #8

label_protocol: For MeDIP-chip experiments, 1 μg of sonicated genomic DNA was immunoprecipitated using a mouse monoclonal anti-5-methylcytosine antibody (Diagenode). The immunoprecipitated DNA (MeDIP DNA) and corresponding input DNA were labeled with Cy5- and Cy3-labeled random 9-mer primers, respectively.

growth_protocol: Human uterine fibroid and matched myometrium tissues were obtained during surgery and processed immediately after collection. Tissue samples were rinsed with PBS to remove blood and stored at −80°C until genomic DNA extraction.

extract_protocol: Genomic DNA was extracted from tissue samples using the DNeasy Blood & Tissue Kit (Qiagen) following the manufacturer's instructions. DNA concentration and purity were assessed using a NanoDrop ND-1000 spectrophotometer. Purified genomic DNA was sonicated to generate fragments of approximately 200–1000 bp prior to methylated DNA immunoprecipitation (MeDIP).

treatment_protocol: No experimental treatment was applied. Samples represent native tissue specimens collected from human subjects.

tag: sample type

value: Purified genomic DNA as total input

value: Purified genomic DNA after IP with anti-5-methylcytosine (5mc) antibody


title: M7

description:
MeDIP-chip two-color microarray
hg19

source_name: Myometrium #7


title: Adu_ctrl_Day21_E1

description: Library name: Adu_ctrl_Day21_E1


title: control group, bio rep2, female

value: PBS


title: M8

description:
MeDIP-chip two-color microarray
hg19

source_name: Myometrium #8


title: MM130012

description:
Library name: MM130012
DNA methylation profiling
CAU_chr1_methylation_matrix.tsv.gz, CAU_chr2_methylation_matrix.tsv.gz, CAU_chr3_methylation_matrix.tsv.gz, CAU_chr4_methylation_matrix.tsv.gz, CAU_chr5_methylation_matrix.tsv.gz, CAU_chr6_methylation_matrix.tsv.gz, CAU_chr7_methylation_matrix.tsv.gz, CAU_chr8_methylation_matrix.tsv.gz, CAU_chr9_methylation_matrix.tsv.gz, CAU_chr10_methylation_matrix.tsv.gz, CAU_chr11_methylation_matrix.tsv.gz, CAU_chr12_methylation_matrix.tsv.gz, CAU_chr13_methylation_matrix.tsv.gz, CAU_chr14_methylation_matrix.tsv.gz, CAU_chr15_methylation_matrix.tsv.gz, CAU_chr16_methylation_matrix.tsv.gz, CAU_chr17_methylation_matrix.tsv.gz, CAU_chr18_methylation_matrix.tsv.gz, CAU_chr19_methylation_matrix.tsv.gz, CAU_chr20_methylation_matrix.tsv.gz, CAU_chr21_methylation_matrix.tsv.gz, CAU_chr22_methylation_matrix.tsv.gz


