title: GBMC-G008_H3K27ac_ChIPseq


title: GBMC-G008_H3K79me2_ChIPseq

status: Public on Jul 03 2026

type: SRA

city: Houston

first: Mahinur

last: Mattohti

state: TX

address: 6670 Bertner Ave

department: Surgery

country: USA

institute: Houston Methodist Research Institute

library_source: genomic

data_processing:
ChIPseq reads were aligned to hg19 genome using bowtie1 with max 1 mismatch, duplicated reads were removed
peaks were called using MACS14 and MACS2 using pvalue cutoff of 1e-5
bigwig files were generated by deeptools bamCoverage normalized by RPKM
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files contains the ChIPseq signal normalized by RPKM. Bed files contain the peaks called by MACS14 and MACS2

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: All cell lines were expanded and maintained in specified growth medium from ATCC or MDACC.

extract_protocol:
Crosslinked samples were thawed on ice and resuspended in RIPA lysis buffer supplemented with protease inhibitor, lysed the cells on ice then sheared the chromatin by sonication. After centrifuge, the clean sonicated cell lysate mixed with protein G magnetic dynabeads (Invitrogen) coupled to antibodies described above and incubated over night at 4 degrees. Samples was washed 5 times with cold RIPA, twice with high salt RIPA, twice with LiCl buffer, twice with TE, and then eluted in elution buffer. The eluate was reverse crosslinked at 65C. Solid-phase reversible immobilization (SPRI) cleanup steps were performed. Beads were washed twice on the magnet with 70% ethanol and then air-dried. The DNA was eluted in EB buffer.
Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and Bioanalyzer 1000 before multiplexing.

tag: tissue

value: GBM cancer cell line

tag: cell line

tag: chip antibody


title: 1h control replicate 2

city: Clayton

first: Rachael

last: Turner

state: Victoria

address: Wellington Road

department: Biochemistry and Molecular Biology

country: Australia

institute: Monash University

description:
Library name: Sample 2
W_C_1h_R2

library_source: transcriptomic

data_processing:
Processing is automated using the Tail Tools pipeline (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools), and proceeds as follows:
Reads are stripped of trailing poly(A) sequence.
Reads are aligned using STAR aligner (v2.6.0A https://github.com/alexdobin/star). Multi-mapping reads are assigned to one location at random.
Alignments are extended where the stripped poly(A) sequence matches As present in the genome. A poly(A) tail is called present if there are at least four untemplated As remaining in the stripped sequence.
Reads aligning to genes are counted. As 3' UTR annotations are not always accurate, reads up to 400 bases down-strand of a gene are counted towards that gene. Total reads per gene, reads with a poly(A) tail per gene, and average poly(A) tail length are tabulated.
Assembly: C. albicans SC5314
Supplementary files format and content: counts.csv is a comma-separated values file containing the raw genetic annotation read count for all samples

molecule: total RNA

organism: Candida albicans

growth_protocol: Wild-type C. albicans cultures were grown on YPD plates (1% yeast extract, 2% peptone, 2% glucose, and 2% agar, 80μg/ml uridine) and hyphal formation induced in MOPS buffered RPMI (Sigma R6504) adjusted to pH 7.0 at 37 °C. Lactate was used at 0.2% (w/v) in RPMI.

extract_protocol:
RNA was extracted using the hot phenol method.
Library construction was by the PAT-seq approach (Harrison et al RNA 2015).

treatment_protocol: Overnight cultures were washed with PBS and diluted to an OD 600  of 0.1 in 4ml RPMI with  16 µg/ml gladiolin or 0.08% DMSO control. Cultures were grown for 1h, 3h or 8h at 37°C, shaking at 200rpm.

tag: genotype

value: WT

tag: treatment

value: DMSO

tag: treatment timepoint

value: 1h control


title: 1h gladiolin replicate 1

description:
Library name: Sample 3
W_T_1h_R1

value: gladiolin

value: 1h gladiolin


title: GBMC-G028_Input DNA


title: GBMC-G008_H3K9me3_ChIPseq


title: GBMC-G008_H3K4me1_ChIPseq


title: snMultiome, Mouse hippocampus, WT, animal 3, rep 3, ATAC

city: Madison

first: Ziyao

last: Zhang

state: WI

address: 1500 Highland Ave, Room 667

institute: University of Wisconsin-Madison

description: Library name: WT_5_snATAC

library_source: genomic single cell

data_processing:
snMultiome data were processed with CellRanger Arc.
Assembly: mm10
Supplementary files format and content: CellRanger Arc output file: atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi, filtered_feature_bc_matrix.h5, raw_feature_bc_matrix.h5

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
Single nuclei suspensin prepared from fresh frozen tissue. Single nuclei were encapsulated in GEMs using the 10x controller and 10x scMultiome gel bead kit A.
The sequencing libraries were constructed following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression user guide (CG000338 Rev F).

value: Hippocampus

tag: cell type

value: Mixed

value: WT/y

value: Naïve


title: snMultiome, Mouse hippocampus, WT, animal 3, rep 2, ATAC

description: Library name: WT_4_snATAC


title: GBMC-G002_Input DNA


title: snMultiome, Mouse hippocampus, WT, animal 3, rep 1, ATAC

description: Library name: WT_3_snATAC


title: GBMC-G002_H3K79me2_ChIPseq


title: snMultiome, Mouse hippocampus, WT, animal 2, ATAC

description: Library name: WT_2_snATAC


title: GBMC-G002_H3K4me3_ChIPseq


title: GBMC-G002_H3K27me3_ChIPseq


title: GBMC-G002_H3K27ac_ChIPseq


title: snMultiome, Mouse hippocampus, WT, animal 1, ATAC

description: Library name: WT_1_snATAC


title: snMultiome, Mouse hippocampus, Mecp2 S80A;S421E, animal 3, rep 2, ATAC

description: Library name: AE_4_snATAC

value: Mecp2 S80A;S421E/y


title: GBMC-G002_H3K9me3_ChIPseq


title: snMultiome, Mouse hippocampus, Mecp2 S80A;S421E, animal 3, rep 1, ATAC

description: Library name: AE_3_snATAC


title: GBMC-G002_H3K4me1_ChIPseq


title: snMultiome, Mouse hippocampus, Mecp2 S80A;S421E, animal 2, ATAC

description: Library name: AE_2_snATAC


title: snMultiome, Mouse hippocampus, Mecp2 S80A;S421E, animal 1, ATAC

description: Library name: AE_1_snATAC

library_source: transcriptomic single cell

molecule: nuclear RNA


title: snMultiome, Mouse hippocampus, WT, animal 3, rep 3, GEX

description: Library name: WT_5_snRNA


title: GBMC-G001_H3K27me3_ChIPseq


title: GBMC-G001_H3K27ac_ChIPseq


title: GBMC-G001_H3K4me3_ChIPseq


title: snMultiome, Mouse hippocampus, WT, animal 3, rep 2, GEX

description: Library name: WT_4_snRNA


title: snMultiome, Mouse hippocampus, WT, animal 3, rep 1, GEX

description: Library name: WT_3_snRNA


title: GBMC-G001_H3K79me2_ChIPseq


title: GBMC-G001_H3K9me3_ChIPseq


title: snMultiome, Mouse hippocampus, WT, animal 2, GEX

description: Library name: WT_2_snRNA


title: GBMC-G001_H3K4me1_ChIPseq


title: snMultiome, Mouse hippocampus, WT, animal 1, GEX

description: Library name: WT_1_snRNA


title: COAD-C027_H3K27me3_ChIPseq

value: Colon cancer cell line


title: COAD-C027_H3K4me3_ChIPseq


title: snMultiome, Mouse hippocampus, Mecp2 S80A;S421E, animal 3, rep 2, GEX

description: Library name: AE_4_snRNA


title: snMultiome, Mouse hippocampus, Mecp2 S80A;S421E, animal 3, rep 1, GEX

description: Library name: AE_3_snRNA


title: COAD-C027_H3K27ac_ChIPseq


title: snMultiome, Mouse hippocampus, Mecp2 S80A;S421E, animal 1, GEX

description: Library name: AE_1_snRNA


title: COAD-C027_H3K9me3_ChIPseq


title: COAD-C027_H3K79me2_ChIPseq


title: snMultiome, Mouse hippocampus, Mecp2 S80A;S421E, animal 2, GEX

description: Library name: AE_2_snRNA


title: scMC38 rep 4

city: Aurora

first: Andrea

last: Bonetto

state: Colorado

department: Pathology

institute: University of Colorado Anschutz Medical Campus

description: Library name: AB67_10

data_processing:
Fastq files were processed using the gammon-bio/rnaseq_pipeline (v1.0.1, https://github.com/gammon-bio/rnaseq_pipeline/tree/v1.0.1)
Read filtering/adapter trimming was performed with fastp (v1.0.1)
Quality control was performed with FastQC (v0.12.1); QC reports were aggregated with MultiQC (v1.30)
Transcripts were mapped and quantified using Salmon (v1.10.3); mapping was to the mouse transcriptome (GRCm39, gene annotation from Ensembl release 115)
Tables with gene counts were generated by the tximport R package (v1.34.0) under R version 4.4.3; Ensembl IDs were mapped to gene symbols using biomaRt (v2.62.0)
Assembly: GRCm39
Supplementary files format and content: Csv file containing gene counts

source_name: skeletal muscle (quadriceps)

extract_protocol:
Total RNA from skeletal muscle (quadriceps) was isolated using the Rneasy Mini Kit (Qiagen)
Universal Plus mRNA-seq library preparation kit with NuQuant (Nugen/Tecan)

treatment_protocol: Mice were innoculated with 1.0 x 10^6 cells (in 200 ul sterile PBS) and sacrificed after 28 days.

value: skeletal muscle (quadriceps)


title: scMC38 rep 3

description: Library name: AB67_9


title: COAD-C027_H3K4me1_ChIPseq


title: COAD-C022_Input DNA


title: scMC38 rep 2

description: Library name: AB67_8


title: COAD-C022_H3K27me3_ChIPseq


title: scMC38 rep 1

description: Library name: AB67_6


title: Control rep 4

description: Library name: AB67_4

value: PBS


title: COAD-C022_H3K4me3_ChIPseq


title: COAD-C022_H3K79me2_ChIPseq


title: Control rep 3

description: Library name: AB67_3


title: Control rep 2

description: Library name: AB67_2


title: COAD-C022_H3K27ac_ChIPseq


title: Control rep 1

description: Library name: AB67_1


title: COAD-C022_H3K4me1_ChIPseq


title: Fibroblasts, RNAseq, pool2, tumours 4 and 5

city: Cambridge

first: Timotheus

last: Halim

address: University of Cambridge Li Ka Shing Centre, Robinson Way

department: CRUK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

description:
Library name: Pool_2_RNA
Pool 2 (tdTom+ and tdTom- cells from 2 samples)

data_processing:
A reference genome was constructed from the GRCm39-2024-A reference with an entry for tdTomato and the WPRE of the Ai9 mouse added using cellranger mkref. Reads were aligned, demultiplexed, and quantified using cellranger multi  (10X Genomics, 9.0.1). Tumours 2 and 3 were pooled together prior to sorting. Sort fractions labelled A are tdTomato+ and B are tdTomato-. Cells with tdTomato expression present in the tdTomato- sort fraction due to sort contamination were subsequently moved into the tdTomato+ group in Seurat.
Assembly: GRCm39-2024-A
Supplementary files format and content: Cell Ranger output files

source_name: Tumour

extract_protocol:
Tumours were mechanically minced and digested in a digestion buffer containing Collagenase I and DNAse I, followed by passing through a 21G needle and filtering through a 70um filter for preparation of single cell suspensions. Single cells were FACS-sorted for Live, CD45- CD31- EpCAM- Pdpn+ Pdgfra+ tdTomato+/- cell populations, before being pooled for on-chip multiplexing (GEM-X OCM 3' Chip Kit v4 4-plex 2 chips PN-1000747)
Single-cell encapsulation and library preparation was performed according to manufacturer's instructions (GEM-X Universal 3' Gene Expression v4 4-plex Reagent Kits). Barcodes: T1A, T4A = OB1; T1B, T4B = OB2; T2A_3A, T5A = OB3; T2B_3B, T5B = OB4.

