title: MCF-7 cell,nc 1

value: breast cancer

value: MCF-7 cell

value: HER2-negative breast cancer cells


title: 1st replicate of H3K4me3 CUT&RUN on parental SALE cells.

status: Public on Jul 14 2025

type: SRA

city: Seattle

first: Alice

last: Berger

state: WA

address: 1100 Fairview Ave N

country: USA

institute: Fred Hutchinson Cancer Center

description: Library name: A8_SALE_par_H3K4me3

library_source: genomic

data_processing:
Trim Galore (https://github.com/FelixKrueger/TrimGalore) was used to examine read quality and trim adapters. Reads were aligned to the reference genome using Bowtie2. Genome coverage profiles were generated using bedtools genomecov. MACS2 was used to call peaks from each sample in both target-only and IgG-controlled modes. Reads from all IgG samples were pooled to create a common control for peak calling. For narrow peaks from transcription factors and H3K4me3, IgG-controlled peaks were kept for downstream analysis if they met the following criteria: overlapping with treatment-only peaks, q-value < 0.01 and enrichment > 2. For broad peaks from H3K27me3, target-only peaks were kept for downstream analysis if they met the follow criteria: overlapping with IgG-controlled peaks, q-value < 0.01 and enrichment > 2.
Assembly: hg38
Supplementary files format and content: .bw files are BigWig files normalized using the counts per millions (CPM) method.
Library strategy: CUT&Run

molecule: genomic DNA

organism: Homo sapiens

source_name: SALE

extract_protocol:
12 million cells per cell line were collected by trypsinization, washed extensively in Wash Buffer (20mM HEPES-NaOH pH 7.5, 150mM NaCl, 0.5mM Spermidine (Cell Signaling Technology), and 1 large Roche complete EDTA-free protease tablet per 50mL solution).
Concanavalin A beads (Bangs Laboratories, ca. no. BP531) were activated through repeated washing in Binding Buffer (20mM HEPES-KOS pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2), and prepared at 10µL per sample. Beads were added under gentle vortex, and incubated rocking at room temperature for 8 minutes. Bead-cell complexes were collected by magnet separation, buffer removed, and bead-cell complexes were resuspended in Antibody Buffer (0.1% Triton-X 100, 2mM EDTA). Each cell line sample was then split into two technical replicates per cell line, per antibody. Primary antibodies were added to a final dilution of 1:100 (see Star Methods) and incubated for 2hrs rotating at 4 ºC. Samples were processed for AutoCUT&RUN by arraying in a 96-well PCR plate and processed on a Beckman Biomek i7 liquid handling instrument equipped with a 96S Super Magnet Plate (Alpaqua SKU A001322) for magnetic separation of samples during wash steps, and a QInstruments ColdPlate heater-cooler thermo block (QInstruments no. 2016-0110) with a 96 well PCR plate adapter (Qinstruments no. 2016-1041) to perform the MNase digestion reaction at 4 °C after the addition of 2 mM CaCl2. MNase digestion reactions are then stopped after 120 min by adding EGTA, which allows Mg2+ addition for subsequent enzymatic reactions. Chromatin fragments released into the supernatant during digestion are then used as the substrate for end-repair and ligation with barcoded Y-adapters. Prior to ligation, the A-tailing step is performed at 58 °C to preserve sub-nucleosomal fragments in the library. End-repair and adapter ligation reactions are performed on a separate thermocycler. Chromatin proteins are then digested with Proteinase K, and adapter ligated DNA fragments are purified on the Biomek i7 using two rounds of pre-PCR Ampure bead cleanup with size selection. PCR enrichment reactions are performed on a thermocycler using the KAPA PCR kit (KAPA Cat#KK2502). Two rounds of post-PCR Ampure bead cleanup with size selection are performed on the Biomek i7 to remove unwanted proteins and self-ligated adapters. The size distributions of AutoCUT&RUN libraries are analyzed on an Agilent 4200 TapeStation, and gated size and quantification values are used to calculate sample library yields for pooling. Up to 96 barcoded AutoCUT&RUN libraries are pooled at equimolar concentration for paired-end 50 × 50 bp sequencing on an Illumina NextSeq P2 platform at the Fred Hutchinson Cancer Center Genomics Shared Resource.

tag: cell line

value: SALE

tag: cell type

value: immortalized small airway lung epithelial cells

tag: genotype

value: parental

tag: antibody


title: RNA-seq of THP-1 macrophages:M.luteus infected-a

city: COLLEGE STATION

first: Doyoung

last: Kwak

state: Texas

address: 302 Ball Street

institute: Texas A&M

description:
Library name: THP-M.luteus-a
RNA isolated from THP-1 macrophages cells infected with Micrococcus luteus and collected at 1hour post infection (replicate 1)

library_source: transcriptomic

data_processing:
Raw sequencing reads in FASTQ format were processed to remove adapter sequences, poly-N reads, and low-quality reads, generating high-quality clean reads. Clean reads from each sample were aligned to the Homo sapiens reference genome (GRCh38.p12) using STAR (v2.5.4b), along with the annotation reference gencode.v30.chr_patch_hapl_scaff.annotation.gff3. Alignment efficiency ranged from 73–87%, yielding 35.9–83.4 million uniquely mapped reads per sample. Uniquely mapped reads were used for gene-level quantification, ensuring that each read was assigned to a single, non-overlapping gene based on its genomic coordinates. Paired-end reads were checked for overlaps to improve mapping accuracy.
Assembly: Reads were aligned to the human reference genome sequence GRCh38.p12 along with the GENCODE annotation file gencode.v30.chr_patch_hapl_scaff.annotation.gff3.
Supplementary files format and content: Processed RNA-seq data files contain raw gene-level counts and are provided in comma-separated values (CSV) format. Each row corresponds to a gene, identified using Ensembl Gene IDs and annotated according to GENCODE v30.

molecule: total RNA

extract_protocol:
Total RNA was extracted using TRIzol™ reagent (Invitrogen) following manufacturer protocols. RNA integrity (RIN) and concentration were assessed using the Agilent 4200 TapeStation system, and only RNA samples with RIN >8 were used for library preparation.
RNA-seq libraries were generated using the TruSeq Stranded Total RNA-Seq Library Kit (Illumina), incorporating rRNA depletion. cDNA synthesis was performed using random primers, and paired-end libraries were constructed following the manufacturer’s instructions.Paired-end sequencing (2 × 150 bp) was performed on the Illumina NovaSeq6000 platform.

treatment_protocol: THP-1 monocytes were differentiated into macrophages using Phorbol 12-myristate 13-acetate (PMA, 100 ng/mL, 48 h) before infection with various bacterial strains. Infections were carried for 1 hour, after which cells were collected for RNA extraction. Bacterial Strains used,Pathogenic strains: Coxiella burnetii Nine Mile Phase II (NMII), Coxiella burnetii NMII dotA::Tn (T4SS mutant), Coxiella burnetii NMII dotB::Tn (T4SS mutant), Enterohemorrhagic Escherichia coli (O157, O157 Δstx), Francisella novicida U112, Pseudomonas aeruginosa PAO1, Staphylococcus aureus JE2, Salmonella enterica subsp. Typhimurium SL1344, Rhizobium radiobacter, Micrococcus luteus, Enterococcus faecalis, Brucella melitensis ΔvjbR. Non-pathogenic controls: Escherichia coli DH5α, Listeria innocua, Bacillus subtilis P31K6.

value: Monocytes

tag: treatment

value: PMA differentiation, followed by infection-1h


title: RNA-seq of THP-1 macrophages:Uninfected-3

description:
Library name: THP-Mock-3
RNA isolated from THP-1 macrophages uninfected cells collected at 1 hour post infection


title: 1st replicate of H3K4me1 CUT&RUN on parental SALE cells.

description: Library name: A7_SALE_par_H3K4me1


title: RNA-seq of THP-1 macrophages:C.burnetiidotB infected-c

description:
Library name: THP-CoxielladotB-c
RNA isolated from THP-1 macrophages cells infected with Coxiella burnetii dotB:: Tn and collected at 1hour post infection (replicate 3)


title: RNA-seq of THP-1 macrophages:R.radiobacter infected-b

description:
Library name: THP-R.radiobacter-b
RNA isolated from THP-1 macrophages cells infected with Rhizobium radiobacter and collected at 1hour post infection (replicate 2)


title: RNA-seq of THP-1 macrophages:R.radiobacter infected-a

description:
Library name: THP-R.radiobacter-a
RNA isolated from THP-1 macrophages cells infected with Rhizobium radiobacter and collected at 1hour post infection (replicate 1)


title: 1st replicate of FOSL1 CUT&RUN on parental SALE cells.

description: Library name: A6_SALE_par_FOSL1_1

value: FOSL1:Abcam ab252421


title: RNA-seq of THP-1 macrophages:R.radiobacter infected-d

description:
Library name: THP-R.radiobacter-d
RNA isolated from THP-1 macrophages cells infected with Rhizobium radiobacter and collected at 1hour post infection (replicate 4)


title: RNA-seq of THP-1 macrophages:Uninfected-2

description:
Library name: THP-Mock-2
RNA isolated from THP-1 macrophages uninfected cells collected at 1 hour post infection


title: 1st replicate of cJUN CUT&RUN on parental SALE cells.

description: Library name: A5_SALE_par_cJUN_1

value: cJUN:CST 9165


title: RNA-seq of THP-1 macrophages:DH5 infected-d

description:
Library name: THP-DH5a-d
RNA isolated from THP-1 macrophages cells infected with Escherichia coli DH5α and collected at 1hour post infection (replicate 4)


title: NK00_V2-9

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

description: Library name: NK00

library_source: other

data_processing:
the sequencing data were demultiplexed, converted to unmapped BAM (uBAM) format, and uploaded into Ion Reporter v.5.20 (Thermo Fisher Scientific)
Assembly: Greengenes database (v.13_5)
Supplementary files format and content: fastQ, and otu_table_total_tss.tsv for processed data
Library strategy: 16S rRNA-seq

molecule: other

organism: unidentified

source_name: gut microbiota

extract_protocol:
DNA was extracted using the QIAsymphony DSP/Virus/Pathogen Midi kit (Qiagen)
The libraries were then prepared using the Ion Plus Fragment Library Preparation Kit (Thermo Fisher Scientific)

tag: tissue

value: gut microbiota

tag: method

tag: region

tag: analysis type

value: validation

tag: family id

tag: patient caregiver


title: NJ75_V2-9

description: Library name: NJ75


title: 1st replicate of panTEAD CUT&RUN on parental SALE cells.