title: M6

description:
MeDIP-chip two-color microarray
hg19

source_name: Myometrium #6


title: F7

description:
MeDIP-chip two-color microarray
hg19

source_name: Fibroid #7


title: Adu_ctrl_Day1_A3

description: Library name: Adu_ctrl_Day1_A3


title: Adu_ctrl_Day1_A2

description: Library name: Adu_ctrl_Day1_A2


title: Adu_ctrl_Day1_A4

description: Library name: Adu_ctrl_Day1_A4


title: Adu_ctrl_Day1_A1

description: Library name: Adu_ctrl_Day1_A1


title: Ado_sds_Day21_H4

description: Library name: Ado_sds_Day21_H4


title: Ado_sds_Day21_H1

description: Library name: Ado_sds_Day21_H1


title: F4

description:
MeDIP-chip two-color microarray
hg19

source_name: Fibroid #4


title: EKODC10.5MHKLM

description: Library name: Sample10

value: spleen

value: primary cell


title: WTDC10.5MHKLM

description: Library name: Sample7


title: M5

description:
MeDIP-chip two-color microarray
hg19

source_name: Myometrium #5


title: Fus_EED_R1

value: breast cancer

value: sorted tumor cells

value: WGD+


title: WTDC10.5X10-6con

description: Library name: Sample2


title: WTDC10.5X10-69.13

description: Library name: Sample1


title: Adu_sds_Day21_F3

description: Library name: Adu_sds_Day21_F3

value: Brain tissue


title: Ado_sds_Day21_H2

description: Library name: Ado_sds_Day21_H2


title: A1_L2_UDI202

description: Library name: Sample11


title: Ado_sds_Day1_D4

description: Library name: Ado_sds_Day1_D4


title: F3

description:
MeDIP-chip two-color microarray
hg19

source_name: Fibroid #3


title: M3

description:
MeDIP-chip two-color microarray
hg19

source_name: Myometrium #3


title: Ado_sds_Day21_H3

description: Library name: Ado_sds_Day21_H3


title: Ribo-seq for RPSA

city: Shenyang

first: Wensu

last: Liu

address: 77 Puhe Road, Shenbei District

institute: China Medical University

description: Library name: siRPSA

data_processing:
(1) Raw reads were quality-trimmed (Trim Galore!); (2) rRNA/tRNA contaminants were removed (SortMeRNA); (3) Reads were aligned to reference genome (STAR); (4) P-site offset was calculated and applied (based on 3-nt periodicity); (5) Read depth was normalized to RPFs per million (RPM); (6) Translation efficiency (TE) was computed as RPFs/RNA-seq reads; (7) ORFs were annotated using custom scripts against RefSeq and Ensembl.
Assembly: Human genome assembly GRCh38/hg38 (ENSEMBL release 110) was used as the reference for read alignment and annotation.
Supplementary files format and content: .xls files with rpkm for all samples
Library strategy: Ribo-Seq

extract_protocol:
Cells were lysed in buffer containing CHX, and total RNA was digested with low-concentration RNase I to degrade unprotected mRNA. Ribosome-protected fragments (RPFs, 26–35 nt) were purified by sucrose cushion ultracentrifugation, followed by phenol-chloroform extraction and ethanol precipitation.
RPFs were dephosphorylated, 3′-adaptors were ligated, and 5′-phosphorylated adaptors were ligated to generate double-stranded cDNA. cDNA was amplified by PCR (12–15 cycles), size-selected (25–35 nt), and purified without gel extraction using SPRI beads. Library quality was assessed via Bioanalyzer (Agilent).

value: prostate cancer


title: IC19 lung fibroblast secretome 3

city: Manchester

first: Amaya

last: Viros

address: Wilmslow Road

department: Skin Cancer Ageing

country: United Kingdom

institute: Cancer Research UK

description: Library name: IC19_lung_3

data_processing:
The RNA sequencing reads underwent quality checking using the FASTQC program. Then, Trim Galore v. 0.6.10 was utilized to inspect and remove adapter contamination. Subsequently, the clean reads were aligned to the human reference genome assembly (GRCh38) using the STAR aligner v.2.5.1b in either single-end or paired-end mode based on the sequencing protocol, with default parameters. The mapped data were then converted to gene level integer read counts using featureCounts and the Ensemble gene annotation (Homo_sapiens.GRCh38.85.gtf).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file contains raw counts for all samples

growth_protocol: Cells were seeded at 80% confluence a day prior to the treatment. Prior to treatment, cells were washed twice with PBS.

extract_protocol:
RNA from cells were extracted using Qiagen RNA extraction kit (Qiagen, Cat no. 74104) as per manual instructions
Libraries were prepared by Azenta/GENEWIZ using their Standard Bulk RNA-Seq workflow with poly(A) selection and sequenced on an Illumina NovaSeq platform (paired-end 2×150 bp)

treatment_protocol: SCC cells were treated for 24 hours with serum free DMEM (control) or serum free conditioned media (DMEM) collected from dermal, oral, or lung fibroblasts. Conditioned media was collected by culturing firboblasts in serum free DMEM for 72 hours before collecting secretome. Serum free DMEM contained 1% penicillin streptomycin, 1x L-glutamine.