value: Tumour

value: 2838c3 PDAC cell line


title: COAD-C021_Input DNA


title: Microglia, snRNAseq

city: San Francisco

first: Haoyue

last: Zhou

state: CA

address: 1650 Owens St

institute: Gladstone Institutes

description: Library name: MG_RNA

data_processing:
Raw sequencing files were processed using the 10x Genomics Cell Ranger multi pipeline (v9.0.1) with default parameters.
Raw count matrices were imported into Seurat (v5.1.0). Nuclei with nFeature_RNA < 200, > 9000, or percent.mt > 10 were removed. Doublets were filtered via DoubletFinder v2.0.6.
Data normalization, scaling, log-transformation, dimensionality reduction (PCA/UMAP), clustering (Louvain, resolution = 0.1), and marker detection (Wilcoxon) were performed in Seurat.
Non-microglia, low quality, and mixed cell population clusters were removed
Assembly: GRCm39
Supplementary files format and content: micro_seurat.rds.gz --> normalized and processed seurat object
Supplementary files format and content: feature_readme_micro.csv --> for demultiplexing for cellranger multi pipeline

source_name: brain

growth_protocol: mice ordered from jackson

extract_protocol:
mouse perfusion, brain dissection, sorting of microglia, 8 brains pooled per replicate
10x GEM-X Single Cell GEX Flex (Multiplex), STEP 1: Probe Hybridization
10x GEM-X Single Cell GEX Flex (Multiplex), STEP 2: GEM Generation & Library Prep

treatment_protocol: inject mice with atto-647-labeled serpina1

value: brain

value: Mixed sample (A1AT+, A1AT-)


title: COAD-C021_H3K27me3_ChIPseq


title: COAD-C021_H3K4me3_ChIPseq


title: Astrocyte, snRNAseq

description: Library name: AST_RNA

data_processing:
Raw sequencing files were processed using the 10x Genomics Cell Ranger multi pipeline (v9.0.1) with default parameters.
Raw count matrices were imported into Seurat (v5.1.0). Nuclei with nFeature_RNA < 200, > 9000, or percent.mt > 20 were removed. Doublets were filtered via DoubletFinder v2.0.6.
Data normalization, scaling, log-transformation, dimensionality reduction (PCA/UMAP), clustering (Louvain, resolution = 0.1), and marker detection (Wilcoxon) were performed in Seurat.
Non-astrocytic, low quality, and mixed cell population clusters were removed
Assembly: GRCm39
Supplementary files format and content: astro_seurat.rds.gz --> normalized and processed seurat object
Supplementary files format and content: feature_readme_astro.csv --> demultiplexing for cellranger multi

extract_protocol:
mouse perfusion, brain dissection, sorting of astrocytes, 8 brains pooled per replicate
10x GEM-X Single Cell GEX Flex (Multiplex), STEP 1: Probe Hybridization
10x GEM-X Single Cell GEX Flex (Multiplex), STEP 2: GEM Generation & Library Prep

treatment_protocol: inject mice with atto-647-labeled apoa1

value: WT

value: Mixed sample (APOA1+, APOA1-)


title: Fibroblasts, RNAseq, pool1, tumours 1 and 2_3

description:
Library name: Pool_1_RNA
Pool 1 (tdTom+ and tdTom- cells from 2 samples)


title: COAD-C021_H3K79me2_ChIPseq


title: sample 18_si_FBL2_3

city: Wuhan

first: Zhang

last: Kui

address: Jinlong Avenue, Jiangxia District     Wuhan Institute of Virology, Chinese Academy of Sciences     Wuhan, Hubei 430200     China

country: China

institute: Wuhan Institute of Virology

description:
Library name: sample 18
master_table_siFBL.csv

data_processing:
Sample 1-18: For sequencing, circularized DNA was amplified via rolling circle amplification to produce DNA nanoballs (DNBs), which were loaded onto patterned nanoarrays. Combinatorial Probe-Anchor Synthesis (cPAS) technology (DNBSEQ platform, BGI) was employed for 150 bp paired-end sequencing. Raw reads were quality-filtered using SOAPnuke to remove low-quality bases and adapters. Clean reads were mapped to the human reference genome (GRCh38/hg38) using HISAT2. Gene expression levels were estimated with RSEM (v1.3.1) and normalized to FPKM values. Differential Expression analysis was performed using DESeq2 (v1.4.5) with hresholds of |log2FC| ≥ 1 and adjusted p-value < 0.05. Enriched KEGG pathways were identified via Hypergeometric testing (Phyper), with significance thresholds set at Q-value ≤ 0.05 after false discovery rate (FDR) correction. All analyses were conducted using the BGI Tom Multi-omics Platform (https://biosys.bgi.com).
Sample 19-22: To identify termination sites characteristic of 2'-O-methylation, raw paired-end reads were first filtered by fastp (v0.23.2) and merged using FLASH (v1.2.11, -p 33 -m 12 -M 300 -x 0.25 -z) to create longer contiguous sequences. The merged reads were then filtered to select those containing the target adapter sequence "agtctcgatttcggaGGGGGGGG", allowing for one nucleotide mismatch to account for potential sequencing errors while maintaining specificity for Nm-detection products. Adapter sequences and any downstream polyG tracts were subsequently trimmed using Cutadapt to isolate the authentic viral sequences. The processed reads were then aligned to the EV71 reference genome (BrCr-TR, GenBank # U22521.1) using Bowtie2 (v2.2.6).
Sample 23-25: Raw multi-fast5 reads were base-called using Guppy (v3.1.5) and converted to single-read fast5 files using the ont_fast5_api (v3.0.2) multi_to_single_fast5 command. Reads were then mapped to the EV71 reference genome (GenBank # JQ804832.1) using Tombo (v1.5.1).
Assembly: GRCh38/hg38,and EV71 genome (GenBank number: U22521.1 or JQ804832.1)
Supplementary files format and content: Sample 1-18: Excel files contain FPKM.
Supplementary files format and content: Sample 19-22: Excel files contain NanoNm rate.
Supplementary files format and content: Sample 23-25: Excel files contain Nm mutation rate.

molecule: polyA RNA

source_name: embryonic rhabdomyosarcoma

growth_protocol: RD/Vero cells were maintained in DMEM supplemented with 10% fetal bovine serum(FBS)at 37 ℃ in a 5% CO2 environment

extract_protocol:
Total RNAs were extracted using TRIzol Reagent (Invitrogen, cat. NO 15596026）
Sample 1-18: For library preparation, mRNA was enriched via oligo(dT) magnetic bead-based selection, fragmented, and subjected to quality control. First- and second-strand cDNA synthesis was performed, followed by 3’ adenylation and adapter ligation. (3) cDNA ends from low-dNTP extension were amplified by nested RACE-PCR. The resulting amplicons were purified and constructed into sequencing libraries for the Illumina platform. (4) Poly(A) RNA was directly ligated to sequencing adapters without reverse transcription. The prepared library was loaded onto a Nanopore flow cell for direct RNA sequencing.  Sample 19-22: Library preparation was performed by two step PCR. First round PCR reaction was set up as follows: DNA (10 ng/μl) 2μl; amplicon PCR forward primer mix (10 μM) 1μl; amplicon PCR reverse primer mix (10 μM) 1μl; 2×PCR Ready Mix 15 μl (total 25μl) (Kapa HiFi Ready Mix). The plate was sealed and PCR performed in a thermal instrument (BIO-RAD, T100TM).The PCR products were checked using electrophoresis in 1 % (w/v) agarose gels in TBE buffer (Tris, boric acid, EDTA). Then we used AMPure XP beads to purify the amplicon product. After that, the second round PCR was performed. PCR reaction was set up as follows: DNA (10 ng/μl) 2μl; universal P7 primer with index(10 μM) 1μl; P5 primer with index(10 μM) 1μl; 2× PCR Ready Mix 15 μl (total 30μl)(Kapa HiFi Ready Mix). Then we used AMPure XP beads to purify the amplicon product. The libraries were then quantified and pooled. Paired-end sequencing of the library was performed on the NovaSeq6000 / MiSeqsequencers with MIseq PE300 model (Illumina, San Diego, CA).  Sample 23-25: Poly(A) mRNA isolation using the GenElute mRNA Miniprep Kit (Sigma-Aldrich). Direct RNA sequencing was performed according to the Oxford Nanopore DRS protocol (SQK-RNA002)

treatment_protocol: For infection, RD/Vero cells were infected with EV71, followed by incubation and harvesting at specified time points. For knockdown, RD cells were transfected with siRNA targeting FBL or control siRNA, followed by EV71 infection.

value: embryonic rhabdomyosarcoma

value: RD

value: cell line


title: COAD-C021_H3K27ac_ChIPseq


title: sample 17_si_FBL2_2

description:
Library name: sample 17
master_table_siFBL.csv


title: COAD-C021_H3K9me3_ChIPseq


title: sample 16_si_FBL2_1

description:
Library name: sample 16
master_table_siFBL.csv


title: COAD-C021_H3K4me1_ChIPseq


title: COAD-C020_Input DNA


title: sample 15_si_FBL1_3

description:
Library name: sample 15
master_table_siFBL.csv


title: sample 14_si_FBL1_2

description:
Library name: sample 14
master_table_siFBL.csv


title: COAD-C020_H3K27me3_ChIPseq


title: COAD-C020_H3K79me2_ChIPseq


title: sample 13_si_FBL1_1

description:
Library name: sample 13
master_table_siFBL.csv


title: sample 12_si_NC_3

description:
Library name: sample 12
master_table_siFBL.csv


title: COAD-C020_H3K27ac_ChIPseq


title: sample 11_si_NC_2

description:
Library name: sample 11
master_table_siFBL.csv


title: COAD-C020_H3K4me3_ChIPseq


title: sample 10_si_NC_1

description:
Library name: sample 10
master_table_siFBL.csv


title: COAD-C020_H3K9me3_ChIPseq


title: sample 9_24hpi_3

description:
Library name: sample 9
master_table_TimeCourse.csv


title: COAD-C020_H3K4me1_ChIPseq


title: sample 7_24hpi_1

description:
Library name: sample 7
master_table_TimeCourse.csv


title: sample 8_24hpi_2

description:
Library name: sample 8
master_table_TimeCourse.csv


title: COAD-C016_H3K27me3_ChIPseq


title: sample 6_6hpi_3

description:
Library name: sample 6
master_table_TimeCourse.csv


title: sample 5_6hpi_2

description:
Library name: sample 5
master_table_TimeCourse.csv


title: COAD-C016_H3K4me3_ChIPseq


title: COAD-C016_H3K79me2_ChIPseq


title: sample 4_6hpi_1

description:
Library name: sample 4
master_table_TimeCourse.csv


title: COAD-C016_H3K27ac_ChIPseq


title: sample 3_mock_3

description:
Library name: sample 3
master_table_TimeCourse.csv

value: mock


title: COAD-C016_H3K9me3_ChIPseq


title: sample 2_mock_2

description:
Library name: sample 2
master_table_TimeCourse.csv


title: COAD-C016_H3K4me1_ChIPseq


title: sample 1_mock_1

description:
Library name: sample 1
master_table_TimeCourse.csv


title: COAD-C015_H3K4me3_ChIPseq


title: COAD-C015_H3K79me2_ChIPseq


title: COAD-C015_H3K27ac_ChIPseq


title: Female,FR,Insulin,P21,rep9

city: Verdun

first: Nicholas

last: O'Toole

state: QC

address: 6875 Boulevard Lasalle

country: Canada

institute: Douglas Mental Health University Institute

description:
Library name: 8B.5_Female_FR_Insulin_mPFC_P21
8B.5_Female_FR_Insulin_mPFC_P21
P21_mPFC_counts.txt

data_processing:
Reads were aligned to the rat genome with STAR
Read counts per gene were computed with STAR
Assembly: Rnor_6.0
Supplementary files format and content: Ensembl gene Ids and read counts, tab delimited
Supplementary files format and content: Differential expression data, tab delimited

organism: Rattus norvegicus

source_name: Medial prefrontal cortex

extract_protocol:
Qiagen AllPrep RNA minikit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Medial prefrontal cortex


title: Female,FR,Insulin,P21,rep10

description:
Library name: 9A.7_Female_FR_Insulin_mPFC_P21
9A.7_Female_FR_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: COAD-C015_H3K9me3_ChIPseq


title: COAD-C015_H3K4me1_ChIPseq


title: Female,FR,Insulin,P21,rep7

description:
Library name: 7A.5_Female_FR_Insulin_mPFC_P21
7A.5_Female_FR_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: COAD-C022_H3K9me3_ChIPseq


title: Female,FR,Insulin,P21,rep6

description:
Library name: 6B.5_Female_FR_Insulin_mPFC_P21
6B.5_Female_FR_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: Female,FR,Insulin,P21,rep5

description:
Library name: 4A.7_Female_FR_Insulin_mPFC_P21
4A.7_Female_FR_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: COAD-C013_Input DNA


title: Female,FR,Insulin,P21,rep8

description:
Library name: 8A.5_Female_FR_Insulin_mPFC_P21
8A.5_Female_FR_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: COAD-C013_H3K27me3_ChIPseq


title: Female,AdLib,Insulin,P21,rep10

description:
Library name: 3B.5_Female_AdLib_Insulin_mPFC_P21
3B.5_Female_AdLib_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: Female,AdLib,Insulin,P21,rep9

description:
Library name: 16C.5_Female_AdLib_Insulin_mPFC_P21
16C.5_Female_AdLib_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: COAD-C013_H3K4me3_ChIPseq


title: COAD-C013_H3K79me2_ChIPseq


title: Female,AdLib,Insulin,P21,rep8

description:
Library name: 15A.6_Female_AdLib_Insulin_mPFC_P21
15A.6_Female_AdLib_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: COAD-C013_H3K27ac_ChIPseq


title: Female,AdLib,Insulin,P21,rep7

description:
Library name: 14B.6_Female_AdLib_Insulin_mPFC_P21
14B.6_Female_AdLib_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: COAD-C013_H3K9me3_ChIPseq


title: COAD-C013_H3K4me1_ChIPseq


title: Female,AdLib,Insulin,P21,rep6

description:
Library name: 14B.5_Female_AdLib_Insulin_mPFC_P21
14B.5_Female_AdLib_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: Female,AdLib,Insulin,P21,rep5