description: Library name: A4_SALE_par_panTEAD_1

value: panTEAD:CST 13295


title: NJ95_V2-9

description: Library name: NJ95


title: NX00_V2-9

description: Library name: NX00


title: NJ65_V2-9

description: Library name: NJ65


title: RNA-seq of THP-1 macrophages:DH5 infected-c

description:
Library name: THP-DH5a-c
RNA isolated from THP-1 macrophages cells infected with Escherichia coli DH5α and collected at 1hour post infection (replicate 3)


title: MCF-7 cell,nc 2

city: changchun

first: long

last: xu

address: xinmin road

country: China

institute: jilin university

data_processing:
In this project, the mRNA with polyA structure in the total RNA was enriched by Oligo(dT) magnetic beads, and the RNA was broken down to 200-300bp fragments by ion interruption. The 200-300bp fragment length was chosen because the splice length is fixed and a shorter interrupted fragment length would result in a higher proportion of splice sequences, thus reducing the proportion of valid data; a longer interrupted fragment length would not be conducive to cluster generation during up-sequencing. The first strand of cDNA was synthesised using RNA as the template and a 6-base random primer and reverse transcriptase, and the first strand cDNA was used as the template for the second strand cDNA synthesis.    Translated with www.DeepL.com/Translator (free version)
After library construction, PCR amplification was used to enrich the library fragments, followed by library selection based on fragment size, which ranged from 300-400 bp. The libraries were then quality checked by an Agilent 2100 Bioanalyzer, and the total library concentration and the effective library concentration were tested. Libraries containing different Index sequences (each sample with a different Index, and finally the downstream data of each sample according to the Index) were mixed proportionally according to the effective concentration of the library and the amount of data required for the library. The mixed libraries are uniformly diluted to 2nM and denatured by alkali to form single-stranded libraries.    Translated with www.DeepL.com/Translator (free version)
After RNA extraction, purification and library construction, these libraries were sequenced using Next-Generation Sequencing (NGS) based on the Illumina HiSeq sequencing platform with Paired-end (PE) sequencing.
Assembly: GRCh38 (hg38)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: breast cancer

extract_protocol:
RNA was harvested using RNeasy Mini Kits (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the ScriptSeq Complete Kit (Epicentre) following manufacturer's protocols.

value: nc

value: Normal cells


title: RNA-seq of THP-1 macrophages:DH5 infected-b

description:
Library name: THP-DH5a-b
RNA isolated from THP-1 macrophages cells infected with Escherichia coli DH5α and collected at 1hour post infection (replicate 2)


title: RNA-seq of THP-1 macrophages:DH5 infected-a

description:
Library name: THP-DH5a-a
RNA isolated from THP-1 macrophages cells infected with Escherichia coli DH5α and collected at 1hour post infection (replicate 1)


title: NJ40_V2-9

description: Library name: NJ40


title: 1st replicate of TAZ CUT&RUN on parental SALE cells.

description: Library name: A3_SALE_par_TAZ_1

value: TAZ:CST 4883


title: 1st replicate of YAP1 CUT&RUN on parental SALE cells.

description: Library name: A2_SALE_par_YAP1_1

value: YAP1:Abcam ab52771


title: RNA-seq of THP-1 macrophages:Uninfected-1

description:
Library name: THP-Mock-1
RNA isolated from THP-1 macrophages uninfected cells collected at 1 hour post infection


title: NJ30_V2-9

description: Library name: NJ30


title: RNA-seq of THP-1 macrophages:M.luteus infected-b

description:
Library name: THP-M.luetus-b
RNA isolated from THP-1 macrophages cells infected with Micrococcus luteus and collected at 1hour post infection (replicate 2)


title: NJ15_V2-9

description: Library name: NJ15


title: RNA-seq of THP-1 macrophages:R.radiobacter infected-c

description:
Library name: THP-R.radiobacter-c
RNA isolated from THP-1 macrophages cells infected with Rhizobium radiobacter and collected at 1hour post infection (replicate 3)


title: NC-2

city: Daqing

first: Jian

last: Mei

state: Heilongjiang Province

address: 39 Xinyang Road

department: Daqing campus

institute: Harbin Medical university

description: Library name: Sample2

data_processing:
STAR (version 2.7.10a)
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Lung

growth_protocol: PAECs were cultured in endothelial cell medium, containing 10% fetal bovine serum and 1% penicillin streptomycin at 37 °C, 5% CO2, and humidified atmosphere.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTSStranded mRNAseq Library Prep Kit for Illumina V2 following manufacturer's protocols.

treatment_protocol: Cells were transfected with U2AF2 overexpression plasmid and NC plasmid for 6 h and then cultured for 24 h, and cells were collected

value: Lung

value: Primary cells

value: Human pulmonary artery endothelial cells


title: U-1

description: Library name: Sample3


title: NI95_V2-9

description: Library name: NI95


title: Sample GSF-L-154 treated with Dht for 48h

city: Kiel

first: Radhika

middle: Bomma

last: Sivaprasad

state: Schleswig Holstein

address: Schwanenweg

department: Institute for Human Genetics

country: Germany

institute: Uniklinik Schleswig Holstein

description:
Library name: GSF-L-154_48h_Dht
raw_counts_cais_samples.tsv
raw_counts_cais_labia-minora_samples.tsv
Normalized_counts_CAIS_samples.xlsx
Normalized_counts_labia-minora_samples.xlsx

data_processing:
Sequencing data conversion and demultiplexing were performed using bcl2fastq2 v2.20 (Illumina). Gene-level count matrices were generated from the FASTQ files using the community-driven nf-core/rnaseq pipeline v3.12.0
The pipeline included adapter trimming (TrimGalore v0.6.7), contamination removal (SortMeRNA v4.3.4 and BBMap-BBSplit v39.01), alignment (STAR 2.7.10a) to hg38, transcript-level quantification (Salmon v1.10.1), and comprehensive quality control (FastQC v0.11.9, RESeQC v3.0.1, dupRadar v1.28.0, and MultiQC v1.14). Transcript-level counts were converted to gene-level counts using tximeta-tximport v1.12.0.
As the samples were processed in two separate sequencing runs (one for male control and one for CAIS samples), batch correction was applied to account for run-specific effects. The datasets were combined and processed together using Salmon (which includes STAR aligner support), ensuring consistent quantification across both batches.
Transcriptomic analysis was performed using Shiny-Seq, an RNA-sequencing analysis pipeline based on DESeq2.
Assembly: hg38
Supplementary files format and content: Raw counts for each sample are provided in a tab-separated values (TSV) file.
Supplementary files format and content: Normalized counts for each sample are provided in an Excel file.

molecule: polyA RNA

source_name: Labia minora

growth_protocol: GSFs were cultured in phenol red free Dulbecco's modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS, MaxSpec), 100 units/ml penicillin/streptomycin, 2 mM L-glutamine and 20 mM HEPES buffer (all purchased from Life Technologies) and incubated at 37°C in a 5% CO2 incubator

extract_protocol:
The cells were lysed in RNA-extraction buffer, and total RNA was extracted using the RNeasy Mini Kit with on-column DNase digestion. 1μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for the mRNA sequencing were prepared using the Illumina Stranded mRNA Prep Ligation kit following the manufacturer's protocol.

treatment_protocol: At 24 hours post-confluence, the medium was replaced with fresh medium containing 0.1% charcoal-stripped FBS, and cells were treated with 10 nM DHT. Control dishes received an equivalent volume of ethanol, and all cultures were incubated at 37°C with 5% CO₂ for 48 or 72 hours.

value: Labia minora

value: Genital skin fibroblast

value: CAIS

value: Dihydrotestosterone

tag: time

value: 48 hours

tag: batch


title: Sample GSF-L-154 treated with Etoh for 72h

description:
Library name: GSF-L-154_72h_Etoh
raw_counts_cais_samples.tsv
raw_counts_cais_labia-minora_samples.tsv
Normalized_counts_CAIS_samples.xlsx
Normalized_counts_labia-minora_samples.xlsx

value: Ethanol

value: 72 hours


title: Sample GSF-L-156 treated with Dht for 72h

description:
Library name: GSF-L-156_72h_Dht
raw_counts_cais_samples.tsv
raw_counts_cais_labia-minora_samples.tsv
Normalized_counts_CAIS_samples.xlsx
Normalized_counts_labia-minora_samples.xlsx


title: cd_TT_rep1

city: New Haven

first: Bluma

middle: J

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

description: Library name: cd_TT_rep1

data_processing:
Reads were filtered for unique sequences using FastUniq, trimmed using cutadapt and aligned to the hg19 genome along with annotations using HISAT.
Aligned reads were filtered to get uniquely mapping reads using SAMtools.
Reads were counted using HTSeq-count using the union mode.
To determine the number of uridine residues inferred from each read and the sites of T-to-C mutations, the aligned bam files were processed in R using Rsamtools.
Genome tracks were generated using STAR aligner and normalized using factors derived from DESeq2 estimateSizeFactors. Tracks were converted to binary format using the toTDF tool from IGVtools.
Assembly: hg19
Supplementary files format and content: tdf
Library strategy: TT-TimeLapse-seq

molecule: nuclear RNA

growth_protocol: DMEM, 10% fetal bovine serum, 2.5 ug/ml Plasmocin , 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
After rinsing twice with ice cold PBS, 1 mL TRIzol reagent (Thermo Fisher Scientific) was added to lyse cells. After incubation at room temperature for 5 min, 200 uL chloroform was added. Samples were vortexed and incubated briefly at room temperature and centrifuged at 12,000 × g, 5 min, 4°C. The aqueous phase was transferred to a new tube and total RNA was isolated by isopropanol precipitation. Genomic DNA was removed using the TURBO DNase Kit (Ambion) and then samples was further cleaned up with RNAclean XP beads (Beckman) following the manufacturer's instructions. 75 ug purified RNA was sheared in 160 uL RNA fragmentation buffer (75 mM Tris pH 7.4, 112.5 mM KCl, 4.5 mM MgCl2) for 3.5 min at 94°C. Sheared RNA was purified with the RNeasy Mini Kit (Qiagen). For each reaction, 50 ug purified RNA was biotinylated by 5 ug MTSEA-biotin-XX (Biotium) for 30 min at room temperature with rotation. Samples were purified again with RNeasy Mini Kit (Qiagen) to remove unreacted MTSEA-biotin-XX. Purified biotinylated RNA was incubated with 10 uL blocked Dynabeads MyOne Streptavidin C1 beads (Thermo Fisher Scientific) for 15 min at room temperature with rotation. Beads were washed with 100 uL High-salt Wash Buffer (100 mM Tris pH 7.4, 10 mM EDTA, 1M NaCl, 0.05% Tween-20) three times and 100 uL TE Buffer (10 mM Tris pH 7.4, 1 mM EDTA) twice. Nascent transcript was eluted in 25 uL Elution Buffer (100 mM DTT, 20 mM HEPES pH 7.4, 1mM EDTA, 100 mM NaCl, 0.05% Tween-20) for 15 min at room temperature with rotation. 20 uL Eluted RNA was added with 0.835 uL 3M sodium acetate pH 5.2, 0.2 uL 500 mM DETA, 1.3 uL TFEA, 1.365 uL waster, 1.5 uL 200mM mCPBA for TimeLapse chemistry, and then purified with 25 uL RNAclean XP beads (Beckman). 18 uL Purified RNA was added with 0.8 uL water, 0.2 uL 1 M DTT, 0.2 uL 1M Tris pH 7.4, 0.4 uL 0.5 M EDTA, 0.4 uL 5 M NaCl for reducing treatment, and then purified with 20 uL RNAclean XP beads (Beckman).
Purified RNA was used for sequencing library prep with the KAPA RNA HyperPrep Kit with RiboErase (Roche KR1351).

treatment_protocol: 1 mM 4-thiouridine was added to culture media in a 15-cm dish for 5 min at 37°C.