value: Cutaneous SCC

value: Lung firboblast secretome


title: Ribo-seq for NC

description: Library name: NC


title: F6

description:
MeDIP-chip two-color microarray
hg19

source_name: Fibroid #6


title: Ado_sds_Day1_D3

description: Library name: Ado_sds_Day1_D3


title: F2

description:
MeDIP-chip two-color microarray
hg19

source_name: Fibroid #2


title: M4

description:
MeDIP-chip two-color microarray
hg19

source_name: Myometrium #4


title: F1

description:
MeDIP-chip two-color microarray
hg19

source_name: Fibroid #1


title: Wildtype neural progenitor cells R1

city: Neuherberg

first: Dierk

last: Niessing

address: Ingolstädter Landstraße 1

department: Institute of Structural Biology

country: Germany

institute: Helmholtz Zentrum München

description: Library name: NPC_WT_replicate1

data_processing:
The prepared libraries were sequenced on a HiSeq 1500 machine (Illumina) in paired-end 60 bp mode, with each library sequenced with 35 million reads (done at Gene Center, LMU Munich).
Data analysis of RNA Sequencing data was done with the public galaxy.eu platform. First, quality control of sequencing results was performed on all samples using the FastQC tool (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were mapped to human genome (GRCh38.p13) using STAR tool.
Reads per gene were analyzed with htseq tool.
Assembly: GRCh38.p13
Supplementary files format and content: Tab delimited files with raw counts

source_name: Neural progenitor cell

extract_protocol:
Each replicate was harvested from one 100% confluent 10 cm culture dish, comprising approximately 3-5x10^6 cells. Cells were first washed with ice-cold 1x PBS, before scraping them off the dish with ice-cold 900 µL TRIzol for resuspension. Cell suspensions were immediately transferred to RNase-free 1.5 mL tubes and stored at -80 °C and handed over to Gene Center (LMU Munich) for RNA extraction, library preparation, and RNA sequencing.
RNA extraction and library preparation were performed using the SMARTer Stranded Total RNA-Seq Kit v3 (Takara).

value: Neural progenitor cell

value: wild type


title: F5

description:
MeDIP-chip two-color microarray
hg19

source_name: Fibroid #5


title: M2

description:
MeDIP-chip two-color microarray
hg19

source_name: Myometrium #2


title: M1

description:
MeDIP-chip two-color microarray
hg19

source_name: Myometrium #1


title: PURA knockout neural progenitor cells R2

description: Library name: NPC_KO_replicate2

value: PURA knockout


title: Ado_sds_Day1_D2

description: Library name: Ado_sds_Day1_D2

source_name: Brain tissue


title: Wildtype induced pluripotent stem cells R4

description: Library name: iPSC_WT_replicate4

source_name: iPSC

value: iPSC


title: Ado_sds_Day1_D1

description: Library name: Ado_sds_Day1_D1


title: PURA knockout neural progenitor cells R4

description: Library name: NPC_KO_replicate4


title: PURA knockout induced pluripotent stem cells R3

description: Library name: iPSC_KO_replicate3


title: PURA knockout induced pluripotent stem cells R1

description: Library name: iPSC_KO_replicate1


title: mouse_colorectal_organoid_NAP_biological_replicate_2

city: Beijing

first: Qingtao

last: Meng

address: No.10, West Tou Tiao, Youan Men Wai, Fengtai District

institute: capital Medical University

description:
Library name: RNA_seq_N2
Colorectal organoid derived from a 6–8-week-old female Mus musculus, treated with NAP, biological replicate 2.

data_processing:
Raw sequencing reads were processed using Trimmomatic (v0.39) to remove adapter sequences and low-quality reads. Clean reads were aligned to the GRCm39 mouse reference genome using HISAT2 (v2.2.1). Gene-level read counts were quantified with featureCounts (Subread v2.0.8).
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file includes raw read counts for each sample.
Supplementary files format and content: Tab-delimited text file includes FPKM expression values for each sample.

source_name: Colorectal organoids

growth_protocol: Female C57BL/6J mice (6–8 weeks old, 20–22 g)