description:
Library name: 13C.1_Female_AdLib_Insulin_mPFC_P21
13C.1_Female_AdLib_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: COAD-C012_Input DNA


title: COAD-C012_H3K4me3_ChIPseq


title: Female,AdLib,Insulin,P21,rep4

description:
Library name: 13B.1_Female_AdLib_Insulin_mPFC_P21
13B.1_Female_AdLib_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: COAD-C012_H3K79me2_ChIPseq


title: Female,FR,Insulin,P21,rep4

description:
Library name: 16A.5_Female_FR_Insulin_mPFC_P21
16A.5_Female_FR_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: Female,AdLib,Insulin,P21,rep3

description:
Library name: 13A.3_Female_AdLib_Insulin_mPFC_P21
13A.3_Female_AdLib_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: COAD-C012_H3K27ac_ChIPseq


title: Female,FR,Insulin,P21,rep3

description:
Library name: 12B.1_Female_FR_Insulin_mPFC_P21
12B.1_Female_FR_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: COAD-C012_H3K9me3_ChIPseq


title: Female,FR,Insulin,P21,rep2

description:
Library name: 12A.5_Female_FR_Insulin_mPFC_P21
12A.5_Female_FR_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: Female,AdLib,Insulin,P21,rep2

description:
Library name: 11A.6_Female_AdLib_Insulin_mPFC_P21
11A.6_Female_AdLib_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: Female,AdLib,Insulin,P21,rep1

description:
Library name: 11A.5_Female_AdLib_Insulin_mPFC_P21
11A.5_Female_AdLib_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: COAD-C012_H3K4me1_ChIPseq


title: COAD-C007_Input DNA


title: Female,FR,Insulin,P21,rep1

description:
Library name: 10A.3_Female_FR_Insulin_mPFC_P21
10A.3_Female_FR_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: COAD-C007_H3K27me3_ChIPseq


title: SCRC-M724_H3K4me1_ChIPseq

value: MPNST cancer cell line


title: Male,FR,Insulin,P21,rep10

description:
Library name: 9A.5_Male_FR_Insulin_mPFC_P21
9A.5_Male_FR_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: COAD-C007_H3K27ac_ChIPseq


title: COAD-C007_H3K9me3_ChIPseq


title: Male,FR,Insulin,P21,rep9

description:
Library name: 8B.7_Male_FR_Insulin_mPFC_P21
8B.7_Male_FR_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: COAD-C007_H3K4me1_ChIPseq


title: Male,FR,Insulin,P21,rep8

description:
Library name: 8A.7_Male_FR_Insulin_mPFC_P21
8A.7_Male_FR_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: COAD-C004_H3K4me3_ChIPseq


title: Male,FR,Insulin,P21,rep6

description:
Library name: 6B.7_Male_FR_Insulin_mPFC_P21
6B.7_Male_FR_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: 1h control replicate 1

description:
Library name: Sample 1
W_C_1h_R1

value: DMSO

value: 1h control


title: Male,FR,Insulin,P21,rep7

description:
Library name: 7A.7_Male_FR_Insulin_mPFC_P21
7A.7_Male_FR_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: COAD-C004_H3K27ac_ChIPseq

value: Colon cancer cell line


title: PAAD-P034_H3K4me3_ChIPseq

value: Pancreatic cancer cell line


title: COAD-C004_H3K9me3_ChIPseq


title: Male,FR,Insulin,P21,rep5

description:
Library name: 4A.5_Male_FR_Insulin_mPFC_P21
4A.5_Male_FR_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: Male,AdLib,Insulin,P21,rep10

description:
Library name: 3B.7_Male_AdLib_Insulin_mPFC_P21
3B.7_Male_AdLib_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: COAD-C004_H3K4me1_ChIPseq


title: Male,AdLib,Insulin,P21,rep9

description:
Library name: 16C.6_Male_AdLib_Insulin_mPFC_P21
16C.6_Male_AdLib_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: COAD-C003_Input DNA


title: COAD-C003_H3K4me3_ChIPseq


title: Male,FR,Insulin,P21,rep4

description:
Library name: 16A.8_Male_FR_Insulin_mPFC_P21
16A.8_Male_FR_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: COAD-C003_H3K79me2_ChIPseq


title: wtCAR2

status: Public on Jul 05 2026

city: Shenzhen

first: Chen

last: Yang

address: 1068 Xueyuan Avenue, Nanshan District, Shenzhen,China

institute: Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences

description: Library name: sample2

data_processing:
QC(Fastq)
alignment to GRCh38.p14 using STAR
read quantificatio(featureCounts)
filter out zero count (50％  of the samples are greater than zero)
normalization(TMM)
Assembly: hg38
Supplementary files format and content: csv file includes raw counts for each Sample

source_name: T cell

extract_protocol:
RNA is extracted from tissues or cells using standard extraction methods, followed by strict quality control of RNA samples. The quality control methods mainly include quantitative analysis using Nanodrop and detection of RNA integrity using Agilent 4200 TapeStation.
By utilizing the structural feature that most mRNA in eukaryotes have polyA tails, Oligo (dT) magnetic beads were used to enrich mRNA with polyA tails. Subsequently, the obtained mRNA was randomly cleaved using divalent cations. The fragmented mRNA was used as a template, and random oligonucleotides were used as primers to synthesize the first strand of cDNA in the 1st Strand Enzyme reverse transcriptase system. The second strand of cDNA was then synthesized using the 2nd Strand Enzyme and dNTPs. After purification, the double stranded cDNA was subjected to terminal repair, followed by the addition of an A tail and the connection of sequencing adapters. cDNA of around 200-300 bp was screened, amplified by PCR, and the PCR product was purified again to obtain a library.

value: PBMC

value: primary CD8+ T cells

value: day5 post transduction


title: Male,AdLib,Insulin,P21,rep8

description:
Library name: 15A.7_Male_AdLib_Insulin_mPFC_P21
15A.7_Male_AdLib_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: COAD-C003_H3K27ac_ChIPseq


title: Male,AdLib,Insulin,P21,rep7

description:
Library name: 14B.8_Male_AdLib_Insulin_mPFC_P21
14B.8_Male_AdLib_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: COAD-C003_H3K9me3_ChIPseq


title: Male,AdLib,Insulin,P21,rep6

description:
Library name: 14B.7_Male_AdLib_Insulin_mPFC_P21
14B.7_Male_AdLib_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: Male,AdLib,Insulin,P21,rep5

description:
Library name: 13C.3_Male_AdLib_Insulin_mPFC_P21
13C.3_Male_AdLib_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: Male,AdLib,Insulin,P21,rep4

description:
Library name: 13B.3_Male_AdLib_Insulin_mPFC_P21
13B.3_Male_AdLib_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: COAD-C003_H3K4me1_ChIPseq


title: COAD-C002_Input DNA


title: Male,AdLib,Insulin,P21,rep3

description:
Library name: 13A.1_Male_AdLib_Insulin_mPFC_P21
13A.1_Male_AdLib_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: COAD-C004_H3K79me2_ChIPseq


title: COAD-C002_H3K79me2_ChIPseq


title: Male,FR,Insulin,P21,rep3

description:
Library name: 12B.2_Male_FR_Insulin_mPFC_P21
12B.2_Male_FR_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: COAD-C002_H3K4me3_ChIPseq


title: COAD-C002_H3K27ac_ChIPseq


title: Male,AdlLib,Insulin,P21,rep1

description:
Library name: 11A.7_Male_AdlLib_Insulin_mPFC_P21
11A.7_Male_AdlLib_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: Male,AdLib,Insulin,P21,rep2

description:
Library name: 11A.8_Male_AdLib_Insulin_mPFC_P21
11A.8_Male_AdLib_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: Male,FR,Insulin,P21,rep2

description:
Library name: 12A.7_Male_FR_Insulin_mPFC_P21
12A.7_Male_FR_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: COAD-C002_H3K9me3_ChIPseq


title: Male,FR,Insulin,P21,rep1

description:
Library name: 10A.1_Male_FR_Insulin_mPFC_P21
10A.1_Male_FR_Insulin_mPFC_P21
P21_mPFC_counts.txt


title: COAD-C002_H3K4me1_ChIPseq


title: BRCA-B052_Input DNA

value: Breast cancer cell line


title: Female,FR,Saline,P21,rep10

description:
Library name: 9A.3_Female_FR_Saline_mPFC_P21
9A.3_Female_FR_Saline_mPFC_P21
P21_mPFC_counts.txt


title: BRCA-B052_H3K27me3_ChIPseq


title: Female,FR,Saline,P21,rep9

description:
Library name: 8B.1_Female_FR_Saline_mPFC_P21
8B.1_Female_FR_Saline_mPFC_P21
P21_mPFC_counts.txt


title: BRCA-B052_H3K4me3_ChIPseq


title: Female,FR,Saline,P21,rep8

description:
Library name: 8A.1_Female_FR_Saline_mPFC_P21
8A.1_Female_FR_Saline_mPFC_P21
P21_mPFC_counts.txt


title: Female,FR,Saline,P21,rep7

description:
Library name: 7A.1_Female_FR_Saline_mPFC_P21
7A.1_Female_FR_Saline_mPFC_P21
P21_mPFC_counts.txt


title: BRCA-B052_H3K27ac_ChIPseq


title: BRCA-B052_H3K79me2_ChIPseq


title: Female,FR,Saline,P21,rep6

description:
Library name: 6B.1_Female_FR_Saline_mPFC_P21
6B.1_Female_FR_Saline_mPFC_P21
P21_mPFC_counts.txt


title: Female,FR,Saline,P21,rep5

description:
Library name: 4A.3_Female_FR_Saline_mPFC_P21
4A.3_Female_FR_Saline_mPFC_P21
P21_mPFC_counts.txt


title: BRCA-B052_H3K9me3_ChIPseq


title: Female,AdLib,Saline,P21,rep10

description:
Library name: 3B.1_Female_AdLib_Saline_mPFC_P21
3B.1_Female_AdLib_Saline_mPFC_P21
P21_mPFC_counts.txt


title: BRCA-B052_H3K4me1_ChIPseq


title: Female,AdLib,Saline,P21,rep9

description:
Library name: 16C.1_Female_AdLib_Saline_mPFC_P21
16C.1_Female_AdLib_Saline_mPFC_P21
P21_mPFC_counts.txt


title: BRCA-B050_Input DNA


title: BRCA-B050_H3K27me3_ChIPseq


title: Female,FR,Saline,P21,rep4

description:
Library name: 16A.1_Female_FR_Saline_mPFC_P21
16A.1_Female_FR_Saline_mPFC_P21
P21_mPFC_counts.txt


title: BRCA-B050_H3K4me3_ChIPseq


title: Platelets, Healthy, Rep4

city: Nashville

first: Matthew

last: Cottam

state: TN

address: 2213 Garland Avenue South 9465

institute: Vanderbilt University

data_processing:
Raw sequencing reads were trimmed and filtered for quality using Trimgalore v0.6.7.
Trimmed reads were aligned to the hg38 reference genome and counted using STAR v2.7.9a with the `--quantMode GeneCounts` option.
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

source_name: Peripheral Blood Platelets

extract_protocol:
Samples were resuspended in 700 µl QIAzol Lysis Reagent (Qiagen GmbH, Hilden, Germany).
RNA was extracted from the platelet-QIAzol Lysis Reagent aliquots by application of the RNeasy Mini kit (Qiagen GmbH, Hilden, Germany; Cat: 1071023) according to the manufacturer’s recommendations.
Library preparation was completed using theNEBNext Ultra II Directional RNA Library Prep Kitand protocol (P/N: E7760L) per manufacturer recommendations.
RNA samples underwent mRNA enrichment using oligo(dT) beads, followed by fragmentation using divalent cations under elevated temperature.
First-strand cDNA synthesis was performed using random hexamer primers, while second-strand cDNA synthesis was carried out using DNA Polymerase I and RNase H. End repair, A-tailing, and adapter ligation were performed to generate the final cDNA library.