value: Triple negative breast cancer

value: 1 mM 4-thiouridine, 5 min


title: PR_no_s4U

description: Library name: PR_no_s4U


title: Sample GSF-L-154 treated with Etoh for 48h

description:
Library name: GSF-L-154_48h_Etoh
raw_counts_cais_samples.tsv
raw_counts_cais_labia-minora_samples.tsv
Normalized_counts_CAIS_samples.xlsx
Normalized_counts_labia-minora_samples.xlsx


title: cd_TT_rep2

description: Library name: cd_TT_rep2


title: RNA-seq_cdPRDM9_rep2

description: Library name: RNA-seq_cdPRDM9_rep2

data_processing:
Data were aligned to the hg19 genome assembly using STAR with default parameters.
Aligned reads were counted using HTSeq.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include raw gene counts for each sample

extract_protocol:
1 x 106 cells were harvested in 1 mL TRIzol reagent (Thermo Fisher Scientific) and homogenized by pipetting. After incubation at room temperature for 5 min, 100 uL BCP was added. Samples were vortexed and incubated briefly at room temperature and centrifuged at 12,000 × g, 15 min, 4°C. The aqueous phase was transferred to a new tube and total RNA was isolated with the RNeasy Micro Plus Kit (Qiagen) following the manufacturer's instructions.
Purified RNA was used for sequencing library prep with the KAPA RNA HyperPrep Kit with RiboErase (Roche KR1351).


title: RNA-seq_cdPRDM9_rep1

description: Library name: RNA-seq_cdPRDM9_rep1


title: MZ88_V2-9

description: Library name: MZ88

value: gut microbiota

value: validation


title: NI85_V2-9

description: Library name: NI85


title: Sample GSF-L-156 treated with Etoh for 72h

description:
Library name: GSF-L-156_72h_Etoh
raw_counts_cais_samples.tsv
raw_counts_cais_labia-minora_samples.tsv
Normalized_counts_CAIS_samples.xlsx
Normalized_counts_labia-minora_samples.xlsx


title: MZ73_V2-9

description: Library name: MZ73


title: RNA-seq_PRDM9_rep1

description: Library name: RNA-seq_PRDM9_rep1


title: RNA-seq_WT_rep2

description: Library name: RNA-seq_WT_rep2

value: WT


title: MZ83_V2-9

description: Library name: MZ83


title: U-2

description: Library name: Sample4


title: RNA-seq_WT_rep1

description: Library name: RNA-seq_WT_rep1


title: Sample GSF-L-154 treated with Dht for 72h

description:
Library name: GSF-L-154_72h_Dht
raw_counts_cais_samples.tsv
raw_counts_cais_labia-minora_samples.tsv
Normalized_counts_CAIS_samples.xlsx
Normalized_counts_labia-minora_samples.xlsx


title: NC-1

description: Library name: Sample1


title: Sample GSF-L-156 treated with Etoh for 48h

description:
Library name: GSF-L-156_48h_Etoh
raw_counts_cais_samples.tsv
raw_counts_cais_labia-minora_samples.tsv
Normalized_counts_CAIS_samples.xlsx
Normalized_counts_labia-minora_samples.xlsx


title: ATAC-seq_WT_rep2

description: Library name: ATAC-seq_WT_rep2

data_processing:
Data were filtered for high‐quality reads using the fastq_quality_filter tool from FASTX‐Toolkit with parameters ‐p 80 ‐q 20 parameters.
Filtered libraries were aligned to the hg19 genome assembly using Bowtie2 with parameters --end‐to‐end --sensitive.
Aligned reads were filtered to get uniquely mapping reads without PCR duplicates using SAMtools with parameters -q 1 -f 3 -F 256.
Bigwig files were generated using the bamCoverage tool from deepTools.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
5 x 104 cells were harvested for each reaction.
ATAC-seq library preparation was carried out using the ATAC-Seq Kit (Active Motif) according to the manufacturer's instructions.


title: NI90_V2-9

description: Library name: NI90


title: ATAC-seq_WT_rep1

description: Library name: ATAC-seq_WT_rep1


title: Sample GSF-L-76 treated with Dht for 72h

description:
Library name: GSF-L-76_72h_Dht
raw_counts_cais_samples.tsv
raw_counts_cais_labia-majora_samples.tsv
Normalized_counts_CAIS_samples.xlsx
Normalized_counts_labia-majora_samples.xlsx

source_name: Labia majora

value: Labia majora


title: MZ43_V2-9

description: Library name: MZ43


title: PR_TT_rep1

description: Library name: PR_TT_rep1


title: PR_TT_rep2

description: Library name: PR_TT_rep2


title: input_PRDM9

description: Library name: input_PRDM9

data_processing:
Data were filtered for high‐quality reads using the fastq_quality_filter tool from FASTX‐Toolkit with parameters ‐p 80 ‐q 20 parameters.
Filtered libraries were aligned to the hg19 genome assembly using Bowtie2 with parameters --end‐to‐end --sensitive.
Aligned reads were filtered to get uniquely mapping reads without PCR duplicates using SAMtools with parameters -q 1 -f 3 -F 256.
ChIP-seq data across different samples were normalized using CHIPIN with parameters raw_read_count type_norm="linear".
Bigwig files were generated using the bamCoverage tool from deepTools.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
3 x 10^6 cells were cross-linked in 1% methanol-free formaldehyde at room temperature for 10 min, and then quenched with 0.114 M Glycine. Fixed cells were resuspended in 300 uL High Salt Lysis/Sonication Buffer (800 mM NaCl, 25 mM Tris pH 7.5, 5 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.5% sodium deoxycholate, 1 x protease inhibitor cocktail) and frozen in -80°C. 20 uL Dynabeads Protein G (Thermo Fisher Scientific) was first incubated with 2 ug antibodies in 20 uL Chromatin Dilution Buffer (25 mM Tris pH 7.5, 5 mM EDTA, 1% Triton X-100, 0.1% SDS, 1 x protease inhibitor cocktail) at room temperature for 3 hours with rotation. Fixed cells were transferred to a Bioruptor Pico Microtube (Diagenode) and sonicated for 10 cycles (30 s on/off) in Bioruptor (Diagenode) at 4°C. 1 mL Chromatin Dilution Buffer was added to sonicated cells, and samples were spun at 13600 x g for 30 min at 4°C to pellet insoluble material. If appropriate, 2 uL SNAP-ChIP spike-ins (EpiCypher) was added to the supernatant. 65 uL soluble chromatin was set aside as input. Dynabead/antibody mix was added to the soluble chromatin and incubated at 4°C overnight with rotation. Then, beads were washed with 1 mL Wash Buffer A (140 mM NaCl, 50 mM HEPES pH 7.9, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate), Wash Buffer B (500 mM NaCl, 50 mM HEPES pH 7.9, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate), and Wash Buffer C (20 mM Tris pH 7.5, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40 Alternative, 0.5% sodium deoxycholate) once each, and TE Buffer (10 mM Tris pH 7.5, 1 mM EDTA) twice. Bound DNA was eluted twice with 100 uL Elution Buffer (10 mM Tris pH 7.5, 1 mM EDTA, 1% SDS) at 65°C for 5 min. Eluted DNA and input samples were incubated with 4 ug RNase A (Millipore Sigma) at 65°C overnight to reverse cross-linking and digest any contaminating RNA. ChIP and input samples were further digested with 40 ug Proteinase K (NEB) at 45°C for 2 hours and then purified with the Zymo ChIP DNA Clean & Concentrator Kit (Zymo Research) following the manufacturer's instructions.
ChIP-seq libraries were prepared using either the KAPA HyperPrep Kit (Roche, KK8504) or the Watchmaker DNA Library Prep Kit (#7K0103-096).

tag: chip antibody


title: Sample GSF-L-76 treated with Etoh for 72h

description:
Library name: GSF-L-76_72h_Etoh
raw_counts_cais_samples.tsv
raw_counts_cais_labia-majora_samples.tsv
Normalized_counts_CAIS_samples.xlsx
Normalized_counts_labia-majora_samples.xlsx


title: Pol2-S5P_cdPRDM9_rep2

description: Library name: Pol2-S5P_cdPRDM9_rep2


title: Pol2-S5P_cdPRDM9_rep1

description: Library name: Pol2-S5P_cdPRDM9_rep1


title: MZ28_V2-9

description: Library name: MZ28


title: RNA-seq_PRDM9_rep2

description: Library name: RNA-seq_PRDM9_rep2


title: Sample GSF-L-76 treated with Dht for 48h

description:
Library name: GSF-L-76_48h_Dht
raw_counts_cais_samples.tsv
raw_counts_cais_labia-majora_samples.tsv
Normalized_counts_CAIS_samples.xlsx
Normalized_counts_labia-majora_samples.xlsx


title: Pol2-S5P_PRDM9_rep1

description: Library name: Pol2-S5P_PRDM9_rep1


title: MZ18_V2-9

description: Library name: MZ18


title: Pol2-S5P_PRDM9_rep2

description: Library name: Pol2-S5P_PRDM9_rep2


title: Sample GSF-L-156 treated with Dht for 48h

description:
Library name: GSF-L-156_48h_Dht
raw_counts_cais_samples.tsv
raw_counts_cais_labia-minora_samples.tsv
Normalized_counts_CAIS_samples.xlsx
Normalized_counts_labia-minora_samples.xlsx


title: Pol2-S5P_WT_rep2

description: Library name: Pol2-S5P_WT_rep2


title: Sample GSF-L-73 treated with Dht for 72h

description:
Library name: GSF-L-73_72h_Dht
raw_counts_cais_samples.tsv
raw_counts_cais_labia-majora_samples.tsv
Normalized_counts_CAIS_samples.xlsx
Normalized_counts_labia-majora_samples.xlsx


title: Sample GSF-L-76 treated with Etoh for 48h

description:
Library name: GSF-L-76_48h_Etoh
raw_counts_cais_samples.tsv
raw_counts_cais_labia-majora_samples.tsv
Normalized_counts_CAIS_samples.xlsx
Normalized_counts_labia-majora_samples.xlsx


title: Pol2_WT_rep2

description: Library name: Pol2_WT_rep2

value: Pol2 (Diagenode, #C15200004)


title: MY98_V2-9

description: Library name: MY98


title: Pol2-S5P_WT_rep1

description: Library name: Pol2-S5P_WT_rep1


title: Pol2_WT_rep1

description: Library name: Pol2_WT_rep1


title: MZ48_V2-9

description: Library name: MZ48


title: H3K27ac_cdPRDM9_rep1

description: Library name: H3K27ac_cdPRDM9_rep1

value: H3K27ac (Abcam, #ab4729)


title: Sample GSF-L-73 treated with Etoh for 72h

description:
Library name: GSF-L-73_72h_Etoh
raw_counts_cais_samples.tsv
raw_counts_cais_labia-majora_samples.tsv
Normalized_counts_CAIS_samples.xlsx
Normalized_counts_labia-majora_samples.xlsx


title: input_cdPRDM9

description: Library name: input_cdPRDM9


title: MY93_V2-9

description: Library name: MY93


title: Sample GSF-L-73 treated with Etoh for 48h

description:
Library name: GSF-L-73_48h_Etoh
raw_counts_cais_samples.tsv
raw_counts_cais_labia-majora_samples.tsv
Normalized_counts_CAIS_samples.xlsx
Normalized_counts_labia-majora_samples.xlsx