extract_protocol:
The colon tissue extracted from mice was cut into small sections. Following a wash with PBS, the small tissue fragments underwent digestion with Gentle Cell Dissociation Reagent (GCDR) (100-1077, Stemcell) in a shaking state at 20 rpm for 20 minutes, and the resulting mixture was filtrated through a 70-μm filter. After a subsequent centrifugation, the pellet was resuspended in cold DMEM/F12 medium (C11330500BT, Gibco). The centrifugation and wash were repeated, and the pellet was suspended in IntestiCult organoid growth medium (06005, Stemcell), and an equivalent volume of Matrigel matrix was added. The mixture was poured into a 24-well plate. Finally, 500 μL of IntestiCult organoid growth medium was added. Total RNA was extracted from all samples using TRIzol™ reagent (Invitrogen, Thermo Fisher Scientific).
RNA-Seq experiment was performed by Novogene, employing standard Illumina sequencing procedures for mRNA-seq. Total RNA was used for mRNA enrichment with poly(T) oligo-attached magnetic beads, followed by fragmentation prior to cDNA synthesis. First-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis. The resulting cDNA underwent end repair, A-tailing, adapter ligation, size selection, PCR amplification, and purification. Library quality and concentration were assessed using a Qubit 2.0 Fluorometer and an Agilent 2100 Bioanalyzer. Quantified libraries will be pooled and sequenced on Illumina platforms (NovaSeq 6000), according to effective library concentration and data amount.

treatment_protocol: Organoids were treated with 10 pM NAP for 48 hours, and control organoids were treated with PBS as vehicle control under identical conditions.

value: Colorectal organoids

value: NAP treatment


title: MAR-3.6.2, 24 hrs 0507 (1)

city: Duarte

first: Le Xuan Truong

last: Nguyen

address: 1500 E. Duarte Road

department: Hematology/Bone Marrow T MC

institute: City of Hope

description: Library name: 52591_HTB-0507 3.6.2 1

data_processing:
NovaSeq Control Software 1.2.0.28691 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.
Assembly: GRCh38.p14 RNA sequences (Transcriptome)
Supplementary files format and content: comma-delimited csv file includes raw counts for each samples

source_name: Bone Marrow Cells

extract_protocol:
RNA was harvested using miRNeasy Mini Kit (Qiagen). DNA digestion was conducted during RNA extraction. 10 ug of total RNA was prepared for the downstream processing for RNA-sequencing.
RNA libraries for RNA-seq were prepared using KAPA mRNA Hyperprep Kit following manufacturer's protocols.

value: Bone Marrow Cells

value: Patient-drived primary CD34+CD38- blast

value: Acute Myeloid Leukemia


title: Vehicle, 24 hrs 0507 (3)

description: Library name: 52590_HTB-0507 Veh 3


title: PURA knockout neural progenitor cells R3

description: Library name: NPC_KO_replicate3


title: Ado_ctrl_Day21_G4

description: Library name: Ado_ctrl_Day21_G4


title: PURA knockout neural progenitor cells R1

description: Library name: NPC_KO_replicate1


title: Ado_ctrl_Day21_G3

description: Library name: Ado_ctrl_Day21_G3


title: Wildtype neural progenitor cells R4

description: Library name: NPC_WT_replicate4


title: Ado_ctrl_Day21_G2

description: Library name: Ado_ctrl_Day21_G2


title: No Treatment 0507 (3)

description: Library name: 52587_HTB-0507 Ctrl 3


title: Ado_ctrl_Day21_G1

description: Library name: Ado_ctrl_Day21_G1


title: Wildtype neural progenitor cells R3

description: Library name: NPC_WT_replicate3


title: Wildtype neural progenitor cells R2

description: Library name: NPC_WT_replicate2


title: Ado_ctrl_Day1_C3

description: Library name: Ado_ctrl_Day1_C3


title: Ado_ctrl_Day1_C2

description: Library name: Ado_ctrl_Day1_C2


title: No Treatment 0507 (1)

description: Library name: 52585_HTB-0507 Ctrl 1


title: BMDM cells, ATRA, rep3 (RNA)

city: Guangzhou

first: dingdang

last: Yu

address: No. 106, Zhongshan 2nd Road, Yuexiu District

institute: Guangdong Provincial People's Hospital

description: Library name: ATRA_RNA_rep3

data_processing:
For ATAC-seq, after trimming the adaptors and low-quality reads with Trim Galore v0.6.6, the remaining reads were align to the mm10 genome using Bowtie 2 v2.3.5.1.
SAMtools v1.11 and Picard v2.23.3 were used to remove low mapping quality reads, mitochondrion DNA and PCR duplicates.
Reads counts adjusted to reads per kilobase per million mapped reads (RPKM) using deeptools v2.5.7.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: bone marrow

extract_protocol:
For ATAC-seq assays,cells were lysed in ice-cold lysis buffer, followed by resuspending in fragmentation buffer and incubation at 37 ℃ for 30 min. The fragmented DNA products were extracted using ATAC DNA Extract Beads.
ATAC-seq library was performed according to the manual of the Hyperactive ATAC‐Seq Library Prep Kit for Illumina (Vazyme, TD711).