tag: disease state

value: healthy

value: Peripheral Blood Platelets


title: BRCA-B050_H3K79me2_ChIPseq


title: Female,AdLib,Saline,P21,rep8

description:
Library name: 15A.1_Female_AdLib_Saline_mPFC_P21
15A.1_Female_AdLib_Saline_mPFC_P21
P21_mPFC_counts.txt


title: BRCA-B050_H3K27ac_ChIPseq


title: Female,AdLib,Saline,P21,rep7

description:
Library name: 14B.2_Female_AdLib_Saline_mPFC_P21
14B.2_Female_AdLib_Saline_mPFC_P21
P21_mPFC_counts.txt


title: Female,AdLib,Saline,P21,rep6

description:
Library name: 14B.1_Female_AdLib_Saline_mPFC_P21
14B.1_Female_AdLib_Saline_mPFC_P21
P21_mPFC_counts.txt


title: BRCA-B050_H3K4me1_ChIPseq


title: Female,AdLib,Saline,P21,rep5

description:
Library name: 13C.7_Female_AdLib_Saline_mPFC_P21
13C.7_Female_AdLib_Saline_mPFC_P21
P21_mPFC_counts.txt


title: Female,AdLib,Saline,P21,rep4

description:
Library name: 13B.6_Female_AdLib_Saline_mPFC_P21
13B.6_Female_AdLib_Saline_mPFC_P21
P21_mPFC_counts.txt


title: BRCA-B047_Input DNA


title: BRCA-B047_H3K27me3_ChIPseq


title: BRCA-B047_H3K4me3_ChIPseq


title: Female,AdLib,Saline,P21,rep3

description:
Library name: 13A.7_Female_AdLib_Saline_mPFC_P21
13A.7_Female_AdLib_Saline_mPFC_P21
P21_mPFC_counts.txt


title: BRCA-B047_H3K79me2_ChIPseq


title: Female,FR,Saline,P21,rep2

description:
Library name: 12A.1_Female_FR_Saline_mPFC_P21
12A.1_Female_FR_Saline_mPFC_P21
P21_mPFC_counts.txt


title: Female,AdLib,Saline,P21,rep2

description:
Library name: 11A.2_Female_AdLib_Saline_mPFC_P21
11A.2_Female_AdLib_Saline_mPFC_P21
P21_mPFC_counts.txt


title: Female,AdLib,Saline,P21,rep1

description:
Library name: 11A.1_Female_AdLib_Saline_mPFC_P21
11A.1_Female_AdLib_Saline_mPFC_P21
P21_mPFC_counts.txt


title: Female,FR,Saline,P21,rep1

description:
Library name: 10A.7_Female_FR_Saline_mPFC_P21
10A.7_Female_FR_Saline_mPFC_P21
P21_mPFC_counts.txt


title: BRCA-B038_Input DNA


title: BRCA-B038_H3K27me3_ChIPseq


title: BRCA-B047_H3K9me3_ChIPseq


title: BRCA-B038_H3K4me3_ChIPseq


title: Male,FR,Saline,P21,rep9

description:
Library name: 8B.3_Male_FR_Saline_mPFC_P21
8B.3_Male_FR_Saline_mPFC_P21
P21_mPFC_counts.txt


title: Male,FR,Saline,P21,rep7

description:
Library name: 7A.3_Male_FR_Saline_mPFC_P21
7A.3_Male_FR_Saline_mPFC_P21
P21_mPFC_counts.txt


title: BRCA-B038_H3K79me2_ChIPseq


title: Male,FR,Saline,P21,rep8

description:
Library name: 8A.3_Male_FR_Saline_mPFC_P21
8A.3_Male_FR_Saline_mPFC_P21
P21_mPFC_counts.txt


title: Male,FR,Saline,P21,rep10

description:
Library name: 9A.1_Male_FR_Saline_mPFC_P21
9A.1_Male_FR_Saline_mPFC_P21
P21_mPFC_counts.txt


title: Male,FR,Saline,P21,rep6

description:
Library name: 6B.3_Male_FR_Saline_mPFC_P21
6B.3_Male_FR_Saline_mPFC_P21
P21_mPFC_counts.txt


title: BRCA-B038_H3K9me3_ChIPseq


title: Male,FR,Saline,P21,rep5

description:
Library name: 4A.1_Male_FR_Saline_mPFC_P21
4A.1_Male_FR_Saline_mPFC_P21
P21_mPFC_counts.txt


title: BRCA-B038_H3K4me1_ChIPseq


title: Male,AdLib,Saline,P21,rep10

description:
Library name: 3B.3_Male_AdLib_Saline_mPFC_P21
3B.3_Male_AdLib_Saline_mPFC_P21
P21_mPFC_counts.txt


title: BRCA-B038_H3K27ac_ChIPseq


title: BRCA-B035_Input DNA


title: Male,AdLib,Saline,P21,rep9

description:
Library name: 16C.3_Male_AdLib_Saline_mPFC_P21
16C.3_Male_AdLib_Saline_mPFC_P21
P21_mPFC_counts.txt


title: Male,FR,Saline,P21,rep4

description:
Library name: 16A.3_Male_FR_Saline_mPFC_P21
16A.3_Male_FR_Saline_mPFC_P21
P21_mPFC_counts.txt


title: Male,AdLib,Saline,P21,rep8

description:
Library name: 15A.3_Male_AdLib_Saline_mPFC_P21
15A.3_Male_AdLib_Saline_mPFC_P21
P21_mPFC_counts.txt


title: BRCA-B035_H3K79me2_ChIPseq


title: BRCA-B035_H3K27me3_ChIPseq


title: BRCA-B035_H3K27ac_ChIPseq


title: BRCA-B035_H3K9me3_ChIPseq


title: BRCA-B035_H3K4me1_ChIPseq


title: Male,AdLib,Saline,P21,rep5

description:
Library name: 13C.5_Male_AdLib_Saline_mPFC_P21
13C.5_Male_AdLib_Saline_mPFC_P21
P21_mPFC_counts.txt


title: Male,AdLib,Saline,P21,rep4

description:
Library name: 13B.4_Male_AdLib_Saline_mPFC_P21
13B.4_Male_AdLib_Saline_mPFC_P21
P21_mPFC_counts.txt


title: BRCA-B034_Input DNA


title: Male,AdLib,Saline,P21,rep3

description:
Library name: 13A.5_Male_AdLib_Saline_mPFC_P21
13A.5_Male_AdLib_Saline_mPFC_P21
P21_mPFC_counts.txt


title: Male,AdLib,Saline,P21,rep2

description:
Library name: 11A.4_Male_AdLib_Saline_mPFC_P21
11A.4_Male_AdLib_Saline_mPFC_P21
P21_mPFC_counts.txt


title: BRCA-B034_H3K27me3_ChIPseq


title: Male,FR,Saline,P21,rep3

description:
Library name: 12B.6_Male_FR_Saline_mPFC_P21
12B.6_Male_FR_Saline_mPFC_P21
P21_mPFC_counts.txt


title: Male,AdLib,Saline,P21,rep1

description:
Library name: 11A.3_Male_AdLib_Saline_mPFC_P21
11A.3_Male_AdLib_Saline_mPFC_P21
P21_mPFC_counts.txt


title: BRCA-B034_H3K9me3_ChIPseq


title: BRCA-B034_H3K79me2_ChIPseq


title: BRCA-B034_H3K4me3_ChIPseq


title: Male,FR,Saline,P21,rep2

description:
Library name: 12A.3_Male_FR_Saline_mPFC_P21
12A.3_Male_FR_Saline_mPFC_P21
P21_mPFC_counts.txt


title: BRCA-B034_H3K27ac_ChIPseq


title: Male,FR,Saline,P21,rep1

description:
Library name: 10A.5_Male_FR_Saline_mPFC_P21
10A.5_Male_FR_Saline_mPFC_P21
P21_mPFC_counts.txt


title: BRCA-B034_H3K4me1_ChIPseq


title: Female,Adlib,Insulin,P0,rep10

description:
Library name: 9A.7_Female_Adlib_Insulin_PFC_P0
9A.7_Female_Adlib_Insulin_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B028_Input DNA


title: Female,Adlib,Insulin,P0,rep8

description:
Library name: 8A.14_Female_Adlib_Insulin_PFC_P0
8A.14_Female_Adlib_Insulin_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B028_H3K27me3_ChIPseq


title: BRCA-B028_H3K4me3_ChIPseq


title: Female,Adlib,Insulin,P0,rep7

description:
Library name: 7A.12_Female_Adlib_Insulin_PFC_P0
7A.12_Female_Adlib_Insulin_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B035_H3K4me3_ChIPseq


title: BRCA-B028_H3K79me2_ChIPseq


title: Female,FR,Insulin,P0,rep10

description:
Library name: 6A.3_Female_FR_Insulin_PFC_P0
6A.3_Female_FR_Insulin_PFC_P0
P0_mPFC_counts.txt


title: Female,Adlib,Insulin,P0,rep9

description:
Library name: 8B.3_Female_Adlib_Insulin_PFC_P0
8B.3_Female_Adlib_Insulin_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B028_H3K27ac_ChIPseq


title: Female,FR,Insulin,P0,rep9

description:
Library name: 5B.5_Female_FR_Insulin_PFC_P0
5B.5_Female_FR_Insulin_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B028_H3K9me3_ChIPseq


title: Female,FR,Insulin,P0,rep8

description:
Library name: 4B.9_Female_FR_Insulin_PFC_P0
4B.9_Female_FR_Insulin_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B028_H3K4me1_ChIPseq


title: Female,Adlib,Insulin,P0,rep6

description:
Library name: 4A.12_Female_Adlib_Insulin_PFC_P0
4A.12_Female_Adlib_Insulin_PFC_P0
P0_mPFC_counts.txt


title: Female,FR,Insulin,P0,rep7

description:
Library name: 2B.8_Female_FR_Insulin_PFC_P0
2B.8_Female_FR_Insulin_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B021_H3K27me3_ChIPseq


title: BRCA-B021_Input DNA


title: BRCA-B021_H3K4me3_ChIPseq


title: Female,FR,Insulin,P0,rep6

description:
Library name: 16B.9_Female_FR_Insulin_PFC_P0
16B.9_Female_FR_Insulin_PFC_P0
P0_mPFC_counts.txt


title: Female,FR,Insulin,P0,rep5

description:
Library name: 16B.8_Female_FR_Insulin_PFC_P0
16B.8_Female_FR_Insulin_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B021_H3K79me2_ChIPseq


title: Female,Adlib,Insulin,P0,rep5

description:
Library name: 16A.16_Female_Adlib_Insulin_PFC_P0
16A.16_Female_Adlib_Insulin_PFC_P0
P0_mPFC_counts.txt


title: Female,FR,Insulin,P0,rep4

description:
Library name: 15B.7_Female_FR_Insulin_PFC_P0
15B.7_Female_FR_Insulin_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B021_H3K27ac_ChIPseq


title: Female,Adlib,Insulin,P0,rep4

description:
Library name: 15A.7_Female_Adlib_Insulin_PFC_P0
15A.7_Female_Adlib_Insulin_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B021_H3K4me1_ChIPseq


title: BRCA-B021_H3K9me3_ChIPseq


title: Female,FR,Insulin,P0,rep3

description:
Library name: 14A.6_Female_FR_Insulin_PFC_P0
14A.6_Female_FR_Insulin_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B020_Input DNA


title: BRCA-B020_H3K27me3_ChIPseq


title: Female,FR,Insulin,P0,rep2

description:
Library name: 14A.5_Female_FR_Insulin_PFC_P0
14A.5_Female_FR_Insulin_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B020_H3K4me3_ChIPseq


title: Female,Adlib,Insulin,P0,rep3

description:
Library name: 13A.9_Female_Adlib_Insulin_PFC_P0
13A.9_Female_Adlib_Insulin_PFC_P0
P0_mPFC_counts.txt


title: Female,FR,Saline,P21,rep3

description:
Library name: 12B.4_Female_FR_Saline_mPFC_P21
12B.4_Female_FR_Saline_mPFC_P21
P21_mPFC_counts.txt


title: BRCA-B047_H3K27ac_ChIPseq


title: COAD-C016_Input DNA


title: BRCA-B047_H3K4me1_ChIPseq


title: Female,FR,Insulin,P0,rep1

description:
Library name: 11B.7_Female_FR_Insulin_PFC_P0
11B.7_Female_FR_Insulin_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B020_H3K79me2_ChIPseq


title: Female,Adlib,Insulin,P0,rep1

description:
Library name: 11A.11_Female_Adlib_Insulin_PFC_P0
11A.11_Female_Adlib_Insulin_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B020_H3K9me3_ChIPseq


title: Female,Adlib,Insulin,P0,rep2

description:
Library name: 12A.13_Female_Adlib_Insulin_PFC_P0
12A.13_Female_Adlib_Insulin_PFC_P0
P0_mPFC_counts.txt


title: Male,Adlib,Insulin,P0,rep10

description:
Library name: 9A.1_Male_Adlib_Insulin_PFC_P0
9A.1_Male_Adlib_Insulin_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B020_H3K27ac_ChIPseq


title: Male,Adlib,Insulin,P0,rep9

description:
Library name: 8A.5_Male_Adlib_Insulin_PFC_P0
8A.5_Male_Adlib_Insulin_PFC_P0
P0_mPFC_counts.txt


title: Male,Adlib,Insulin,P0,rep8

description:
Library name: 7A.3_Male_Adlib_Insulin_PFC_P0
7A.3_Male_Adlib_Insulin_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B020_H3K4me1_ChIPseq


title: BRCA-B019_H3K27me3_ChIPseq


title: Male,Adlib,Insulin,P0,rep7

description:
Library name: 6B.3_Male_Adlib_Insulin_PFC_P0
6B.3_Male_Adlib_Insulin_PFC_P0
P0_mPFC_counts.txt


title: Control_06

type: RNA

city: Beijing

first: Siyuan

last: Guo

state: Beijing

address: No. 9 Fanjiacun Road, Fengtai District

department: Department of Oral and Maxillofacial Plastic and Traumatic Surgery

institute: Beijing Stomatological Hospital, Capital Medical University

description: Gene expression data of peripheral blood from normal controls

hyb_protocol: Following labeling, fragmented cDNA was hybridized for 16 hr at 45C on GeneChip Clariom D Human Assay. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: Peripheral blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: condition