title: MY78_V2-9

description: Library name: MY78


title: H3K27ac_PRDM9_rep1

description: Library name: H3K27ac_PRDM9_rep1


title: MY68_V2-9

description: Library name: MY68


title: H3K27ac_WT_rep2

description: Library name: H3K27ac_WT_rep2


title: MY63_V2-9

description: Library name: MY63


title: H3K4me3_mSOX9

description: Library name: H3K4me3_mSOX9


title: H3K27ac_WT_rep1

description: Library name: H3K27ac_WT_rep1


title: MZ08_V2-9

description: Library name: MZ08


title: Sample GSF-S-35 treated with Dht for 72h

description:
Library name: GSF-S-35_72h_Dht
raw_counts_control_samples.tsv
raw_counts_control_scrotum_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_scrotum_samples.xlsx

source_name: Scrotum

value: Scrotum

value: Control


title: Sample GSF-S-35 treated with Etoh for 72h

description:
Library name: GSF-S-35_72h_Etoh
raw_counts_control_samples.tsv
raw_counts_control_scrotum_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_scrotum_samples.xlsx


title: H3K4me3_mFOXQ1

description: Library name: H3K4me3_mFOXQ1


title: Sample GSF-S-35 treated with Dht for 48h

description:
Library name: GSF-S-35_48h_Dht
raw_counts_control_samples.tsv
raw_counts_control_scrotum_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_scrotum_samples.xlsx


title: MY58_V2-9

description: Library name: MY58


title: MY53_V2-9

description: Library name: MY53


title: Sample GSF-S-35 treated with Etoh for 48h

description:
Library name: GSF-S-35_48h_Etoh
raw_counts_control_samples.tsv
raw_counts_control_scrotum_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_scrotum_samples.xlsx


title: H3K4me3_acCREs

description: Library name: H3K4me3_acCREs


title: H3K4me3_UOs

description: Library name: H3K4me3_UOs


title: H3K4me3_cdPRDM9_rep2

description: Library name: H3K4me3_cdPRDM9_rep2


title: H3K4me3_PEs

description: Library name: H3K4me3_PEs


title: H3K27ac_cdPRDM9_rep2

description: Library name: H3K27ac_cdPRDM9_rep2


title: Sample GSF-L-73 treated with Dht for 48h

description:
Library name: GSF-L-73_48h_Dht
raw_counts_cais_samples.tsv
raw_counts_cais_labia-majora_samples.tsv
Normalized_counts_CAIS_samples.xlsx
Normalized_counts_labia-majora_samples.xlsx


title: H3K4me3_WT_rep2

description: Library name: H3K4me3_WT_rep2


title: H3K4me3_PRDM9_rep1

description: Library name: H3K4me3_PRDM9_rep1


title: MY48_V2-9

description: Library name: MY48


title: H3K4me3_PRDM9_rep2

description: Library name: H3K4me3_PRDM9_rep2


title: Sample GSF-S-28 treated with Dht for 72h

description:
Library name: GSF-S-28_72h_Dht
raw_counts_control_samples.tsv
raw_counts_control_scrotum_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_scrotum_samples.xlsx


title: MY43_V2-9

description: Library name: MY43


title: H3K27ac_PRDM9_rep2

description: Library name: H3K27ac_PRDM9_rep2


title: MY38_V2-9

description: Library name: MY38


title: H3K4me3_WT_rep1

description: Library name: H3K4me3_WT_rep1


title: Sample GSF-S-28 treated with Etoh for 72h

description:
Library name: GSF-S-28_72h_Etoh
raw_counts_control_samples.tsv
raw_counts_control_scrotum_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_scrotum_samples.xlsx


title: Sample GSF-S-28 treated with Dht for 48h

description:
Library name: GSF-S-28_48h_Dht
raw_counts_control_samples.tsv
raw_counts_control_scrotum_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_scrotum_samples.xlsx


title: H3K4me2_WT_rep2

description: Library name: H3K4me2_WT_rep2

value: H3K4me2 (Abcam, #ab7766)


title: H3K4me2_WT_rep1

description: Library name: H3K4me2_WT_rep1


title: H3K4me1_cdPRDM9_rep2

description: Library name: H3K4me1_cdPRDM9_rep2


title: Sample GSF-S-28 treated with Etoh for 48h

description:
Library name: GSF-S-28_48h_Etoh
raw_counts_control_samples.tsv
raw_counts_control_scrotum_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_scrotum_samples.xlsx

value: Genital skin fibroblast


title: H3K4me1_PRDM9_rep2

description: Library name: H3K4me1_PRDM9_rep2


title: H3K4me1_cdPRDM9_rep1

description: Library name: H3K4me1_cdPRDM9_rep1


title: H3K4me3_cdPRDM9_rep1

description: Library name: H3K4me3_cdPRDM9_rep1


title: Sample GSF-S-33 treated with Dht for 72h

description:
Library name: GSF-S-33_72h_Dht
raw_counts_control_samples.tsv
raw_counts_control_scrotum_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_scrotum_samples.xlsx


title: H3K4me1_PRDM9_rep1

description: Library name: H3K4me1_PRDM9_rep1


title: Sample GSF-S-33 treated with Etoh for 72h

description:
Library name: GSF-S-33_72h_Etoh
raw_counts_control_samples.tsv
raw_counts_control_scrotum_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_scrotum_samples.xlsx


title: H3K4me1_WT_rep2

description: Library name: H3K4me1_WT_rep2


title: MY23_V2-9

description: Library name: MY23


title: MP38_V2-9

description: Library name: MP38


title: Sample GSF-S-33 treated with Dht for 48h

description:
Library name: GSF-S-33_48h_Dht
raw_counts_control_samples.tsv
raw_counts_control_scrotum_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_scrotum_samples.xlsx


title: MP23_V2-9

description: Library name: MP23


title: MP18_V2-9

description: Library name: MP18


title: Sample GSF-S-41 treated with Etoh for 72h

description:
Library name: GSF-S-41_72h_Etoh
raw_counts_control_samples.tsv
raw_counts_control_scrotum_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_scrotum_samples.xlsx


title: Sample GSF-S-33 treated with Etoh for 48h

description:
Library name: GSF-S-33_48h_Etoh
raw_counts_control_samples.tsv
raw_counts_control_scrotum_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_scrotum_samples.xlsx


title: MO83_V2-9

description: Library name: MO83


title: MO78_V2-9

description: Library name: MO78


title: H3K4me1_WT_rep1

description: Library name: H3K4me1_WT_rep1


title: Sample GSF-S-41 treated with Dht for 48h

description:
Library name: GSF-S-41_48h_Dht
raw_counts_control_samples.tsv
raw_counts_control_scrotum_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_scrotum_samples.xlsx


title: MO63_V2-9

description: Library name: MO63


title: Sample GSF-S-41 treated with Etoh for 48h

description:
Library name: GSF-S-41_48h_Etoh
raw_counts_control_samples.tsv
raw_counts_control_scrotum_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_scrotum_samples.xlsx


title: Sample GSF-S-41 treated with Dht for 72h

description:
Library name: GSF-S-41_72h_Dht
raw_counts_control_samples.tsv
raw_counts_control_scrotum_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_scrotum_samples.xlsx


title: Sample GSF-S-170 treated with Dht for 72h

description:
Library name: GSF-S-170_72h_Dht
raw_counts_control_samples.tsv
raw_counts_control_scrotum_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_scrotum_samples.xlsx


title: MO73_V2-9

description: Library name: MO73


title: MM97_V2-9

description: Library name: MM97


title: Sample GSF-S-170 treated with Etoh for 72h

description:
Library name: GSF-S-170_72h_Etoh
raw_counts_control_samples.tsv
raw_counts_control_scrotum_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_scrotum_samples.xlsx


title: Sample GSF-S-170 treated with Dht for 48h

description:
Library name: GSF-S-170_48h_Dht
raw_counts_control_samples.tsv
raw_counts_control_scrotum_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_scrotum_samples.xlsx


title: MY33_V2-9

description: Library name: MY33


title: MM87_V2-9

description: Library name: MM87


title: MM77_V2-9

description: Library name: MM77


title: Sample GSF-S-170 treated with Etoh for 48h

description:
Library name: GSF-S-170_48h_Etoh
raw_counts_control_samples.tsv
raw_counts_control_scrotum_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_scrotum_samples.xlsx


title: MM62_V2-9

description: Library name: MM62


title: MY28_V2-9

description: Library name: MY28


title: MM52_V2-9

description: Library name: MM52


title: Sample GSF-S-3 treated with Etoh for 72h

description:
Library name: GSF-S-3_72h_Etoh
raw_counts_control_samples.tsv
raw_counts_control_scrotum_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_scrotum_samples.xlsx


title: MM47_V2-9

description: Library name: MM47


title: Sample GSF-S-3 treated with Dht for 48h

description:
Library name: GSF-S-3_48h_Dht
raw_counts_control_samples.tsv
raw_counts_control_scrotum_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_scrotum_samples.xlsx


title: MM47_B_V2-9

description: Library name: MM47_B


title: Sample GSF-S-3 treated with Dht for 72h

description:
Library name: GSF-S-3_72h_Dht
raw_counts_control_samples.tsv
raw_counts_control_scrotum_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_scrotum_samples.xlsx


title: RNA AML06_NUP98r

city: Vienna

first: Kaan

last: Boztug

state: Vienna

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute

description: RNA-seq

data_processing:
Unaligned split bam files were merged using Picard v3.0.0
UMI sequences from unaligned bam files were read from "BC" tags and put into "RX" tags using a custom Python script
Unaligned bam files were then converted to fastq format using Picard v3.0.0
and filtered with fastp v0.23.3
and subsequently aligned to the GRCh38 reference genome using STAR v2.7.10 as bam files
aligned reads were then sorted using Picard v3.0.0 and and transfrred RX tags to the aligned bam fioles using GATK v4.4.0
Read mate infoation, grouping by UMIs and calling of molecular consensus sequences was performed with fgbio v2.1.0
Then the aligend bam files were converted to fastq files again and  counts were then quantified using Salmon v1.9.0
Assembly: GRCh38
Supplementary files format and content: Processed files contain read counts per gene as quantified with salmon quant v1.9.0

source_name: Bone marrow

growth_protocol: Fresh-frozen bone marrow mononuclear cells were rapidly thawed and resuspended in IMDM. Cells were subsequently washed once with PBS. Blasts populations were identified via flow-cytometry using a routine diagnostics panel and subsequently  sorted for DNA- and RNA- isolation and library prepration.