treatment_protocol: 200 nM ATRA or DMO for 24hr

value: bone marrow

value: BMDM

value: macrophage

value: WT

value: ATRA


title: Ado_ctrl_Day1_C1

description: Library name: Ado_ctrl_Day1_C1

value: Brain tissue


title: PURA knockout induced pluripotent stem cells R4

description: Library name: iPSC_KO_replicate4


title: Ado_ctrl_Day1_C4

description: Library name: Ado_ctrl_Day1_C4


title: mouse_colorectal_organoid_NAP_biological_replicate_6

description:
Library name: RNA_seq_N6
Colorectal organoid derived from a 6–8-week-old female Mus musculus, treated with NAP, biological replicate 6.


title: mouse_colorectal_organoid_NAP_biological_replicate_4

description:
Library name: RNA_seq_N4
Colorectal organoid derived from a 6–8-week-old female Mus musculus, treated with NAP, biological replicate 4.


title: FG214-H175I-EN

type: protein

first: Stephen

last: Gisselbrecht

state: MA

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics, Department of Medicine

institute: Brigham and Women's Hospital

hyb_protocol: First, microarrays were double stranded by on-slide primer extension, as described in Berger et al. (Berger et al. Nat Biotechnol. 2006 (PMID 16998473)). The primer extension mixture contains Cy3-conjugated dUTP, to allow for quantification of the relative amount of double stranded DNA on each spot. Double stranded microarrays were pre-wetted in standard phosphate buffered saline (PBS) (10mM PO43-, 137 mM NaCl, 2.7 mMKCl, pH7.4) / 0.01% Triton-X 100 for 5 minutes. PBS / 2% (wt/vol) nonfat dried milk (Sigma) was applied to individual chambers of an eight-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarray was incubated for 1 hour at room temperature. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% (vol/vol) Triton X-100 for 2 min. Proteins were diluted in a 75-μl protein binding mixture containing PBS / 2% (wt/vol) milk or EN (138 mM potassium glutamate, pH 7.2, 12 mM sodium bicarbonate, 0.8 mM magnesium chloride) / 2% (wt/vol) milk, 51.3 ng/μl salmon testes DNA (Sigma), 0.2 μg/μl bovine serum albumin (New England Biolabs), 32.67 micromolar zinc acetate, and, where indicated, 500 mM imidazole. Pre-incubated protein binding mixtures were applied to individual chambers of an eight-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 hour at room temperature. Microarrays were again washed once with PBS/ 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS/ 0.01% (vol/vol) Triton X-100 for 2 minutes. Alexa-488-conjugated mouse monoclonal anti-HA antibody (Invitrogen A-21287) was diluted to 50μg/ml in PBS / 2% (wt/vol) milk and applied to individual chambers of an eight-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 30 minutes at room temperature. Microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each incubation step, microarrays and cover slips were disassembled in a staining dish filled with the first wash solution. All washes were performed in Coplin jars at room temperature on an orbital shaker at 125 rpm. Following each series of washes, microarrays were rinsed in PBS and slowly removed to ensure removal of detergent and uniform drying.

scan_protocol: Cy3 signal was scanned to assess double-stranding efficiency and Alexa488 signal was scanned at multiple photomultiplier tube gain settings on a Molecular Devices GenePix 4400A microarray scanner.

data_processing: The scanned images were analyzed with GenePix software to produce separate .gpr files for each chamber associating background-subtracted median signal intensity at a probe to probe sequence; scans were combined with Masliner and the resulting file was normalized to Cy3 signal and analyzed with the Universal PBM Analysis Suite (Berger et al., Nature Biotechnology 2006) to report Enrichment scores and Median Signal Intensity for each 8-mer in the processed data files.