value: Control

value: blood

tag: gender

value: male


title: BRCA-B019_Input DNA


title: BRCA-B019_H3K4me3_ChIPseq


title: BRCA-B019_H3K79me2_ChIPseq


title: Male,FR,Insulin,P0,rep9

description:
Library name: 5B.3_Male_FR_Insulin_PFC_P0
5B.3_Male_FR_Insulin_PFC_P0
P0_mPFC_counts.txt


title: Male,FR,Insulin,P0,rep10

description:
Library name: 6A.1_Male_FR_Insulin_PFC_P0
6A.1_Male_FR_Insulin_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B019_H3K27ac_ChIPseq


title: Male,FR,Insulin,P0,rep8

description:
Library name: 4B.1_Male_FR_Insulin_PFC_P0
4B.1_Male_FR_Insulin_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B019_H3K9me3_ChIPseq


title: BRCA-B019_H3K4me1_ChIPseq


title: Male,Adlib,Insulin,P0,rep6

description:
Library name: 4A.1_Male_Adlib_Insulin_PFC_P0
4A.1_Male_Adlib_Insulin_PFC_P0
P0_mPFC_counts.txt


title: Male,FR,Insulin,P0,rep7

description:
Library name: 2B.1_Male_FR_Insulin_PFC_P0
2B.1_Male_FR_Insulin_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B015_H3K27me3_ChIPseq


title: Male,FR,Insulin,P0,rep6

description:
Library name: 1AFR.2_Male_FR_Insulin_PFC_P0
1AFR.2_Male_FR_Insulin_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B015_Input DNA


title: Male,Adlib,Insulin,P0,rep5

description:
Library name: 16A.4_Male_Adlib_Insulin_PFC_P0
16A.4_Male_Adlib_Insulin_PFC_P0
P0_mPFC_counts.txt


title: Male,FR,Insulin,P0,rep5

description:
Library name: 16B.5_Male_FR_Insulin_PFC_P0
16B.5_Male_FR_Insulin_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B015_H3K4me3_ChIPseq


title: Male,AdLib,Saline,P21,rep7

description:
Library name: 14B.4_Male_AdLib_Saline_mPFC_P21
14B.4_Male_AdLib_Saline_mPFC_P21
P21_mPFC_counts.txt


title: Male,AdLib,Saline,P21,rep6

description:
Library name: 14B.3_Male_AdLib_Saline_mPFC_P21
14B.3_Male_AdLib_Saline_mPFC_P21
P21_mPFC_counts.txt


title: BRCA-B015_H3K79me2_ChIPseq


title: IgG-DMSO

first: Yuan

last: Qi

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

description: Library name: IgG-pH74-DMSO

data_processing:
Sequence reads quality were checked by fastqc, and trimmed for adaptor /low quality sequencie using trim-galore (--paired -stringency 5 -length 27)
Trimmed reads were aligned to hg19 using bwa mem with default parameters
Aligned bam files were sorted and filtered by samtools with -q 10 option.
bam files were converted to bw files using bamCoverage reads per genomic content (1x normalization) with effective genome size of 2451960000.
Assembly: hg19
Supplementary files format and content: bigWig, processed alignment
Library strategy: CUT&Run

extract_protocol:
Cells were harvested and washed twice with wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and EDTA-free protease inhibitor cocktail). The cells were then incubated overnight with the rabbit anti-P300 antibody (1:50, Cell Signaling, Cat# 54062, RRID:AB_2799450) in the buffer (Wash buffer supplemented with 0.05% digitonin and 2 mM EDTA) at 4 °C. The following day, the supernatant was removed by centrifugation and the cell pellets were washed once with Dig-wash buffer (Wash buffer containing 0.05% digitonin). The cell pellets were then incubated with Protein A-MNase (700 ng/mL in Dig-wash buffer) for 1 h by rotation at 4 °C. After three washes, the cell pellets were resuspended in 100 μl Dig-wash buffer with 2 μl of 100 mM CaCl2, incubated at 0 °C for 30 min and then the reactions were stopped by the addition of 100 μl 2×STOP buffer (340 mM NaCl, 20 mM EDTA pH 8.0, 4 mM EGTA, 0.05% digitonin, 50 μg/mL RNase A, 50 μg/mL glycogen and 2 pg/mL heterologous spike-in yeast DNA). The supernatant DNA was collected after centrifugation and further purified using phenol–chloroform–isoamyl alcohol (Sigma, Cat#: p3803), chloroform extraction and ethanol precipitation.
The CUT&RUN-seq library construction was performed using 10 ng CUT&RUN DNA and a NEBNext ultra DNA library prep kit (NEB, Cat#: E7645); the CUT&RUN-seq libraries were sequenced in a 50 bp paired-end sequencing on a NextSeq 1000 system (Illumina), using Illumina's NextSeq 1000 P2 Reagents (#20046811) following the manufacturer's instructions.

value: Human Epithelial Ovarian Cancer Cell Line


title: Male,FR,Insulin,P0,rep4

description:
Library name: 15B.1_Male_FR_Insulin_PFC_P0
15B.1_Male_FR_Insulin_PFC_P0
P0_mPFC_counts.txt


title: Male,FR,Insulin,P0,rep3

description:
Library name: 14A.1_Male_FR_Insulin_PFC_P0
14A.1_Male_FR_Insulin_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B015_H3K27ac_ChIPseq


title: BRCA-B015_H3K9me3_ChIPseq


title: Male,Adlib,Insulin,P0,rep4

description:
Library name: 15A.3_Male_Adlib_Insulin_PFC_P0
15A.3_Male_Adlib_Insulin_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B015_H3K4me1_ChIPseq


title: BRCA-B014_Input DNA


title: Male,Adlib,Insulin,P0,rep3

description:
Library name: 13A.1_Male_Adlib_Insulin_PFC_P0
13A.1_Male_Adlib_Insulin_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B014_H3K4me3_ChIPseq


title: Male,FR,Insulin,P0,rep1

description:
Library name: 11B.3_Male_FR_Insulin_PFC_P0
11B.3_Male_FR_Insulin_PFC_P0
P0_mPFC_counts.txt


title: Male,Adlib,Insulin,P0,rep2

description:
Library name: 12A.6_Male_Adlib_Insulin_PFC_P0
12A.6_Male_Adlib_Insulin_PFC_P0
P0_mPFC_counts.txt


title: Male,Adlib,Insulin,P0,rep1

description:
Library name: 11A.4_Male_Adlib_Insulin_PFC_P0
11A.4_Male_Adlib_Insulin_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B014_H3K27me3_ChIPseq


title: Male,FR,Insulin,P0,rep2

description:
Library name: 11C.4_Male_FR_Insulin_PFC_P0
11C.4_Male_FR_Insulin_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B014_H3K9me3_ChIPseq


title: BRCA-B014_H3K27ac_ChIPseq


title: Female,Adlib,Saline,P0,rep10

description:
Library name: 9A.5_Female_Adlib_Saline_PFC_P0
9A.5_Female_Adlib_Saline_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B014_H3K79me2_ChIPseq


title: Female,Adlib,Saline,P0,rep9

description:
Library name: 8B.2_Female_Adlib_Saline_PFC_P0
8B.2_Female_Adlib_Saline_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B014_H3K4me1_ChIPseq


title: Female,Adlib,Saline,P0,rep8

description:
Library name: 8A.9_Female_Adlib_Saline_PFC_P0
8A.9_Female_Adlib_Saline_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B013_Input DNA


title: Female,Adlib,Saline,P0,rep7

description:
Library name: 7A.10_Female_Adlib_Saline_PFC_P0
7A.10_Female_Adlib_Saline_PFC_P0
P0_mPFC_counts.txt


title: Female,FR,Saline,P0,rep10

description:
Library name: 6A.7_Female_FR_Saline_PFC_P0
6A.7_Female_FR_Saline_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B013_H3K4me3_ChIPseq


title: BRCA-B013_H3K79me2_ChIPseq


title: Female,FR,Saline,P0,rep9

description:
Library name: 5B.4_Female_FR_Saline_PFC_P0
5B.4_Female_FR_Saline_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B013_H3K27ac_ChIPseq


title: Female,FR,Saline,P0,rep8

description:
Library name: 4B.11_Female_FR_Saline_PFC_P0
4B.11_Female_FR_Saline_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B013_H3K9me3_ChIPseq


title: BRCA-B013_H3K4me1_ChIPseq


title: Female,FR,Saline,P0,rep7

description:
Library name: 4B.10_Female_FR_Saline_PFC_P0
4B.10_Female_FR_Saline_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B010_Input DNA


title: Female,FR,Saline,P0,rep6

description:
Library name: 2B.11_Female_FR_Saline_PFC_P0
2B.11_Female_FR_Saline_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B010_H3K4me3_ChIPseq


title: Female,Adlib,Saline,P0,rep5

description:
Library name: 16A.12_Female_Adlib_Saline_PFC_P0
16A.12_Female_Adlib_Saline_PFC_P0
P0_mPFC_counts.txt


title: Female,Adlib,Saline,P0,rep6

description:
Library name: 4A.14_Female_Adlib_Saline_PFC_P0
4A.14_Female_Adlib_Saline_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B010_H3K27ac_ChIPseq


title: BRCA-B010_H3K79me2_ChIPseq


title: Female,FR,Saline,P0,rep5

description:
Library name: 16B.7_Female_FR_Saline_PFC_P0
16B.7_Female_FR_Saline_PFC_P0
P0_mPFC_counts.txt


title: Female,FR,Saline,P0,rep4

description:
Library name: 15B.5_Female_FR_Saline_PFC_P0
15B.5_Female_FR_Saline_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B010_H3K4me1_ChIPseq


title: Female,Adlib,Saline,P0,rep4

description:
Library name: 15A.5_Female_Adlib_Saline_PFC_P0
15A.5_Female_Adlib_Saline_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B008_Input DNA


title: BRCA-B008_H3K4me3_ChIPseq


title: Female,FR,Saline,P0,rep2

description:
Library name: 14A.7_Female_FR_Saline_PFC_P0
14A.7_Female_FR_Saline_PFC_P0
P0_mPFC_counts.txt


title: Female,FR,Saline,P0,rep3

description:
Library name: 14A.8_Female_FR_Saline_PFC_P0
14A.8_Female_FR_Saline_PFC_P0
P0_mPFC_counts.txt


title: Female,Adlib,Saline,P0,rep3

description:
Library name: 13A.11_Female_Adlib_Saline_PFC_P0
13A.11_Female_Adlib_Saline_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B008_H3K79me2_ChIPseq


title: BRCA-B008_H3K27ac_ChIPseq


title: Female,Adlib,Saline,P0,rep2

description:
Library name: 12A.10_Female_Adlib_Saline_PFC_P0
12A.10_Female_Adlib_Saline_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B003_Input DNA


title: Female,FR,Saline,P0,rep1

description:
Library name: 11B.5_Female_FR_Saline_PFC_P0
11B.5_Female_FR_Saline_PFC_P0
P0_mPFC_counts.txt


title: Female,Adlib,Saline,P0,rep1

description:
Library name: 11A.8_Female_Adlib_Saline_PFC_P0
11A.8_Female_Adlib_Saline_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B003_H3K4me3_ChIPseq


title: BRCA-B003_H3K79me2_ChIPseq


title: BRCA-B008_H3K4me1_ChIPseq


title: Male,Adlib,Saline,P0,rep8

description:
Library name: 8B.1_Male_Adlib_Saline_PFC_P0
8B.1_Male_Adlib_Saline_PFC_P0
P0_mPFC_counts.txt


title: Male,Adlib,Saline,P0,rep7

description:
Library name: 8A.2_Male_Adlib_Saline_PFC_P0
8A.2_Male_Adlib_Saline_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B003_H3K27ac_ChIPseq


title: Male,Adlib,Saline,P0,rep6

description:
Library name: 7A.1_Male_Adlib_Saline_PFC_P0
7A.1_Male_Adlib_Saline_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B003_H3K4me1_ChIPseq


title: BRCA-B003_H3K27me3_ChIPseq


title: Male,Adlib,Saline,P0,rep9

description:
Library name: 9A.3_Male_Adlib_Saline_PFC_P0
9A.3_Male_Adlib_Saline_PFC_P0
P0_mPFC_counts.txt


title: Male,Adlib,Saline,P0,rep5

description:
Library name: 6B.1_Male_Adlib_Saline_PFC_P0
6B.1_Male_Adlib_Saline_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B001_Input DNA


title: Male,FR,Saline,P0,rep10

description:
Library name: 6A.2_Male_FR_Saline_PFC_P0
6A.2_Male_FR_Saline_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B001_H3K27me3_ChIPseq


title: Male,FR,Saline,P0,rep9

description:
Library name: 5B.1_Male_FR_Saline_PFC_P0
5B.1_Male_FR_Saline_PFC_P0
P0_mPFC_counts.txt


title: BRCA-B001_H3K4me3_ChIPseq


title: Nthy, EZH1 Q571R, ATAC, rep2

city: Seoul

first: Hanbyeol

last: Kim

address: Daehak-ro 103

country: South Korea

institute: Seoul National University

description: Library name: Nthy_EZH1_Q571R_ATAC_rep2

data_processing:
Adapter sequences were trimmed using fastp and reads were aligned to the human (hg38) and E. coli (k12) reference genomes using Bowtie2. Mitochondrial reads and reads mapping to the ENCODE black list were removed. BAM files were normalized using RPKM to account for differences in sequencing depth. Subsequently, these values were further adjusted using scaling factors derived from reads mapping to the E. coli genome (originating from residual DNA in the Tn5 transposase preparation) were used to calculate scaling factors. Bigwig files were generated using deepTools and visualized using the Integrative Genomics Viewer (IGV). Heatmaps were generated with deepTools to visualize chromatin accessibility patterns across conditions.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Nthy-ori 3-1

growth_protocol: RPMI, 10% fetal bovine serum, 2mM glutamine, 1x antibiotics/antimycotics. Cells were cultured at 37°C at 5% CO2.