extract_protocol:
RNA was isolated jointly using the Quiagen AllPrep DNA/RNA mini kit (Cat no 80204) according to the manufacturer's protocols. Amplification of cDNA was was performed with the SmartSeq2 protocol
Library construction was performed using the Twist Library Preparation EF Kit (Twist Biosciences) according to the manufacturer's recommendations

value: Bone marrow

value: leukemic blast

tag: sequencing batch


title: RNA AML57_UBTF

description: RNA-seq

value: trisomy 8, UBTF


title: Sample GSF-F-123 treated with Dht for 72h

description:
Library name: GSF-F-123_72h_Dht
raw_counts_control_samples.tsv
raw_counts_control_foreskin_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_foreskin_samples.xlsx

source_name: Foreskin

value: Foreskin

value: Dihydrotestosterone


title: RNA AML31_BCRABL1

description: RNA-seq


title: MM37_V2-9

description: Library name: MM37


title: RNA AML17_NUP98r

description: RNA-seq


title: RNA AML04_NK

description: RNA-seq

value: normal karyotype


title: RNA AML12_NUP98r

description: RNA-seq


title: MM43_V2-9

description: Library name: MM43


title: RNA AML43_NK

description: RNA-seq


title: Sample GSF-F-123 treated with Dht for 48h

description:
Library name: GSF-F-123_48h_Dht
raw_counts_control_samples.tsv
raw_counts_control_foreskin_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_foreskin_samples.xlsx

value: 48 hours


title: Sample GSF-F-123 treated with Etoh for 72h

description:
Library name: GSF-F-123_72h_Etoh
raw_counts_control_samples.tsv
raw_counts_control_foreskin_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_foreskin_samples.xlsx

value: Ethanol

value: 72 hours


title: MM32_V2-9

description: Library name: MM32

value: gut microbiota

value: validation


title: RNA AML24_UBTF

description: RNA-seq


title: MM22_V2-9

description: Library name: MM22


title: RNA AML82_NK

description: RNA-seq


title: Sample GSF-F-123 treated with Etoh for 48h

description:
Library name: GSF-F-123_48h_Etoh
raw_counts_control_samples.tsv
raw_counts_control_foreskin_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_foreskin_samples.xlsx


title: MM07_V2-9

description: Library name: MM07


title: RNA AML67_KMT2Ar

description: RNA-seq


title: RNA AML28_NK

description: RNA-seq


title: Sample GSF-F-122 treated with Dht for 72h

description:
Library name: GSF-F-122_72h_Dht
raw_counts_control_samples.tsv
raw_counts_control_foreskin_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_foreskin_samples.xlsx


title: RNA AML23_KMT2Ar

description: RNA-seq


title: MM02_V2-9

description: Library name: MM02


title: RNA AML65_KMT2Ar

description: RNA-seq


title: Sample GSF-F-122 treated with Etoh for 72h

description:
Library name: GSF-F-122_72h_Etoh
raw_counts_control_samples.tsv
raw_counts_control_foreskin_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_foreskin_samples.xlsx


title: Sample GSF-S-3 treated with Etoh for 48h

description:
Library name: GSF-S-3_48h_Etoh
raw_counts_control_samples.tsv
raw_counts_control_scrotum_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_scrotum_samples.xlsx


title: MI46_V2-9

description: Library name: MI46


title: RNA AML50_GLISr

description: RNA-seq


title: RNA AML52_KMTA2Ar

description: RNA-seq


title: Sample GSF-F-122 treated with Dht for 48h

description:
Library name: GSF-F-122_48h_Dht
raw_counts_control_samples.tsv
raw_counts_control_foreskin_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_foreskin_samples.xlsx


title: RNA AML87_NK

description: RNA-seq


title: MI36_V2-9

description: Library name: MI36


title: Sample GSF-F-122 treated with Etoh for 48h

description:
Library name: GSF-F-122_48h_Etoh
raw_counts_control_samples.tsv
raw_counts_control_foreskin_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_foreskin_samples.xlsx


title: RNA AML89_RUNX1

description: RNA-seq


title: MI26_V2-9

description: Library name: MI26


title: RNA AML98_CBFB

description: RNA-seq


title: RNA AML60_CBFB

description: RNA-seq


title: RNA AML07_KMT2Ar

description: RNA-seq


title: RNA AML54_KMT2Ar

description: RNA-seq


title: Sample GSF-F-119 treated with Dht for 72h

description:
Library name: GSF-F-119_72h_Dht
raw_counts_control_samples.tsv
raw_counts_control_foreskin_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_foreskin_samples.xlsx


title: MI06_V2-9

description: Library name: MI06


title: MI11_V2-9

description: Library name: MI11


title: Sample GSF-F-119 treated with Etoh for 72h

description:
Library name: GSF-F-119_72h_Etoh
raw_counts_control_samples.tsv
raw_counts_control_foreskin_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_foreskin_samples.xlsx


title: RNA AML26_CBFB

description: RNA-seq


title: RNA AML66_CBFB

description: RNA-seq


title: Sample GSF-F-119 treated with Etoh for 48h

description:
Library name: GSF-F-119_48h_Etoh
raw_counts_control_samples.tsv
raw_counts_control_foreskin_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_foreskin_samples.xlsx


title: MH96_V2-9

description: Library name: MH96


title: RNA AML44_NUP98r

description: RNA-seq


title: RNA AML13_KMT2Ar

description: RNA-seq


title: MI01_V2-9

description: Library name: MI01


title: Sample GSF-F-139 treated with Dht for 72h

description:
Library name: GSF-F-139_72h_Dht
raw_counts_control_samples.tsv
raw_counts_control_foreskin_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_foreskin_samples.xlsx


title: RNA AML84_complex

description: RNA-seq

value: complex


title: Sample GSF-F-139 treated with Etoh for 72h

description:
Library name: GSF-F-139_72h_Etoh
raw_counts_control_samples.tsv
raw_counts_control_foreskin_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_foreskin_samples.xlsx


title: D10_NKG2A_90

city: NANTES

first: Enora

last: Ferron

address: 34 boulevard Jean Monnet

department: Research

country: France

institute: Etalissement Français du Sang

data_processing:
Base calling : bcl2fastq2 v2.20 Data filtering, alignment and UMI count done with SRP pipeline : Eric Charpentier, Marine Cornec, Solenne Dumont et al. 3’ RNA sequencing for robust and low-cost gene expression profiling, 28 January 2021, PROTOCOL (Version 1) available at Protocol Exchange [https://doi.org/10.21203/rs.3.pex-1336/v1] read trimming: cutadapt v4.5 Alignment : bwa v0.7.17 ; bwa aln -M 0 | bwa samse Read counts : custom python script count.py using pysam : https://bio.tools/3SRP
Assembly: hg38
Supplementary files format and content: Count matrix containing raw UMI counts, one sample per column for a total of 69 column, raw names are HGNC approved genes symbol

source_name: PBMC

growth_protocol: Collection of blood samples, PBMCs were thawed on the day prior to cell sorting and NK cells were stained with labelled mAbs

extract_protocol:
Total RNA was extracted using Trizol and RNA Integrity Number (RIN) score was determined with a 2100 Bioanalyzer (Agilent).
RNAseq library have been prepared following the 3’SRP method published by : Eric Charpentier, Marine Cornec, Solenne Dumont et al. 3’ RNA sequencing for robust and low-cost gene expression profiling, 28 January 2021, PROTOCOL (Version 1) available at Protocol Exchange [https://doi.org/10.21203/rs.3.pex-1336/v1]

treatment_protocol: Cell sorting of NK cell subsets : NKG2A-KIR-, NKG2A+KIR-, NKG2A+KIR2DL1+, NKG2A+KIR2DL3+. CD57 and KIR3DL1 were excluded from the gating strategy.

value: PBMC

value: Natural Killer cell


title: D25_NKG2A_86


title: MH91_V2-9

description: Library name: MH91


title: MH56_V2-9

description: Library name: MH56


title: D16_NKG2A_94


title: Sample GSF-F-139 treated with Dht for 48h

description:
Library name: GSF-F-139_48h_Dht
raw_counts_control_samples.tsv
raw_counts_control_foreskin_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_foreskin_samples.xlsx

value: Control


title: MH51_V2-9

description: Library name: MH51


title: D12_NKG2A_82


title: D25_KIRneg_85


title: D9_NKG2A_74


title: MH46_V2-9

description: Library name: MH46


title: Sample GSF-F-139 treated with Etoh for 48h

description:
Library name: GSF-F-139_48h_Etoh
raw_counts_control_samples.tsv
raw_counts_control_foreskin_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_foreskin_samples.xlsx


title: D17_NKG2A_6


title: MH41_V2-9

description: Library name: MH41


title: Sample GSF-F-119 treated with Dht for 48h

description:
Library name: GSF-F-119_48h_Dht
raw_counts_control_samples.tsv
raw_counts_control_foreskin_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_foreskin_samples.xlsx


title: RNA AML63_NUP98

description: RNA-seq


title: D25_NKG2A_66


title: Sample GSF-F-138 treated with Etoh for 72h

description:
Library name: GSF-F-138_72h_Etoh
raw_counts_control_samples.tsv
raw_counts_control_foreskin_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_foreskin_samples.xlsx


title: D14_NKG2A_70


title: Sample GSF-F-138 treated with Dht for 72h

description:
Library name: GSF-F-138_72h_Dht
raw_counts_control_samples.tsv
raw_counts_control_foreskin_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_foreskin_samples.xlsx


title: RNA AML88_mono7

description: RNA-seq

value: monosomy 7


title: MH16_V2-9

description: Library name: MH16


title: Sample GSF-F-138 treated with Dht for 48h

description:
Library name: GSF-F-138_48h_Dht
raw_counts_control_samples.tsv
raw_counts_control_foreskin_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_foreskin_samples.xlsx

value: Genital skin fibroblast


title: MH01_V2-9

description: Library name: MH01


title: D7_NKG2A_50


title: D24_NKG2A_62


title: Sample GSF-F-138 treated with Etoh for 48h

description:
Library name: GSF-F-138_48h_Etoh
raw_counts_control_samples.tsv
raw_counts_control_foreskin_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_foreskin_samples.xlsx


title: D23_NKG2A_54


title: MB67_V2-9

description: Library name: MB67


title: Sample GSF-F-121 treated with Dht for 72h

description:
Library name: GSF-F-121_72h_Dht
raw_counts_control_samples.tsv
raw_counts_control_foreskin_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_foreskin_samples.xlsx


title: MB72_V2-9

description: Library name: MB72


title: D6_NKG2A_42


title: D21_NKG2A_38


title: D20_NKG2A_30


title: Sample GSF-F-121 treated with Etoh for 72h

description:
Library name: GSF-F-121_72h_Etoh
raw_counts_control_samples.tsv
raw_counts_control_foreskin_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_foreskin_samples.xlsx


title: D5_NKG2A_34


title: D1_NKG2A_2


title: MB57_V2-9

description: Library name: MB57


title: D4_NKG2A_26


title: Sample GSF-F-121 treated with Etoh for 48h

description:
Library name: GSF-F-121_48h_Etoh
raw_counts_control_samples.tsv
raw_counts_control_foreskin_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_foreskin_samples.xlsx


title: D19_NKG2A_22


title: MB47_V2-9

description: Library name: MB47


title: D3_NKG2A_18


title: MB52_V2-9

description: Library name: MB52


title: Sample GSF-F-121 treated with Dht for 48h

description:
Library name: GSF-F-121_48h_Dht
raw_counts_control_samples.tsv
raw_counts_control_foreskin_samples.tsv
Normalized_counts_control_samples.xlsx
Normalized_counts_foreskin_samples.xlsx


title: HFrEF_11

city: Stanford

first: Mark

middle: Emile

last: Pepin

state: CA

address: 870 Quarry road

department: Cardiovascular Medicine

institute: Stanford University

data_processing:
The sequencing quality was evaluated using FastQC (0.11.9) before and after adapter trimming to ensure PHRED < 30 via TrimGalore (0.4.4). Sequenced reads were aligned to the CT- and GA-converted human hg38 (GRCh38.p12) genome assemblies using Bismark [42] to quantify the relative alignment of methylated and unmethylated CpGs, respectively.
Assembly: GRCh38.p12
Supplementary files format and content: The R package methylKit (1.8.0) was used for this purpose, and statistical significance of differential methylation was assumed based on an over-correction adjusted Chi-squared test.