molecule: protein

organism: Fimbriimonas ginsengisoli

source_name: bacterial expression and purification

label_protocol: Agilent microarrays (AMADID #030236) containing all 10-nt sequences were made double-stranded by primer annealing and on-array extension with Cy3-labelled nucleotides to monitor double-stranding efficiency; HA-tagged proteins were detected with Alexa488-labelled anti-HA antibody.

growth_protocol: Constructs of FG214 wild type and H175I were generated with C-terminal human influenza hemagglutinin (HA) and 6His tags.

extract_protocol: The cells were lysed by sonification, and the lysate was cleared by centrifuging at 10,000 x g for 30 minutes at 4°C. The supernatant was collected and filtered through a 0.2 µm syringe filter. For affinity purification, the protein was loaded onto a 5 mL HisTrap (Cytiva) column preequilibrated with Buffer A. The column was washed with 10 column volumes (CVs) of Buffer A before eluting the protein with buffer B (50mM Tris-HCl pH 8.0, 500 mM NaCl, 500 mM imidazole). The eluate was applied to a Superdex 200 10/300 (Cytiva) column preequilibrated with assay buffer (50 mM sodium phosphate pH 7.0 and 50 mM NaCl).

treatment_protocol: FG214 was recombinantly expressed in BL21(DE3) E. coli (Stratagene) in M9 minimal media plus 1 mM 5-aminolevulinic acid at 16°C overnight. Expression was induced with 1 mM isopropyl β-D-1-thiogalactopyranoside.

value: bacterial


title: mouse_colorectal_organoid_NAP_biological_replicate_3

description:
Library name: RNA_seq_N3
Colorectal organoid derived from a 6–8-week-old female Mus musculus, treated with NAP, biological replicate 3.


title: mouse_colorectal_organoid_NAP_biological_replicate_5

description:
Library name: RNA_seq_N5
Colorectal organoid derived from a 6–8-week-old female Mus musculus, treated with NAP, biological replicate 5.


title: PURA knockout induced pluripotent stem cells R2

description: Library name: iPSC_KO_replicate2


title: Vehicle, 24 hrs 415 (3)

description: Library name: 52581_HTB-415 Veh 3


title: MAR-3.6.2, 24 hrs 0507 (3)

description: Library name: 52593_HTB-0507 3.6.2 3


title: FG214-WT-EN


title: Wildtype induced pluripotent stem cells R1

description: Library name: iPSC_WT_replicate1


title: BMDM cells, H3K27ac, DMSO, rep1

description: Library name: DMSO_H3K27ac_rep1

data_processing:
For ATAC-seq, after trimming the adaptors and low-quality reads with Trim Galore v0.6.6, the remaining reads were align to the mm10 genome using Bowtie 2 v2.3.5.1.
SAMtools v1.11 and Picard v2.23.3 were used to remove low mapping quality reads, mitochondrion DNA and PCR duplicates.
Reads counts adjusted to reads per kilobase per million mapped reads (RPKM) using deeptools v2.5.7.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: Cut&Tag

tag: cut&tag antibody

value: DMSO


title: mouse_colorectal_organoid_control_biological_replicate_4

description:
Library name: RNA_seq_C4
Colorectal organoid derived from a 6–8-week-old female Mus musculus, no treatment, biological replicate 4.

value: Control


title: Wildtype induced pluripotent stem cells R3

description: Library name: iPSC_WT_replicate3

tag: genotype

value: wild type


title: mouse_colorectal_organoid_control_biological_replicate_5

description:
Library name: RNA_seq_C5
Colorectal organoid derived from a 6–8-week-old female Mus musculus, no treatment, biological replicate 5.


title: input

description: Library name: sample2

data_processing:
Raw FASTQ reads were aligned to the mouse reference genome (mm10) using Bowtie2 (v2.4.4) with default parameters (--very-sensitive). Duplicate reads were marked and removed using Picard Tools (v2.26.0). Peak calling was performed using MACS2 (v2.2.7.1) with the callpeak command (parameters: -q 0.01 --extsize 200 --nomodel), using the IgG sample as control. Peaks were annotated to genomic features (promoters, introns, exons, intergenic regions) using the ChIPseeker package (v1.34.1) in R.
Assembly: mm10
Supplementary files format and content: .gz.bw

source_name: spleen

extract_protocol:
Splenocytes were cross-linked with 1% formaldehyde, quenched with glycine, and lysed. Chromatin was sheared to 200-500 bp by sonication. Immunoprecipitation was performed overnight with anti-E47 antibody or IgG control coupled to Protein G beads. Beads were washed, cross-links were reversed at 65°C overnight, and DNA was purified using QIAquick PCR Purification Kit.
DNA was purified using the QIAquick PCR Purification Kit. Libraries were constructed using the VAHTS TGS DNA Library Prep Kit  (Vazyme) following manufacturer's protocols.