extract_protocol:
ATAC-seq was performed as previously described. Briefly, 50,000 cells were harvested and washed with ice-cold PBS. The supernatant was removed, and the cell pellet was resuspended in 50 µL of lysis buffer (10 mM Tris-HCl [pH 7.4], 3 mM MgCl2, 10 mM NaCl, and 0.1% NP-40). Nuclei were collected and resuspended in 50 µL of transposition reaction buffer (10 mM TAPS [pH 8.5], 5 mM MgCl2, and 10% DMF) containing adaptor-loaded Tn5 transposase. The reaction was incubated at 37°C for 30 min in a thermomixer set to 1,000 rpm. To terminate tagmentation, 10 µL of clean-up buffer (900 mM NaCl and 300 mM EDTA [pH 8.0]) was added.
Tagmented DNA was purified using the MinElute PCR Purification Kit and quantified via qPCR. Libraries were amplified using the KAPA HiFi HotStart PCR Kit with index primers and purified using SPRIselect DNA Size Selection Reagent. Sequencing was performed on an Illumina NovaSeq X (100 bp paired-end) or NovaSeq X Plus (150 bp paired-end) platform.

value: Nthy-ori 3-1

value: Thyroid follicular epithelial cell

value: EZH1 Q571R overexpression


title: Male,FR,Saline,P0,rep8

description:
Library name: 4B.5_Male_FR_Saline_PFC_P0
4B.5_Male_FR_Saline_PFC_P0
P0_mPFC_counts.txt

value: Medial prefrontal cortex


title: Zahra_1_kPa-plus_serum-2

status: Public on Jul 04 2026

city: Heidelberg

first: Rida

last: Zahra

address: Im Neuenheimer Feld 230

department: Centre for Organismal Studies (COS), Cytoskeleton, Cell division and Signalling Unit

country: Germany

institute: Heidelberg University

description: Library name: Sample 2

data_processing:
Quality of the raw data was assessed with FastQC.The adapter sequence was trimmed with Trimmomatic 0.39.
Assembly: After removal of the adapter sequence, reads were mapped against human genome hg38 using STAR with an annotation file from GENCODE (version 21). Later, SAMtools was used to sort the genearated BAM files and counting was done by QoRTs.
Supplementary files format and content: Raw counts are available in the form of .txt files or .csv files

growth_protocol: RPE1 cells were cultured in DMEM F12 supplemented with 10% FBS, 2 mM L-glutamine and 0.348% sodium bicarbonate with 5% CO2 at 37C.

extract_protocol:
Total RNA was harvested using NucleoSpin® RNA Plus (Macherey-Nagel) kit according to the manufacturer´s protocol.
Library peparation was carried out using TruSeq Stranded kit at the NGS core facility of German Cancer research center (DKFZ), Heidelberg, Germany according to the manufacturer´s protocol.

treatment_protocol: Bulk RNA sequencing was performed on RPE1 cells cultured on 1 kPa polyacrylamide hydrogel (coated with fibronectin) or glass-control (glass coated with fibronectin only) in the presence of serum for 24 hours. Furthermore, transcriptomic profile of serum starved cells with respect to their cyclin control was also analyzed. For that, RPE1 cells (cultured on uncoated glass) were serum starved for 6 and 24 hours and cyclin cells (0 hours of serum-starvation samples) were used as their respective controls.

value: Retinal pigment epithelial cells


title: BRCA-B001_H3K79me2_ChIPseq


title: Nthy, EZH1 Q571R, ATAC, rep1

description: Library name: Nthy_EZH1_Q571R_ATAC_rep1


title: Nthy, EZH1 WT, ATAC, rep2

description: Library name: Nthy_EZH1_WT_ATAC_rep2

value: EZH1 WT overexpression


title: Male,FR,Saline,P0,rep7

description:
Library name: 2B.5_Male_FR_Saline_PFC_P0
2B.5_Male_FR_Saline_PFC_P0
P0_mPFC_counts.txt


title: Control rep3

city: JEONJU

first: SOO MI

last: KIM

state: JEONBUK

address: GUNGIRO 20

department: PHYSIOLOGY

institute: JEONBUK NATIONAL UNIVERSITY

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Human HepG2 cell line

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Hepatocellular carcinoma cell line


title: Full-thickness skin wound, non-diabetic, rep 4

first: Craig

last: Duvall

address: 2414 Highland Ave

department: Biomedical Engineering

description: Library name: R9_G_24_1

data_processing:
Data processing was completed by Novogene Co, Ltd - Bulk RNA-seq was conducted using the Illumina NovaSeq X Plus Series platform. Raw reads were processed with fastp software to remove adaptor sequences and retain clean reads. Clean reads were mapped against the Sus scrofa reference genome (Sscrofa11.1) using HISAT2 (version 2.2.1). Mapped reads were then assembled using StringTie (version 2.2.3) and quantified using featureCounts (version 2.0.6).
Assembly: Sscrofa11.1
Supplementary files format and content: Tab-delimited text file includes FPKM values for each Sample

organism: Sus scrofa

source_name: Dermal wound/skin

extract_protocol:
Excised tissue from biopsy punches was stored in RNAlater™ Stabilization Solution (Invitrogen) at -80 °C until the time of RNA isolation. Total RNA was extracted by lysing tissue in TRIzol™ Reagent (Invitrogen) using a TissueLyser II (QIAGEN). The tissue homogenate was phase-separated with chloroform, and the aqueous RNA phase was further purified using a RNeasy Mini Kit (QIAGEN) per the manufacturer’s recommendations.
Library construction was completed by Novogene Co, Ltd. - Messenger RNAwaspurified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: Dermal wound/skin

tag: phenotype

value: Non-diabetic

tag: time

value: Day 10


title: Male,FR,Saline,P0,rep6

description:
Library name: 1AFR.1_Male_FR_Saline_PFC_P0
1AFR.1_Male_FR_Saline_PFC_P0
P0_mPFC_counts.txt


title: Full-thickness skin wound, non-diabetic, rep 3

description: Library name: R6_G_24_1


title: Full-thickness skin wound, non-diabetic, rep 2

description: Library name: L8_G_24_1


title: BRCA-B001_H3K9me3_ChIPseq

data_processing:
ChIPseq reads were aligned to hg19 genome using bowtie1 with max 1 mismatch, duplicated reads were removed
peaks were called using MACS14 and MACS2 using pvalue cutoff of 1e-5
bigwig files were generated by deeptools bamCoverage normalized by RPKM
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files contains the ChIPseq signal normalized by RPKM. Bed files contain the peaks called by MACS14 and MACS2

extract_protocol:
Crosslinked samples were thawed on ice and resuspended in RIPA lysis buffer supplemented with protease inhibitor, lysed the cells on ice then sheared the chromatin by sonication. After centrifuge, the clean sonicated cell lysate mixed with protein G magnetic dynabeads (Invitrogen) coupled to antibodies described above and incubated over night at 4 degrees. Samples was washed 5 times with cold RIPA, twice with high salt RIPA, twice with LiCl buffer, twice with TE, and then eluted in elution buffer. The eluate was reverse crosslinked at 65C. Solid-phase reversible immobilization (SPRI) cleanup steps were performed. Beads were washed twice on the magnet with 70% ethanol and then air-dried. The DNA was eluted in EB buffer.
Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and Bioanalyzer 1000 before multiplexing.

value: Breast cancer cell line


title: BRCA-B001_H3K27ac_ChIPseq


title: Full-thickness skin wound, non-diabetic, rep 1

description: Library name: L5_G_24_1


title: Full-thickness skin wound, diabetic, rep 6

description: Library name: R9_D_24_2

value: Diabetic


title: Full-thickness skin wound, diabetic, rep 7

description: Library name: R14_D_24_2


title: BRCA-B001_H3K4me1_ChIPseq


title: Male,Adlib,Saline,P0,rep4

description:
Library name: 16A.1_Male_Adlib_Saline_PFC_P0
16A.1_Male_Adlib_Saline_PFC_P0
P0_mPFC_counts.txt


title: Nthy, EZH1 WT, ATAC, rep1

description: Library name: Nthy_EZH1_WT_ATAC_rep1


title: mammary_gland_chromatin_mouse45

city: Paris

first: Céline

last: Vallot

address: 26 Rue D'Ulm

country: France

institute: Institut Curie

description:
Library name: mammary_gland_chromatin_mouse45
Chromatin part of the plate

data_processing:
Raw single-cell epigenomics data were pre-processed using the sc-epigenome pipeline of Curie institute (v2.0.0, https://github.com/bioinfo-pf-curie/scepigenome)
Raw transcriptomic data were processed using the scRNA-smartseq3 Nextflow pipeline of Curie Institute (https://github.com/bioinfo-pf-curie/scRNA-SmartSeq3).
Assembly: mm10
Supplementary files format and content: fagment files for chromatin
Supplementary files format and content: full length and umi-only count matrices for rna
Library strategy: CUT&Tag

source_name: mammary gland

growth_protocol: Mice were sacrificed by cervical dislocation. Six mammary glands (numbers 2, 3, and 4 from each side) were collected and pooled. The pooled tissues were roughly chopped using dissecting scissors, followed by finer mincing with two scalpels. Single-cell dissociation was achieved through enzymatic digestion using 3 mg ml–1 collagenase I (Roche, 11088793001) and 100 U m–1 hyaluronidase (Sigma-Aldrich, H3506) in complete media (HBSS 24020117; 5% FBS) for 2 h under agitation (170 rpm) at 37°C. Cells were then treated with pre-warmed (37°C) PBS 0.25% trypsin-versen (Thermo Fisher Scientific, 15040-033) for 1 min 30s, with pipetting for 45s. Twas further processed with 5 mg ml–1 dispase (Sigma-Aldrich, D4693) and DNase 0.1 mg ml–1 (Roche, 11284932001) in complete media for 6 min at 37°C. Red blood cells were lysed using red blood cell lysis buffer (Thermo Fisher Scientific, 00-4333-57), and the suspension was filtered through a 40 µm cell strainer before cell counting and FACS staining. The cells were stained in the dark at 4°C for 20 min. Stained cells were resuspended at 10 million cells ml–1 in cytometry media (PBS with 1% BSA and 2 mM EDTA).  Three control mice were sorted with the following antibodies: anti-CD45-APC (1:50, BioLegend, 103112), anti-CD31-APC (1:50, BioLegend, 102510), anti-CD24-BV421 (1:50, BioLegend, 101826) and anti-CD49f-PE-Cy7 (1:50, BioLegend, 313622) to stain one million cells.  Sorting was performed using a SH800 sorter with a 100 µm chip, and epithelial cells (CD45-, CD31-, CD24 medium/high, CD49f medium/high) were collected in a 384-well plate, with one cell per well, using a custom single-cell sorting mode (60% mask). Two control mice were sorted with an expanded FACS panel comprising the following antibodies: anti-CD45-BV510 (1:500, BioLegend, 103138), CD31-BV510 (1:100, BD Biosciences, 563089); anti-CD29-PE-Dazzle594 (1:500, BioLegend, 102245), EpCAM-PE-Cy7 (1:500, BioLegend, 118215), Tspan8-BUV395 (1:100, BD Biosciences, 748043). Dead cells were excluded using Zombie NIR Fixable Viability Dye (1:5000, BioLegend, 423106); according to the manufacturer’s instructions. When the expanded panel was applied, 10 million cells were stained to enable capture of the rare Tspan8+ cell population. Cell sorting was performed on a BD Aria Fusion cell sorter. Epithelial cells (CD45-, CD31-, EpCAM medium/high, CD29 medium/high) were index-sorted into 384-well plates at one cell per well. Wells were allocated as follows: 50% luminal cells (CD45-, CD31-, EpCAM high, CD29 medium), 25% Tspan8⁺ basal cells (CD45-, CD31, EpCAM low, CD29 high, Tspan8+), and 25% Tspan8- basal cells (CD45-, CD31-, EpCAM low, CD29 high, Tspan8-).