source_name: peripheral blood

extract_protocol:
A total of 15 mL of peripheral venous blood was collected in EDTA vacuettes through venipuncture from AF patients (at hospitalization time and before any treatment administration) and from HS. Blood samples were centrifuged at 1900 x g 10 min at + 4°C within 1 hour and aliquots of plasma were stored at -80°C for long-term storage. Peripheral blood mononuclear cells (PBMCs) were isolated via density centrifugation using Ficoll-Paque™ PLUS (Cytiva) according to the manufacturer’s protocol. CD4+ T cells were purified starting from 5x107/mL of  PBMCs by negative immunomagnetic selection using EasySep™ Human CD4+ T Cell Isolation Kit (STEMCELL Technologies) as previously described.
To perform genome-wide DNA methylation analysis, genomic DNA from 10 AF patients and 11 HS (set population) were analyzed by RRBS at the Genomix4Life S.r.l. (Baronissi, Salerno, Italy). DNA concentrations for each sample was assayed with Qubit fluorometer (Thermo Fisher Scientific) and its quality assessed with the TapeStation 4200 system (Agilent Technologies, Inc.). Indexed libraries were prepared starting from 100 ng/ea purified DNA with Ovation RRBS Methyl-Seq System (Tecan Group Ltd.) according to the manufacturer’s instructions. Libraries were quantified using the TapeStation 4200 system (Agilent Technologies, Inc.) and Qubit fluorometer (Thermo Fisher Scientific), then pooled such that each index-tagged sample was present in equimolar amounts. The pooled samples were subject to cluster generation and sequencing using an Illumina NextSeq 550Dx (Illumina, Inc.) in a 2x76 paired-end format.

value: peripheral blood

value: pBMC

tag: phenotype

value: HFrEF


title: D8_NKG2A_58


title: D2_NKG2A_10


title: D2_KIRneg_9


title: HFpEF_11

value: HFpEF


title: D22_NKG2A_46


title: D10_KIRneg_89


title: MB42_V2-9

description: Library name: MB42


title: D12_KIRneg_81


title: D9_KIRneg_73


title: HFrEF_10


title: MB07_V2-9

description: Library name: MB07


title: D17_KIRneg_5


title: D24_KIRneg_61


title: HFrEF_9


title: MB03_V2-9

description: Library name: MB03


title: D23_KIRneg_53


title: MA97_V2-9

description: Library name: MA97


title: D18_NKG2A_14


title: D7_KIRneg_49


title: D6_KIRneg_41


title: D22_KIRneg_45


title: HFpEF_9


title: D21_KIRneg_37


title: MA82_V2-9

description: Library name: MA82


title: MA92_V2-9

description: Library name: MA92


title: HFrEF_8


title: MB12_V2-9

description: Library name: MB12


title: HFpEF_8


title: D5_KIRneg_33


title: D20_KIRneg_29


title: MA62_V2-9

description: Library name: MA62


title: HFrEF_7


title: D19_KIRneg_21


title: D1_KIRneg_1


title: D3_KIRneg_17


title: HFpEF_7


title: HFpEF_10


title: D8_KIRneg_57


title: MA52_V2-9

description: Library name: MA52


title: MA42_V2-9

description: Library name: MA42


title: HFrEF_6


title: D16_2DL3_95


title: MA37_V2-9

description: Library name: MA37


title: D18_KIRneg_13


title: D17_2DL3_7


title: D24_2DL3_63


title: D11_2DL3_59


title: MA32_V2-9

description: Library name: MA32


title: HFrEF_5


title: D23_2DL3_55


title: D1_2DL3_3


title: D4_KIRneg_25


title: MA07_V2-9

description: Library name: MA07


title: HFpEF_5


title: MA02_V2-9

description: Library name: MA02


title: D4_2DL3_27


title: HFrEF_4


title: D3_2DL3_19


title: LZ92_V2-9

description: Library name: LZ92


title: D5_2DL3_35


title: HFpEF_4


title: D18_2DL3_15


title: D19_2DL3_23


title: D2_2DL3_11


title: HFrEF_3


title: D17_2DL1_8


title: HFpEF_3


title: LZ82_V2-9

description: Library name: LZ82


title: HFpEF_6


title: D13_2Dl1_68


title: LZ72_V2-9

description: Library name: LZ72


title: D24_2DL1_64


title: HFrEF_2


title: D11_2DL1_60


title: LZ67_V2-9

description: Library name: LZ67


title: HFpEF_2


title: D23_2DL1_56


title: D1_2DL1_4


title: vitiligo hk14SCF/HRM mice, week12, 3

city: Kyoto

first: Shinji

last: Tsukada

address: 93, Awatacho, Chudoji, Shimogyo-ku

department: Pharmacological Research Group

country: Japan

institute: Maruho Co., Ltd.

description: Library name: Sample7

data_processing:
DRAGEN Bio-IT Platform (v 3.7.5)
Assembly: mm39
Supplementary files format and content: excel file including raw counts and TPM for each sample

organism: Mus musculus

source_name: skin

growth_protocol: Bone marrow dendritic cells were isolated from the hind limbs of C57BL/6J mice and cultured for one week in DC medium (RPMI+10% FBS+1% GlutaMax+1% P/S+ trace amounts of β-ME). During the culture period, IL-4 and GM-CSF were added to induce differentiation into BMDCs. On the final day of culture, the BMDCs were pulsed with 10μM of hgp100 for 3 hours, and then the cells were harvested.

extract_protocol:
RNA was harvested using Rneasy Fibrous Tissue Mini Kit (Qiagen). 1.0 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNAseq were prepared using SMART-Seq v4 Ultra Low Input RNA following manufacture's protocols .

treatment_protocol: Cultured BMDCs and PMEL CD8+ T cells isolated from the spleen of PMEL transgenic mice were each transferred at 1.5×10^6 cells into hk14-SCF Tg mice.

value: skin

value: 12 week after vitiligo-induction


title: vitiligo hk14SCF/HRM mice, week7, 2

description: Library name: Sample6

value: 7 week after vitiligo-induction


title: HFmrEF_2


title: PF94_V2

description: Library name: PF94

source_name: other

value: other

value: mock


title: HFrEF_1


title: PF93_V2

description: Library name: PF93


title: D21_2DL1_40


title: D15_2DL1_44


title: PF92_V2

description: Library name: PF92


title: vitiligo hk14SCF/HRM mice, week7, 1

description: Library name: Sample5


title: LZ87_V2-9

description: Library name: LZ87

value: gut microbiota


title: hk14SCF/HRM mice, 3

description: Library name: Sample3

value: non-treatment


title: hk14SCF/HRM mice, 4

description: Library name: Sample4


title: HFpEF_1


title: HFmrEF


title: D14_2DL1_72


title: D5_2DL1_36


title: D20_2DL1_32


title: hk14SCF/HRM mice, 2

description: Library name: Sample2


title: HS_11


title: NJ75_V2_V2-9

description: Library name: NJ75_V2

value: CAREGIVER


title: hk14SCF/HRM mice, 1

description: Library name: Sample1


title: PF91_V2

description: Library name: PF91


title: PA60_V2

description: Library name: PA60


title: NJ60_V2-9

description: Library name: NJ60

value: PATIENT


title: D20_2DL3_31

value: PBMC

value: Natural Killer cell


title: NSC_TMut_EhmCseq

city: New York

first: Meelad

middle: M

last: Dawlaty

state: New York

address: 1301 Morris Park Ave, Price 419, Bronx

institute: Albert Einstein College of Medicine

description: Library name: NSC_TMut_EhmCseq

data_processing:
The negative control lambda DNA mapping rate was <1%. T4 mapping rate was >80% confirming reaction efficiency. Adaptors were trimmed using trim galore (v0.6.7) and trimmed reads were mapped to mouse genome mm10 using Bismark (v0.23.1) with default parameters. Duplicated reads were removed using deduplicate_bismark and methylation status of each cytosine was extracted with bismark_methylation_extractor. DhmR analysis was done using the methpipe package following the methpipe manual.
Samtools was used to convert SAM to BAM, sort and index corresponding BAM files. Bigwig files for DNA methylation and hydroxymethylation were generated using bedGraphToBigWig, and used to generate line plots and heatmaps with plotProfile and plotHeatmap. HypoDhMR peaks were annotated with the R package "ChIPseeker".
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: EhmC-seq

source_name: Neural stem cells

extract_protocol:
DNA was extracted from NS cells using Zymo Quick-DNA Miniprep Kit.
Libraries were prepped using the NEBNext E5hmC-seq kit.

value: Neural stem cells

value: Tet-TMut


title: NSC_TFoCa_EhmCseq

description: Library name: NSC_TFoCa_EhmCseq

value: Tet-TFoCa


title: HS_8

value: peripheral blood

value: pBMC

value: Control


title: NJ55_V2-9

description: Library name: NJ55


title: D18_2DL1_16


title: HS_7


title: NSC_WT_EhmCseq

description: Library name: NSC_WT_EhmCseq

value: WT


title: HEK293A cell, HINT1 KO, rep_3

city: Tianjin

first: Xiaofang

last: Zhang

state: Tianjin

address: No. 92 Weijin Road, Nankai District

institute: Tianjin University

data_processing:
The RNA-seq raw data were processed via the online platform Galaxy(https://usegalaxy.org).
Sequence reads were trimmed using Trim Galore! function.(parameter-Is this library paired- or single-end?:paired-end)(Galaxy Version 0.6.7+galaxy0)
Quantification were performed using Salmon quant function.(parameter-Transcripts FASTA file: gencode.v44.transcripts.fa.gz)(parameter-Is this library mate-paired?:paired-end)(Galaxy Version 1.10.1+galaxy2)
Summarized transcript-level data were performed using tximport function.(Galaxy Version 1.22.0)
Assembly: Homo_sapiens.GRCh38.109.gtf.gz
Supplementary files format and content: An Excel files include quantification values for each Sample.
Supplementary files format and content: An Excel files include gene ID and gene name for each Sample.