value: spleen

value: primary cell

value: input


title: mouse_colorectal_organoid_control_biological_replicate_3

description:
Library name: RNA_seq_C3
Colorectal organoid derived from a 6–8-week-old female Mus musculus, no treatment, biological replicate 3.

value: Colorectal organoids


title: Vehicle, 24 hrs 0507 (2)

description: Library name: 52589_HTB-0507 Veh 2

value: Bone Marrow Cells


title: MAR-3.6.2, 24 hrs 0507 (2)

description: Library name: 52592_HTB-0507 3.6.2 2

value: Patient-drived primary CD34+CD38- blast


title: BMDM cells, H3K4me3, DMSO, rep1

description: Library name: DMSO_H3K4me3_rep1


title: intestinal MPS Mock 3

city: Bunkyo-ku

first: Kazuo

last: Takayama

state: Tokyo

address: Yushima 1-5-45

country: Japan

institute: Institute of Science Tokyo

description: Library name: intestinal MPS Mock 3

data_processing:
Sequencing was performed on an Illumina NextSeq 2000 platform with the paired-end mode.
Illumina RTA version 4.12.2 and  bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
Adapter sequences and low-quality bases were trimmed from the raw reads by cutadapt v4.6. The trimmed reads were mapped to the human reference genome sequences (hg38) using STAR v2.7.11a with the GENCODE (release 32, GRCh38.p13) gtf file.
The uniquely and properly mapped reads were used for further analysis. Raw read counts were calculated using htseq-count v2.0.5 with the GENCODE gtf file. Gene expression levels were determined as transcripts per million (TPM).
Assembly: hg38
Supplementary files format and content: Matrix table with TPM for every gene and every sample

source_name: ES cell-derived intestinal MPS

extract_protocol:
Total RNA was isolated using ISOGENE (Cat# 319-90211, NIPPON GENE).
Library preparation was performed using an Illumina Stranded mRNA Prep,Ligation Kit (Cat# 20040532, Illumina) according to the manufacturer’s instructions.

treatment_protocol: The human ES cell-derived intestinal MPS was infected with EV-A71 (0.1 multiplicity of infection (MOI)) and cultured for 7 days.

value: ES cell-derived intestinal MPS

value: intestinal MPS

value: mock

tag: time

value: 7 dpi


title: intestinal MPS Mock 1

description: Library name: intestinal MPS Mock 1


title: Vehicle, 24 hrs 0507 (1)

description: Library name: 52588_HTB-0507 Veh 1

value: Acute Myeloid Leukemia


title: BMDM cells, RPB1, DMSO, rep2

description: Library name: DMSO_RPB1_rep2

value: bone marrow

value: BMDM

value: macrophage

value: WT


title: ND15755 donor, male, age 65, non-diseased, left ventricle, ATAC, replicate 2

city: Philadelphia

first: William

last: Gao

state: PA

address: 415 Curie Blvd

department: Genetics

institute: UNIVERSITY OF PENNSYLVANIA

description: Library name: LV-NDRI15755_5k

library_source: genomic single cell

data_processing:
Processing of these raw data are described in "RNA/internal_datasets" and "ATAC/internal_datasets" of this github repository:  https://github.com/wgao688/Human-cardiac-multiome-analysis. Briefly, the raw FASTQ files were aligned to the hg38 reference genome using STARSolo (v2.7.11a) to produce count matrices for snRNA-seq. These count matrices were then used for downstream analyses (see Github repository and Methods section). For snATAC-seq, cellranger-atac (cellranger-atac-2.1.0) was used to produce fragment files, which were the inputs for downstream processing with SnapATAC2.
Assembly: GRCh38, version 44 (Ensembl 110)
Supplementary files format and content: "Processed data are named GSE290367_integrated_RNA_adata.h5ad.gz" and GSE290367_integrated_RNA_adata.h5ad.gz". These include the aggregated datasets after combining all internal data (denoted as "Penn") with external datasets. This corresponds to the datasets described in Fig. 1a (RNA) and Fig. 2a (ATAC). The processing scripts are located in the "RNA/" and "ATAC/" directories of this github repository: https://github.com/wgao688/Human-cardiac-multiome-analysis"