extract_protocol:
The plate was subjected to the multiome OneCell CUT&Tag protocol, as described in Schwager & Moutaux et. al 2026.
Combination of OneCell CUT&Tag with single-cell full-length transcriptomics, as described in (Schwager, Moutaux et al., 2026)

value: mammary gland

value: epithelial

value: no

tag: library type

value: DNA


title: Male,FR,Saline,P0,rep4

description:
Library name: 15B.3_Male_FR_Saline_PFC_P0
15B.3_Male_FR_Saline_PFC_P0
P0_mPFC_counts.txt


title: Full-thickness skin wound, diabetic, rep 4

description: Library name: R3_D_24_2


title: Full-thickness skin wound, diabetic, rep 5

description: Library name: R5_D_24_2


title: mammary_gland_chromatin_mouse3

description:
Library name: mammary_gland_chromatin_mouse3
Chromatin part of the plate


title: Oral_Biopsy_CrohnsDiseasePatient_Experiment1_GEX

city: Kiel

first: Philipp

last: Hofmann

address: Michaelisstraße 5

department: Institute of Medical Immunology

institute: Christian-Albrecht-University of Kiel

description:
Library name: Oral_CD_Experiment1_GEX
10X Genomics
GEX (5’ 10X Genomics) library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
Raw sequencing base calls were converted to FASTQ files using cellranger mkfastq. The resulting FASTQ files were then processed with Cell Ranger (v7.1.0) and aligned to the GRCh38 human reference genome (Cell Ranger 2020-A release). Paired single-cell RNA and single-cell TCR data were processed using cellranger multi, utilizing the Cell Ranger VDJ reference 7.1.0 for TCR read alignment. Sample-specific demultiplexing for single cell experiments involving hashtag antibodies was achieved by employing a modified Cell Ranger workflow, adapting the 3’ CellPlex pipleline for 5’ chemistry as described in the 10X Genomics online protocol (https://www.10xgenomics.com/analysis-guides/demultiplexing-and-analyzing-5’-immune-profiling-libraries-pooled-with-hashtags). Briefly, a customized cell multiplexing oligo reference was created, specifying each hashtag antibody sequence and incorporating an updated sequence pattern “^NNNNNNNNNN(BC)NNNNNNNNN” to define the barcode position within the hashtag antibody FASTQ files. An initial run of cellranger multi was performed using FASTQ files for the gene expression and hashtag antibody libraries along with the customized cell multiplexing oligo reference to enable sample demultiplexing. The resulting sample-specific BAM files were converted to FASTQ format using 10X Genomics bamtofastq (v1.4.1) and utilized in a second cellranger multi run to allow fully demultiplexed processing of paired single-cell RNA and TCR data.
Assembly: GRCh38
Supplementary files format and content: CellRanger count pipeline output: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CellRanger vdj pipeline output: filtered_contig_annotations.csv

source_name: Oral tissue

extract_protocol:
C. albicans-reactive CD154+ Tmem from peripheral blood or CD3+CD4+CD45RO+ cells from tissues were sorted with FACS and labeled with barcoded hashtag antibodies for sample multiplexing. In brief, PBMCs were stimulated with C. albicans, Th17 targets and Non-Th17 Targets for 6 h in the presence of 1 μg ml−1 of CD40 and 1 μg ml−1 of CD28 pure antibody. Cells were labeled with CD154-Biotin, followed by anti-biotin MicroBeads, and magnetically enriched by MS Columns (all from Miltenyi Biotec). Cells were stained on the column with TotalSeq-C anti-human hashtag antibodies (LNH-94, 1:50) in the presence of Human TruStain FcX (1:20) in 50 μl of staining volume. Columns were washed twice, and cells were eluted with 1000 μl of sterile filtered 1x PBS supplemented with 0.5% (v/v) human AB-serum. Subsequently, cells were sorted via FACS into precoated, low-bind collection tubes, containing sterile, filtered 1xPBS supplemented with 0.5% (v/v) human AB-serum. For intestinal tissue, up to four biopsies were pooled, whereas single biopsies were used  for oral samples (from the roof of the mouth, 4mm). Intestinal and oral biopsies were processed by mincing the tissue with scalpels and enzymatically digesting in 1mL of HBSS Ca2+Mg+ (Gibco) supplemented with 0.5% (v/v) human AB-serum (GemCell), 100 IU/mL penicillin, 100 mg/mL streptomycin, 0.25 mg/mL amphotericin B (Antibiotic Antimycotic Solution, Sigma Aldrich), 20uL/mL DNAseI (CellSystems), 1mg/mL collagenase type CLS IV (Biochrom). Tissue digestion was performed at 37°C while shaking for 30 minutes. Cells were passed through a sterile filter and stained with fluorochrome-conjugated antibodies to CD4-Vioblue or CD4-FITC, CD3-PE or CD3-VioGreen, CD45-AlexaFlour700, CD8/CD14/CD20-PerCP (Dump channel), CD45RO-APC, CLA-BV605 and Integrin-b7-PE-Vio770. Oral samples were stained with TotalSeq-C anti-human hashtag antibodies (LNH-94, 1:50) in the presence of Human TruStain FcX (1:20) in 50 μl of staining volume. Cells were sorted via FACS into precoated, low-bind collection tubes, containing sterile, filtered 1xPBS supplemented with 0.5% (v/v) human AB-serum.  After sorting, cells reactive for each antigen or oral cells derived from multiple donors were combined for sample multiplexing. FACS-enriched cells fractions from intestinal samples were processed individually.
FACS-enriched cells were loaded on a Chromium Next GEM Chip K (10X Genomics) for processing with the Chromium Next GEM Single Cell 5′ Kit v2 according to the manufacturer’s instructions. Sequencing libraries were generated as detailed in the manufacturer’s user guide (CG000511 Rev D).

value: Oral tissue

value: CD4+ T cells

value: Healthy Control and Crohn's disease patient

value: mixed sample (Oral CD4 +Tcells from CD3, CD4. CD5)

value: mRNA


title: Male,Adlib,Saline,P0,rep3

description:
Library name: 15A.1_Male_Adlib_Saline_PFC_P0
15A.1_Male_Adlib_Saline_PFC_P0
P0_mPFC_counts.txt

value: Medial prefrontal cortex


title: Control rep2

description: replicate 2


title: Full-thickness skin wound, diabetic, rep 3

description: Library name: L11_D_24_2


title: Full-thickness skin wound, diabetic, rep 2

description: Library name: L8_D_24_2


title: mammary_gland_chromatin_mouse2

description:
Library name: mammary_gland_chromatin_mouse2
Chromatin part of the plate


title: Male,FR,Saline,P0,rep3

description:
Library name: 14A.3_Male_FR_Saline_PFC_P0
14A.3_Male_FR_Saline_PFC_P0
P0_mPFC_counts.txt


title: mammary_gland_chromatin_mouse1

description:
Library name: mammary_gland_chromatin_mouse1
Chromatin part of the plate


title: Mouse ovary immune cells PCOS TCR

first: Chenlei

last: Xu

address: No. 38 Xueyuan Road, Haidian District

institute: Peking University

description:
Library name: pcos-10XTCR
Single-cell TCR V(D)J library from mouse ovarian immune cells in the PCOS model group, paired with the corresponding GEX library.

data_processing:
Raw sequencing data from gene expression libraries were processed using Cell Ranger v8.0.0 to generate gene-barcode expression matrices.
Raw sequencing data from TCR V(D)J libraries were processed using Cell Ranger v8.0.0 using the vdj_GRCm38_alts_ensembl-5.0.0 reference.
Filtered feature-barcode matrices were used for downstream single-cell RNA-seq analysis.
Single-cell RNA-seq data were analyzed using Seurat. Cells were filtered based on quality control metrics, followed by normalization, feature selection, dimensionality reduction, clustering, and cell type annotation.
TCR clonotype information was obtained from Cell Ranger V(D)J output files and integrated with the corresponding single-cell gene expression data.
Assembly: GRCm38/mm10
Supplementary files format and content: Processed gene expression data files include 10x Genomics feature-barcode matrices for each sample, including barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files containing cell barcodes, gene annotations, and raw UMI count matrices.
Library strategy: TCR-seq

source_name: ovary

growth_protocol: Female wild-type mice were maintained under specific-pathogen-free conditions with free access to food and water.

extract_protocol:
Ovaries were collected from control and PCOS model mice and dissociated into single-cell suspensions. Ovarian immune cells were enriched or sorted according to the experimental design. Cell viability and concentration were assessed before single-cell library preparation.
Single-cell gene expression libraries were prepared using the 10x Genomics Chromium Single Cell 5' Gene Expression platform. Single-cell TCR V(D)J libraries were prepared from the same cell suspensions using the 10x Genomics Chromium Single Cell V(D)J enrichment workflow according to the manufacturer's instructions.

treatment_protocol: Female mice in the PCOS model group were treated with letrozole to induce a PCOS-like phenotype, while control mice received vehicle treatment.

value: ovary

value: ovarian immune cells

value: wild type

value: PCOS model

tag: batch

value: batch 1


title: Full-thickness skin wound, diabetic, rep 1

description: Library name: L6_D_24_2

value: Dermal wound/skin

value: Day 10


title: Spatial Transcriptomics, Spleen set_2

city: Aachen

first: Mohamed

last: Saad

address: Pauwelsstraße 30

department: Institut für Zell- und Tumorbiologie

institute: Uniklinik RWTH Aachen

description: Library name: TMA_set_2

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger (v2.0.0) pipeline.
Assembly: GRCm39-2024-A
Supplementary files format and content: barcodes.tsv.gz : list of spatial barcodes
Supplementary files format and content: features.tsv.gz : list of gene Ids
Supplementary files format and content: matrix.mtx.gz : gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: TMA_overview.xlsx : Spatial location of each TMA
Supplementary files format and content: OverviewBF.tif : Bright field tissue image
Supplementary files format and content: high_res.qptiff : High quality image
Library strategy: Spatial Transcriptomics

source_name: Spleen

growth_protocol: BM cells from CD45.1 donor (male and female) mice were isolated 48h prior to transplantation. C-kit enriched cells were transduced with 1) ThPO lentivirus or  empty vector (EV) control lentivirus, or with 2) MPL retrovirus or EV control retrovirus, depending on mouse model. Gli1CreERT;tdTomato recipients (male and female) were injected with tamoxifen (4x30mg, every 48h) in corn oil/ 3% ethanol intraperitoneally. Three weeks after the last tamoxifen injection, 15-20 week old recipients were 1) lethally irradiated using twice 5Gy, 4h apart, or 2) sublethally irradiated using 5Gy before receiving 0.5 x106 transduced C-kit+ donor cells by intravenous injection. Blood was collected biweekly starting 4 weeks after transplantation and basic blood parameters were measured. Remaining blood was further processed for flow cytometry. For the ThPO model, spleen volume was measured by weekly ultrasound under isoflurane anesthesia using the Visualsonics Vevo3100 starting 4 weeks after transplantation. The software Vevo LAB (v5.7.1) was used for analysis. Mice were sacrificed at 1) 4 weeks (early) or 8-10 weeks (late/endstage) post-transplant or at 2) 4-5 weeks post-transplant. For each analysis, a control group, sacrificed on the same day, was used for comparison. CD45.1 C-kit+ donor cells were lentiviral transduced with ThPO or EV control. WT and C3KO mice (male and female) were lethally irradiated using twice 6Gy before receiving 0.5 x106 transduced C-kit+ donor cells by intravenous injection. WT and C3KO mice receiving CD45.1 C-kit+ donor cells retroviral transduced with MPL or EV control were irradiated sublethally using once 6Gy. Blood was collected biweekly starting 4 weeks after transplantation and analysed in the same way as described above. ThPO and EV control mice were sacrificed 6 weeks (middle) or 8 weeks (late/endstage) post-transplant. MPL and EV control mice were sacrificed 4 weeks post-transplant.

extract_protocol:
Visium HD spatial transcriptomics were performed with paraffin-embedded spleen sections. Two areas per spleen with n = 3 spleens per condition (4 conditions; WT and C3KO; ThPO-late and empty vector control each) were used for the experiment. One area of spleens from one set of conditions was sequenced as one batch (n = 12 spleen areas per batch).
Spatial transcriptome sequencing librairies were prepared with 10xGenomics Visium CytAssist Spatial Gene Expression Slides & Reagent kit according to manufacturer’s construction. Visium V4 Slides FFPE v2 were used.

value: Spleen


title: Spatial Transcriptomics, Spleen set_1

description: Library name: TMA_set_1


title: zygotes_onecell_multiome_h3k4me1_batch2

description:
Library name: zygotes_onecell_multiome_h3k4me1_batch2
L548_Zygote_rH3K4me1.fragments.tsv.gz
L548_Zygote_rH3K4me1.bigwig

data_processing:
Raw single-cell epigenomics data were pre-processed using the sc-epigenome pipeline of Curie institute (v2.0.0, https://github.com/bioinfo-pf-curie/scepigenome)
Raw transcriptomic data were processed using the scRNA-smartseq3 Nextflow pipeline of Curie Institute (https://github.com/bioinfo-pf-curie/scRNA-SmartSeq3).
Assembly: mm10
Supplementary files format and content: fragment files (chromatin)
Supplementary files format and content: full-length and umi-only count matrices (rna)
Supplementary files format and content: Chromatin pseudobulk bigwig
Supplementary files format and content: Example single-cell chromatin and RNA bigwigs for same single cells
Library strategy: CUT&Tag

source_name: zygote

extract_protocol:
Zygotes were manually dispensed in 2µl of M2 medium with 0.2µl Dynabeads Myone Carboxylic (Fisher, 10563775) and kept on ice. After a 5 min centrifugation at 800g at 4°C, the supernatant was removed using the magnetic plate and replaced by 2µl of lysis buffer. Plates were then frozen at -80°C. Multiome OneCell CUT&Tag experiment was performed in two biological replicates, each corresponding to zygotes from one mouse.
Combination of OneCell CUT&Tag with single-cell full-length transcriptomics, as described in (Moutaux, Schwager et al., 2025)

value: zygote

value: mouse zygote


title: Mouse ovary immune cells PCOS GEX

description:
Library name: pcos-10X5
Single-cell gene expression library from mouse ovarian immune cells in the PCOS model group.