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS  and 1% penicillin-streptomycin, and maintained at 37°C and 5% CO2.

extract_protocol:
RNA was harvested using RNAiso Plus from Takara (Japan). More than 2 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard lllumina protocols.

value: Human Embryonic Kidney 293a

value: HINT1 knockout type


title: MY38_V2_V2-9

description: Library name: MY38_V2


title: HS_5


title: HEK293A cell, HINT1 KO, rep_1


title: MY33_V2_V2-9

description: Library name: MY33_V2


title: HEK293A cell, HINT1 KO, rep_2


title: HS_4


title: NSC_WT_EmCseq

description: Library name: NSC_WT_EmCseq

data_processing:
The negative control lambda DNA mapping rate was <1%. pUC19 mapping rate was >80% confirming reaction efficiency. Adaptors were trimmed using trim galore (v0.6.7) and trimmed reads were mapped to mouse genome mm10 using Bismark (v0.23.1) with default parameters. Duplicated reads were removed using deduplicate_bismark and methylation status of each cytosine was extracted with bismark_methylation_extractor. DMR analysis was done using the methpipe package following the methpipe manual.
Samtools was used to convert SAM to BAM, sort and index corresponding BAM files. Bigwig files for DNA methylation and hydroxymethylation were generated using bedGraphToBigWig, and used to generate line plots and heatmaps with plotProfile and plotHeatmap.Hyper DMR peaks were annotated with the R package "ChIPseeker".
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: EM-seq

extract_protocol:
DNA was extracted from NSC cells using Zymo Quick-DNA Miniprep Kit.
Libraries were prepped using the NEBNext EM-seq kit.


title: HS_6


title: NSC_TMut_EmCseq

description: Library name: NSC_TMut_EmCseq


title: MM42_V2_V2-9

description: Library name: MM42_V2


title: HEK293A cell, HINT1 WT, rep_3

value: wild type


title: HS_10


title: HS_3


title: M3

city: Changsha

first: Qi

last: Tian

state: Hunan

address: No. 59, Xiangchun Road, Changsha City, Hunan Province

department: Department of Obstetrics & Gynecology

institute: Hunan Provincial Maternal and Child Health Care Hospital

description: Library name: Sample 9

library_source: transcriptomic single cell

data_processing:
The UMI count matrix was converted into a Seurat object by the R package Seurat (version 4.3.0). Cells with UMI numbers <1000 or with detected genes < 500 or with over 20% mitochondrial-derived UMI counts were considered low-quality cells and were removed. Genes detected in less than 5 cells were removed for downstream analyses.
After quality control, the UMI count matrix was log normalized. Then top 2000 variable genes were used to create potential Anchors with FindIntegrationAnchors function of Seurat. Subsequently, IntegrateData function was used to integrate data. To reduce the dimensionality of the scRNA-Seq dataset, principal component analysis (PCA) was performed on an integrated data matrix. With Elbowplot function of Seurat, top 50 PCs were used to perform the downstream analysis. The main cell clusters were identified with the FindClusters function offered by Seurat, with resolution set as default (res = 0.4). Finally, cells were clustered into 10 major cell types. And then they were visualized with UMAP plots. To identify the cell type for each cluster, we detected gene markers for each cell clusters using the “FindAllMarkers” function in Seurat package (v4.3.0) on a natural log scale was at least 0.5 and the difference of percent of detected cells was at least 0.25 and adjusted p-value was less than 0.05, then we annotated cell types using ScType tools.
Differentially expressed genes (DEGs) were determined with the FindMarkers/FindAllMarkers function from the Seurat package (one-tailed Wilcoxon rank sum test, pvalues adjusted for multiple testing using the Bonferroni correction). For computing DEGs, all genes were probed that the expression difference on a natural log scale was at least 0.5 and the difference of percent of detected cells was at least 0.15 and adjusted p-value was less than 0.05.
The modules of TFs were identified by the SCENIC python workflow (version 0.11.2) using default parameters (http://scenic. aertslab.org). A human/mouse TF gene list was used from the resources of pySCENIC (https://github.com/aertslab/pySCENIC/tree/master/resources). Activated TFs were identified in the AUC matrix, and differentially activated TFs were selected using R package limma based on the fold change (logFC ≥ 0.5 or ≤ -0.5) and false discovery rate (FDR ≤ 0.05). To identify cluster-specific regulons (especially for analyses with many cell types, where some regulons are common to multiple of them) we used the Regulon Specificity Score (RSS).
Assembly: GRCm39
Supplementary files format and content: UMI count matrix of each sample.

source_name: large intestine tissue of Chlamydia-treated mouse

growth_protocol: C57BL/6J female mice, aged 5-6 weeks, were sourced from Vital River in Beijing and maintained under controlled environmental conditions (temperature: 22 °C; light/dark cycle: 12 hours each). Following a one-week acclimatization period in the laboratory, these mice were used for experiments that received approval from the Ethics Committee of the Institute of the 3rd Xiangya Hospital, Central South University, adhering to the guidelines set by the Chinese Council on Animal Care.

extract_protocol:
The scRNA-seq data included 59,197 cells from 3 Control samples, 3 De_Chlamydia-treated samples and 3 Chlamydia-treated mouse large intestine tissue samples. Mice aged 6 to 7 weeks received intragastric inoculations of purified C. muridarum EBs (either live  or heat deactivated), with each mouse receiving 2 × 10^5 inclusion-forming units (IFUs). The naïve control group was administered a sucrose-phosphate-glutamic acid (SPG) vehicle.
Single-cell cDNA libraries were generated as described in Single cell 3’ whole transcriptome amplification (WTA) protocol (BD Rhapsody,USA) using successfully prepared single-cell suspensions. Single cells washed three times, pooled, counted and subsequently loaded onto a cartridge, lysed inside the wells followed by mRNA capture on cell capture beads according to manufacturer instructions. Cell Capture Beads were retrieved and washed prior to performing reverse transcription and treatment with Exonuclease I. cDNA underwent extension using the WTA extension primers, and purified using SPRIselect magnetic beads (B23318, Beckman Coulter,USA).The quantity of PCR products was determined by Qubit 4.0 with Qubit dsDNA HS Assay (Q32854, Thermo Fisher Scientific,USA). For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina Novaseq 6000 system for 150 nt paired-end sequencing.

treatment_protocol: The C. muridarum strains used in this research were derived from the Nigg3 strain (GenBank accession number CP009760.1). We cultured Chlamydia in HeLa cells, followed by purification of elementary bodies (EBs) using established protocols. These EBs were aliquoted and stored at -80 °C. For deactivation, EBs underwent a 30-minute heat treatment at 56 °C. Mice aged 6 to 7 weeks received intragastric inoculations of purified C. muridarum EBs (either live or heat deactivated), with each mouse receiving 2 × 10^5 inclusion-forming units (IFUs). The naïve control group was administered a sucrose-phosphate-glutamic acid (SPG) vehicle.

value: mice infected with chlamydia


title: D4_2DL1_28


title: HS_9


title: HEK293A cell, HINT1 WT, rep_2


title: HS_2


title: M2

description: Library name: Sample 8

value: large intestine tissue of Chlamydia-treated mouse


title: NI95_V2_V2-9

description: Library name: NI95_V2

value: gut microbiota


title: NI90_V2_V2-9

description: Library name: NI90_V2


title: HEK293A cell, HINT1 WT, rep_1


title: MH86_V2-9

description: Library name: MH86

value: CAREGIVER


title: HS_1


title: NSC_TFoCa_EmCseq

description: Library name: NSC_TFoCa_EmCseq


title: MH81_V2-9

description: Library name: MH81

value: PATIENT


title: J3

description: Library name: Sample 6

source_name: large intestine tissue of De_Chlamydia-treated mouse

value: mice infected with inactivated chlamydia


title: HS_18


title: GW39_1_Arc

city: San Francisco

first: Aunoy

last: Poddar

institute: UCSF

description: 10X Genomics

data_processing:
Alignment: FASTQ files were aligned using CellRanger 7.1.0 software from 10X genomics.
Ambient RNA Correction: CellBender 0.2.2 was used to correct for ambient RNA contamination
UMI Filtering, Doublet Removal, and high quality cells were performed on processed data files provided here. Details can be found in accompanying manuscript.
Assembly: GRCh38
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Arc region

extract_protocol:
Frozen sections were transferred from tubes in dry ice to ice cold lysis buffer (0.01M Tris-HCl, 0.14M NaCl, 1mM CaCl2, 0.02M MgCl2, 0.03% Tween-20, 0.01% BSA, 10% Nuclei Ez Lysis Buffer (Sigma), 0.2U/μL Protector RNAse inhibitor (Sigma) in DEPC-treated water) and the tissue was dissociated using a glass dounce homogenizer (Thomas Scientific, Cat # 3431D76). Tissue homogenates were transferred to a separate 30 mL thick wall polycarbonate ultracentrifuge tube (Beckman Coulter, Cat # 355631). Sucrose solution (1.8 M sucrose, 3 mM MgAc2, 1 mM DTT, 10 mM Tris-HCl in DEPC-treated water) was added at the bottom of the tube and homogenates were centrifuged at 107,000 x g for 2.5 hours at 4°C. The supernatant was discarded, and the nuclei pellet was incubated in 200 μL of wash/resuspension buffer (WRB: 1% BSA, 0.2U/μL Protector RNAse inhibitor in DEPC-based PBS) for 20 min on ice before resuspending the pellet
Gene expression and barcode libraries were prepared in parallel using the Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics) according to manufacturer's instructions. A detailed step-by-step protocol can be found on dx.doi.org/10.17504/protocols.io.kqdg369keg25/v2.

value: Arc region


title: MH76_V2-9

description: Library name: MH76

data_processing:
the sequencing data were demultiplexed, converted to unmapped BAM (uBAM) format, and uploaded into Ion Reporter v.5.20 (Thermo Fisher Scientific)
Assembly: Greengenes database (v.13_5)
Supplementary files format and content: fastQ, and otu_table_total_tss.tsv for processed data
Library strategy: 16S rRNA-seq

extract_protocol:
DNA was extracted using the QIAsymphony DSP/Virus/Pathogen Midi kit (Qiagen)
The libraries were then prepared using the Ion Plus Fragment Library Preparation Kit (Thermo Fisher Scientific)


title: HS_17


title: HS_16


title: GW30_Arc

description: 10X Genomics


title: J2

description: Library name: Sample 5

value: large intestine tissue of De_Chlamydia-treated mouse


title: J1

description: Library name: Sample 4


title: HS_15


title: C3

description: Library name: Sample 3

source_name: large intestine tissue of Control mouse

value: large intestine tissue of Control mouse

value: Uninfected mice


title: Group3c

type: RNA

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were nomanized by RMA with Parteck Genomic Suit 6.6

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: mRNA is  converted to cDNA and amplified using NuGEN pico amplification kit

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

treatment_protocol: cell treated with control, G1, G2 and G1+G2 respectively.

tag: strain

value: HL-60 Cell


title: MM37_V2_V2-9

description: Library name: MM37_V2

source_name: gut microbiota


title: MH61_V2-9

description: Library name: MH61


title: HS_14

value: peripheral blood

value: pBMC


title: MH46_V2_V2-9

description: Library name: MH46_V2


title: C2

description: Library name: Sample 2


title: Group3a.


title: MH31_V2-9

description: Library name: MH31


title: Group2c.


title: M1

description: Library name: Sample 7


title: HS_13

value: Control


title: GW39_2_Arc

description: 10X Genomics


title: TGFβ1FKO , mouse dermal fibrobalsts- 4

city: Cologne

first: Sebastian

last: Willenborg

state: NRW

address: Kerpener Str. 62

department: Dermatology

institute: University of Cologne

description:
Library name: KO4
PE150 mode

data_processing:
Base-calling was performed using CASAVA 1.8. with default parameters.
Sequence reads were trimmed for adaptor sequence/low-quality sequence, Reads were removed when uncertain nucleotides constitute more than 10 per cent of either read, when low-quality nucleotides (Base Quality less than 5) constitute more than 50 per cent of the read or with adapter contamination.
The index of the reference genome was built by aligning paired-end clean reads to the reference genome  using Hisat2 v2.0.5. The featureCounts v1.5.0-p3 was used to count the number of reads mapped to each gene.
Statistical analysis of the results was done with R 4.3.2 (R Core Team, 2023) using R Studio 2023.09.1+494 (Posit Team, 2023) and the R packages: DESeq2 1.42.0 and clusterProfiler 4.10.0 .
Lowly expressed transcripts with an overall sum below the threshold (five times the number of samples) were removed.
Differential expression analysis of two groups (four biological replicates per group) was performed using the DESeq2 R package (1.42.0). The resulting P-values were then adjusted using the Benjamini and Hochberg’s method to control the false discovery rate. Genes with an adjusted P-value ≤ 0.05 and a log2FC threshold of 0.6 found by DESeq2 were assigned as differentially expressed.
Reads were aligned to the Mus musculus reference genome GRCm38/mm10 using HISAT2. Ensembl gene IDs were used for feature annotation.
Assembly: GRCm38/mm10
Supplementary files format and content: .csv file with baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, gene symbol, entrez IDs, uniport IDs and sample normalized counts.
Supplementary files format and content: Quantitative data for each sample provided in the processed data file are normalized counts.