source_name: heart

extract_protocol:
Nuclei isolation from flash frozen human donor hearts
All 19 snRNA-seq libraries were generated using the Dropseq protocol. All 11 snATAC-seq libraries were generated using the 10X Genomics ATAC v1 kit.

value: heart


title: No Treatment 0507 (2)

description: Library name: 52586_HTB-0507 Ctrl 2


title: No Treatment 415 (1)

description: Library name: 52576_HTB-415 Ctrl 1


title: K1647 donor, male, age 34, non-diseased, left ventricle, ATAC, replicate 2

description: Library name: LV-K1647-run-2


title: MAR-3.6.2, 24 hrs 415 (1)

description: Library name: 52582_HTB-415 3.6.2 1


title: BMDM cells, ATRA, rep2 (RNA)

description: Library name: ATRA_RNA_rep2

value: ATRA


title: BMDM cells, RPB1, DMSO, rep1

description: Library name: DMSO_RPB1_rep1

value: DMSO


title: FG214-H175I-EN+imidazole

value: bacterial


title: BMDM cells, ATRA, rep1 (RNA)

description: Library name: ATRA_RNA_rep1


title: spCHIP

description: Library name: sample1

value: spleen

value: primary cell


title: K1584 donor, male, age 22, non-diseased, left ventricle, ATAC, replicate 1

description: Library name: LV-K1584-run-1


title: MAR-3.6.2, 24 hrs 415 (2)

description: Library name: 52583_HTB-415 3.6.2 2

value: Bone Marrow Cells


title: Vehicle, 24 hrs 415 (2)

description: Library name: 52580_HTB-415 Veh 2

value: Patient-drived primary CD34+CD38- blast


title: K1488 donor, male, age 81, non-diseased, left ventricle, ATAC, replicate 2

description: Library name: LV-K1488-run-2


title: Vehicle, 24 hrs 415 (1)

description: Library name: 52579_HTB-415 Veh 1


title: BMDM cells, H3K4me3, ATRA, rep2

description: Library name: ATRA_H3K4me3_rep2


title: BMDM cells, DMSO, rep1 (RNA)

description: Library name: DMSO_RNA_rep1


title: Wildtype induced pluripotent stem cells R2

description: Library name: iPSC_WT_replicate2

value: iPSC

value: wild type


title: BMDM cells, H3K27ac, DMSO, rep2

description: Library name: DMSO_H3K27ac_rep2


title: mouse_colorectal_organoid_NAP_biological_replicate_1

description:
Library name: RNA_seq_N1
Colorectal organoid derived from a 6–8-week-old female Mus musculus, treated with NAP, biological replicate 1.

value: Colorectal organoids

value: NAP treatment


title: intestinal MPS EV-A71 2

description: Library name: intestinal MPS EV-A71 2

value: ES cell-derived intestinal MPS

value: intestinal MPS

value: EV-A71 infected

value: 7 dpi


title: BMDM cells, H3K4me3, ATRA, rep1

description: Library name: ATRA_H3K4me3_rep1

value: bone marrow

value: BMDM

value: macrophage

value: WT


title: intestinal MPS EV-A71 3

description: Library name: intestinal MPS EV-A71 3


title: K1727 donor, male, age 40, non-diseased, left ventricle, ATAC, replicate 1

description: Library name: K1727-LV-1

value: heart


title: BMDM cells, RPB1, ATRA, rep2

description: Library name: ATRA_RPB1_rep2

value: ATRA


title: K1727 donor, male, age 40, non-diseased, left ventricle, ATAC, replicate 2

description: Library name: K1727-LV-2


title: Penn_F4 donor, male, gestational week 10, non-diseased, whole heart, ATAC

description: Library name: Fetal-wholeHeart-10wk


title: FG214-WT-PBS+imidazole

value: bacterial