data_processing:
Raw sequencing data from gene expression libraries were processed using Cell Ranger v8.0.0 to generate gene-barcode expression matrices.
Raw sequencing data from TCR V(D)J libraries were processed using Cell Ranger v8.0.0 using the vdj_GRCm38_alts_ensembl-5.0.0 reference.
Filtered feature-barcode matrices were used for downstream single-cell RNA-seq analysis.
Single-cell RNA-seq data were analyzed using Seurat. Cells were filtered based on quality control metrics, followed by normalization, feature selection, dimensionality reduction, clustering, and cell type annotation.
TCR clonotype information was obtained from Cell Ranger V(D)J output files and integrated with the corresponding single-cell gene expression data.
Assembly: GRCm38/mm10
Supplementary files format and content: Processed gene expression data files include 10x Genomics feature-barcode matrices for each sample, including barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files containing cell barcodes, gene annotations, and raw UMI count matrices.


title: Male,FR,Saline,P0,rep2

description:
Library name: 11C.1_Male_FR_Saline_PFC_P0
11C.1_Male_FR_Saline_PFC_P0
P0_mPFC_counts.txt


title: Mouse ovary immune cells control TCR

description:
Library name: control-10XTCR
Single-cell TCR V(D)J library from mouse ovarian immune cells in the control group, paired with the corresponding GEX library.

value: control


title: Male,FR,Saline,P0,rep1

description:
Library name: 11B.1_Male_FR_Saline_PFC_P0
11B.1_Male_FR_Saline_PFC_P0
P0_mPFC_counts.txt


title: transplantations_chromatin_p14

description:
Library name: transplantations_chromatin_p14
Chromatin part of the plate

data_processing:
Raw single-cell epigenomics data were pre-processed using the sc-epigenome pipeline of Curie institute (v2.0.0, https://github.com/bioinfo-pf-curie/scepigenome)
Raw transcriptomic data were processed using the scRNA-smartseq3 Nextflow pipeline of Curie Institute (https://github.com/bioinfo-pf-curie/scRNA-SmartSeq3).
Assembly: mm10
Supplementary files format and content: fragment files (chromatin)
Supplementary files format and content: full-length and umi-only count matrices (rna)
Library strategy: CUT&Tag

growth_protocol: Mammary cell preparation for transplantation. Mammary glands from K14cre/RosaYFP34,35 adult female mice were dissected and the lymph nodes removed before processing. Tissues were washed in HBSS, and chopped into pieces of 1 mm3. The tissues were placed in HBSS plus 300 U/ml collagenase (Sigma) plus 300 mg/ml hyaluronidase (Sigma) and digested for 2 h at 37°C under shaking. EDTA at a final concentration of 5mM was added for 10 min to the resultant organoid suspension, followed by 0.25% Trypsin-EGTA for 2 min before filtration through a 40-mm mesh, two successive washes in 2% FBS/PBS and labelling. Unisuspension of cells were incubated in 250 ml (per 5 millions cells) of 2% FBS/PBS with primary antibodies for 30 min, with shaking every 10 min. Primary antibodies were washed with 2% FBS/PBS cells were resuspended in 2.5 mg/ml DAPI (Invitrogen) before analysis. Primary antibodies used were: APC-Cy7-conjugated anti-Epcam (1/100, clone G8.8, Biolegend), AF700-conjugated anti-CD29 (1/100, clone HMB1-1, Biolegend), APC-conjugated anti-CD45 (1/100, clone 30-F11, eBiosciences), APC-conjugated anti-CD31(1/100, clone 390, eBiosciences), APC-conjugated anti-CD140a (1/100, clone APA5, eBiosciences). Data analysis and cell sorting was performed on a FACSAria III sorter using the FACS DiVa software (BD Biosciences). Dead cells were excluded with DAPI; CD45+, CD31+ and CD140a+ cells were excluded (Lin-) before analysis of the YFP+ cells. Basal cells were defined as Lin-YFP+Epcam+CD29high population while luminal cells were defined as Lin-YFP+Epcam+CD29low. Sorted basal cells were collected in 300 ul DMEM 50%/FBS 50%.  Mammary fat-pad transplantation. 10.000 sorted basal YFP+ cells were resuspended in 10 ul DMEM 25%/FBS 25%/Matrigel 50% and injected into the number 4 glands of 4-week-old NOD/SCID female mice that had been cleared of endogenous epithelium, using a 26g Hamilton syringe. Transplanted glands were harvested 4.5 days after grafting and processed as described in the 2 previous sections for sorting of YFP+ cells.

value: mammary gland

value: fresh tissue

value: epithelial

value: no

value: DNA


title: Male,Adlib,Saline,P0,rep1

description:
Library name: 11A.1_Male_Adlib_Saline_PFC_P0
11A.1_Male_Adlib_Saline_PFC_P0
P0_mPFC_counts.txt

data_processing:
Reads were aligned to the rat genome with STAR
Read counts per gene were computed with STAR
Assembly: Rnor_6.0
Supplementary files format and content: Ensembl gene Ids and read counts, tab delimited
Supplementary files format and content: Differential expression data, tab delimited

value: Medial prefrontal cortex


title: Male,Adlib,Saline,P0,rep2

description:
Library name: 12A.1_Male_Adlib_Saline_PFC_P0
12A.1_Male_Adlib_Saline_PFC_P0
P0_mPFC_counts.txt


title: transplantations_chromatin_p13

description:
Library name: transplantations_chromatin_p13
Chromatin part of the plate


title: Mouse ovary immune cells control GEX

description:
Library name: control-10X5
Single-cell gene expression library from mouse ovarian immune cells in the control group.

value: ovary


title: mammary_gland_rna_mouse45

description:
Library name: mammary_gland_rna_mouse45
RNA part of the plate

data_processing:
Raw single-cell epigenomics data were pre-processed using the sc-epigenome pipeline of Curie institute (v2.0.0, https://github.com/bioinfo-pf-curie/scepigenome)
Raw transcriptomic data were processed using the scRNA-smartseq3 Nextflow pipeline of Curie Institute (https://github.com/bioinfo-pf-curie/scRNA-SmartSeq3).
Assembly: mm10
Supplementary files format and content: fagment files for chromatin
Supplementary files format and content: full length and umi-only count matrices for rna

value: mRNA


title: Female,Adlib,Insulin,Adult,rep10

description:
Library name: 9B.8_Female_Adlib_Insulin_mPFC_Adult
9B.8_Female_Adlib_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: transplantations_chromatin_p12

description:
Library name: transplantations_chromatin_p12
Chromatin part of the plate


title: mammary_gland_rna_mouse23

description:
Library name: mammary_gland_rna_mouse23
RNA part of the plate


title: Male,Adlib,Insulin,Adult,rep10

description:
Library name: 9B.4_Male_Adlib_Insulin_mPFC_Adult
9B.4_Male_Adlib_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: transplantations_chromatin_p11

description:
Library name: transplantations_chromatin_p11
Chromatin part of the plate


title: transplantations_chromatin_p10

description:
Library name: transplantations_chromatin_p10
Chromatin part of the plate


description:
Library name: zygotes_onecell_multiome_rna_for_h3k4me1_batch2
10XlikeMatrix_read.tar.gz
10XlikeMatrix_umi.tar.gz

data_processing:
Raw single-cell epigenomics data were pre-processed using the sc-epigenome pipeline of Curie institute (v2.0.0, https://github.com/bioinfo-pf-curie/scepigenome)
Raw transcriptomic data were processed using the scRNA-smartseq3 Nextflow pipeline of Curie Institute (https://github.com/bioinfo-pf-curie/scRNA-SmartSeq3).
Assembly: mm10
Supplementary files format and content: fragment files (chromatin)
Supplementary files format and content: full-length and umi-only count matrices (rna)
Supplementary files format and content: Chromatin pseudobulk bigwig
Supplementary files format and content: Example single-cell chromatin and RNA bigwigs for same single cells


title: transplantations_chromatin_p9

description:
Library name: transplantations_chromatin_p9
Chromatin part of the plate


description:
Library name: zygotes_onecell_multiome_rna_for_h3k4me1_batch1
10XlikeMatrix_read.tar.gz
10XlikeMatrix_umi.tar.gz


title: Female,FR,Insulin,Adult,rep10

description:
Library name: 5B.8_Female_FR_Insulin_mPFC_Adult
5B.8_Female_FR_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: Male,Adlib,Insulin,Adult,rep9

description:
Library name: 6A.4_Male_Adlib_Insulin_mPFC_Adult
6A.4_Male_Adlib_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: Female,Adlib,Insulin,Adult,rep9

description:
Library name: 6A.8_Female_Adlib_Insulin_mPFC_Adult
6A.8_Female_Adlib_Insulin_mPFC_Adult
Adult_mPFC_counts.txt


title: transplantations_chromatin_p8

description:
Library name: transplantations_chromatin_p8
Chromatin part of the plate


title: transwell,DMSO treated 3

city: shanghai

first: Yong

middle: hui

last: Chen

address: 160, Pujian Road

institute: Renji hospital

description:
Library name: sample6
DMSO_3

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM and count values for each sample

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using 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 is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are 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 are 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 library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: DMSO


title: transplantations_chromatin_p7

description:
Library name: transplantations_chromatin_p7
Chromatin part of the plate


title: WT_FSK_Rep3

city: Seattle

first: Meagan

middle: Nicole

last: Esbin

state: WA

address: 850 Republican St. S280

department: Obstetrics & Gynecology

institute: University of Washington School of Medicine

description: Library name: Sample 10

data_processing:
Raw data were assessed using FastQC
FASTQ files were pseudoaligned to the hg38 transcriptome using Salmon to quantify transcripts in mapping-based mode (salmon quant -i) using decoy-aware mapping with gencode.v39. transcripts.fa.
Differential gene expression analysis was performed with EdgeR in Jupyter Notebook. Raw counts were filtered to remove genes with fewer than 10 reads per sample or fewer than 15 reads summed across all samples. Counts per million reads (CPM) was calculated for the filtered count data using the EdgeR function cpm. Statistical comparisons between individual sample conditions were made using EdgeR makeContrasts and then glmQLFit. The reported P-values and FDR values were corrected with adjust.method = “BH,” and differentially expressed genes are reported with an adjusted FDR of <0.05.
For visualization, the STAR program was used to map .fastq reads onto the hg38 genome to generate .bam files for each sample. These .bam files were converted to .bigWig files using bedtools and merged (summed) across the three replicates of each sample type.
Assembly: hg38
Supplementary files format and content: Comma separated values file containing CPM-normalized count data for each Sample by NCBI Gene ID and ifferential gene expression analysis output from EdgeR with the Log2 Fold-Change (FC)  and Benjamini-Hochberg (BH) corrected False Discovery Rate (FDR) for each gene comparing Forskolin-treated ZBTB10 KO vs. Forskolin-treated WT cells. Comparisons are noted as (FSK_KOvsWT) where positive FC values indicates higher gene expression in Forskolin-treated ZBTB10 KO cells.
Supplementary files format and content: Bigwig files to be used for Genome track visualization (i.e. IGV viewer) of binned reads mapped across the human genome merged (summed) across the 3 replicates for each sample type.

source_name: BeWo

growth_protocol: BeWo cells (ATCC CCL-98) were cultured at 37°C and 5% CO2 in F-12K medium (Corning or ATCC) supplemented with 10% fetal bovine serum and 10 U/mL penicillin–streptomycin. Cells were passaged by trypsinization every 2–4 days and split at a ratio of 1:3–1:5. Media was changed completely every 24–36 h.

extract_protocol:
RNA was extracted from each well using 500 µL of Trizol followed by two sequential chloroform extractions followed by ethanol precipitation per the Trizol user guide (Thermo Fisher MAN0001271).
Total RNA was depleted of rRNA using the Illumina rRNA depletion kit (NEB E6310) and then prepared for Illumina sequencing using the NEBNext Ultra II directional RNA library preparation kit for Illumina (E7760) per the manufacturer's protocol. Sequencing was performed by MedGenome on an Illumina NovaSeq with paired-end 150 bp reads.

treatment_protocol: BeWo cells were plated at 300,000 cells per well into a 6 well plate and allowed to settle 6 h to overnight. Cells were then treated with 0.1% DMSO or 20 μM Forskolin for 48 h. Media for all treatments was changed at 24 h.

value: BeWo

value: choriocarcinoma

value: wild-type

value: 20uM FSK, 48hr


title: transplantations_chromatin_p5

description:
Library name: transplantations_chromatin_p5
Chromatin part of the plate


title: WT_DMSO_Rep3

description: Library name: Sample 9


title: transplantations_chromatin_p4

description:
Library name: transplantations_chromatin_p4
Chromatin part of the plate