source_name: Primary dermal fibroblasts

growth_protocol: Primary dermal fibroblasts isolated from tamoxifen-fed adult mice were cultured in serum-free conditions (serum replacement medium) for 72 h on fibronectin.

extract_protocol:
RNA was extracted from primary dermal fibroblasts using RNeasy Plus Micro Kit (Qiagen, cat. no. 74034) according to manufacturer’s protocol. Paired-end sequencing was performed at Novogene (UK) on Illumina platform (PE150, 20 million reads).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non-directional library. The non-directional library was complete after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: Primary dermal fibroblasts

tag: cell line

value: Primary cells


title: C1

description: Library name: Sample 1


title: Group2b.


title: HS_12

tag: cell type


title: TGFβ1FKO , mouse dermal fibrobalsts- 3

description:
Library name: KO3
PE150 mode

tag: genotype


title: Group2a.


title: MH11_V2-9

description: Library name: MH11


title: 11HS healthy control

value: healthy control


title: MH71_V2-9

description: Library name: MH71


title: MB97_V2-9

description: Library name: MB97


title: Group3b.


title: Group1c.


title: TGFβ1FKO , mouse dermal fibrobalsts- 2

description:
Library name: KO2
PE150 mode


title: MB42_V2_V2-9

description: Library name: MB42_V2


title: 10HS healthy control


title: 10AF atrial fibrillation

value: atrial fibrillation


title: TGFβ1FKO , mouse dermal fibrobalsts- 1

description:
Library name: KO1
PE150 mode


title: MB32_V2-9

description: Library name: MB32


title: 9HS healthy control


title: MA77_V2-9

description: Library name: MA77


title: Control, mouse dermal fibroblasts -4

description:
Library name: WT4
PE150 mode


title: Group1a


title: Conc

source_name: CK


title: 9AF atrial fibrillation


title: Control, mouse dermal fibroblasts -3

description:
Library name: WT3
PE150 mode


title: MA72_V2-9

description: Library name: MA72


title: Control, mouse dermal fibroblasts -2

description:
Library name: WT2
PE150 mode


title: Conb


title: 8HS healthy control


title: Cona.


title: 8AF atrial fibrillation


title: MA32_V2_V2-9

description: Library name: MA32_V2


title: ILC1/3Ps-2 from fetal liver of WT mice

city: Nanjing

first: Jiarui

last: Li

state: Jiangsu

address: Xianlin road #138

institute: Nanjing University of Chinese Medicine

description:
Library name: Sample 8
ILC1/3Ps from fetal liver of WT mice

data_processing:
The raw gene expression data were analyzed using the R toolkit.
Further differential analysis was executed by DE-seq (v3.26.8).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: fetal liver

extract_protocol:
To obtain CLP (Lin–CD45+CD127+Flt3+CD25– live cells), ILCP (Lin–CD45+CD127+Flt3–α4β7+CD25–PD-1+CD94– live cells) and ILC1/3P (Lin–CD45+CD127+Flt3–α4β7+CD25–PD-1–CD94+ live cells) were sorted from the fetal liver of WT B6 mice. Mononuclear cells (MNCs) were incubated with anti-CD45 mAbs for 30 min at 4°C. Subsequently, MNCs were incubated with anti-PE beads for 60 min at 4°C. Nextly, MNCs were incubated with the indicated antibodies for 30 min at 4°C. 7AAD was added to the MNCs suspension, which was subsequently sorted using a FACSAria Fusion (BD Biosciences, San Diego, USA). The purity of the sorted cell populations was >  90%. Purified live cells were labelled with 0.4% Trypan blue to determine their viability (> 90% before processing for RNA-seq). Purified cells were gently transferred into lysis buffer, and reverse transcription was performed using a SMARTer Ultra Low RNA Kit (Clontech) directly in the cell lysate.
Single-cell cDNA was amplified using an Advantage 2 PCR Kit (Clontech) according to the manufacturer’s protocol. cDNA library was sequenced using the NovaSeq6000.

value: fetal liver

value: lymphocytes

value: 6-8 weeks old

value: B6 WT

value: no


title: MH26_V2-9

description: Library name: MH26

value: gut microbiota

value: CAREGIVER


title: 7HS healthy control


title: UUATAC-seq datasets of Zebrafish_CaudalFin

city: Hangzhou

first: Guoji

last: Guo

state: Zhejiang

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

institute: Center for Stem Cell and Regenerative Medicine

description:
Library name: UUATAC_Zebrafish_CaudalFin
single-nucleus ATAC profile of Zebrafish_CaudalFin

data_processing:
The FASTQ files generated by MGI sequencer were split by the T7 index using the software splitBarcode (version 0.1.6, https://github.com/MGI-tech-bioinformatics/splitBarcode). Reads with barcode base quality lower than 10 or more than two mismatches per index were removed. Then the cell barcode was tagged into the query name of each reads using Drop-Seq tools  (version 2.5.1, https://github.com/broadinstitute/Drop-seq). The cell barcode of each read pair consists of four components: T7 index, Hy AS barcode, Hy B barcode and Tn5 barcode (128, 768, 8 and 192 indexes, respectively). We corrected each barcode to its original sequence if only one base was mismeasured in each barcode component. Bam files with tagged barcodes were split by Tn5 barcodes and then merged by tissue information. Different samples were marked by different Tn5 barcodes. Subsequently, reads were aligned to reference genomes of zebrafish (danRer11) using BWA (version 0.7.15, https://github.com/lh3/bwa) with default parameters in paired-end mode to obtain the bam file.
To deal with the Tn5 insertion bias, we performed the function alignmentSieve of deepTools (version 3.5.1, https://github.com/deeptools/deepTools) to shift each read. Next, paired-reads with mapping quality higher than 30 were converted to fragments. And then nonduplicate fragments with length range from 10bp to 1000bp were extracted. We generated one fragment file for each tissue.
Assembly: danRer11
Supplementary files format and content: BED files recording coordinates of fragments captured by UUATAC-seq

organism: Danio rerio

source_name: Caudal fin

extract_protocol:
Whole organs were then dissected in the following order: brain, spleen, heart, swim bladder, tail fin, liver, ovary (female), gill, muscle, intestine and pancreas, and testis (male). The samples were quickly transferred into cold DPBS, washed and then manually pulverized using a mortar and pestle within a liquid nitrogen bath. The pulverized tissues were suspended in 1mL of Nuclear Isolation Buffer (NIB) and followed by incubation for 1.5-3 min to isolate the nuclei. The suspension of each tissue was transferred to 15 mL centrifuge tubes pre-filled with 5mL of WB (wash buffer, 0.2% BSA, 3 mM MgCl2 in DPBS), filtered through 40 μm strainers and centrifuged at 650 × g for 5 min at 4°C. We resuspended the nuclei in 1 mL of WB and filtered the suspension through 20 μm size strainers, pelleted at 650 × g for 5 min and resuspended in the appropriate amount of DPBS to give a final concentration of 25,000 nuclei per microlitre.
Library preparations were performed with the UUATAC-seq protocol

treatment_protocol: Zebrafish was anesthetized in a mixture of ice water.

value: Caudal fin

value: Wild-type


title: KIRI rep3

city: wenzhou

first: Longwei

last: Zhao

address: University-Town, Wenzhou, Zhejiang, P.R.China

institute: Wenzhou Medical university

description:
Library name: sample6
KIRI-3-FPKM

data_processing:
After library construction, initial quantification was performed using Qubit 2.0 Fluorometer. Libraries were diluted to 1.5 ng/μl, followed by insert size analysis on Agilent 2100 Bioanalyzer. Upon confirming expected insert sizes, qRT-PCR was used for accurate quantification of effective library concentration (>2 nM) to ensure quality.
Upon passing QC, qualified libraries were pooled based on effective concentration and desired sequencing depth for Illumina sequencing. The process utilizes Sequencing by Synthesis (SBS) technology. During sequencing, four fluorescently-labeled dNTPs, DNA polymerase, and adapter primers are added to the flow cell for amplification. As each sequencing cluster extends the complementary strand, incorporation of a fluorescent dNTP releases a corresponding signal. The sequencer captures these fluorescence signals, which are then converted into sequencing peaks through software analysis to determine the sequence.
Eukaryotic mRNA sequencing was performed on the HiSeq platform to analyze the complete transcriptome of specific tissues/cells. Library preparation followed the Illumina TruSeq™ RNA Sample Prep Kit protocol.
Assembly: GRCm39
Supplementary files format and content: The text file contains count values, FPKM values, and gene names for each sample.

source_name: nephridial tissue

extract_protocol:
Kidney tissues were homogenized in TRIzol, chloroform-separated, and RNA was precipitated (isopropanol), ethanol-washed, and resuspended. Alternatively, the RNeasy Mini Kit (Qiagen) was used with on-column DNase digestion to ensure genomic DNA removal.
RNA libraries were prepared for sequencing using standard illumina protocols

value: nephridial tissue

value: Mouse whole kidney cells

value: total kidney cells

value: WT

value: single batch


title: ILC1/3Ps-1 from fetal liver of WT mice

description:
Library name: Sample 7
ILC1/3Ps from fetal liver of WT mice


title: 7AF atrial fibrillation

value: peripheral blood

value: pBMC


title: KIRI rep2

description:
Library name: sample5
KIRI-2-FPKM


title: UUATAC-seq datasets of Zebrafish_SwimBladder

description: single-nucleus ATAC profile of Zebrafish_SwimBladder

library_source: genomic single cell

source_name: Swim bladder

value: Swim bladder

value: AB

tag: developmental stage

value: 16 weeks


title: ILCPs-3 from fetal liver of WT mice

description:
Library name: Sample 6
ILCPs from fetal liver of WT mice

value: fetal liver

value: lymphocytes

value: 6-8 weeks old

tag: treatment


title: KIRI rep1

description:
Library name: sample4
KIRI-1-FPKM

tag: tissue


title: UUATAC-seq datasets of Zebrafish_Spleen

description: single-nucleus ATAC profile of Zebrafish_Spleen

source_name: Spleen

value: Spleen


title: 6HS healthy control

value: healthy control


title: ILCPs-2 from fetal liver of WT mice

description:
Library name: Sample 5
ILCPs from fetal liver of WT mice

value: B6 WT

value: no


title: 6AF atrial fibrillation

value: atrial fibrillation


title: UUATAC-seq datasets of Zebrafish_Ovary

description: single-nucleus ATAC profile of Zebrafish_Ovary

source_name: Ovary

value: Ovary

value: Wild-type


title: ILCPs-1 from fetal liver of WT mice

description:
Library name: Sample 4
ILCPs from fetal liver of WT mice


title: 5HS healthy control

source_name: peripheral blood


title: Tacrolimus KIRI rep3

description:
Library name: sample3
TC-3-FPKM

value: nephridial tissue

value: Mouse whole kidney cells

value: total kidney cells

value: WT

value: tacrolimus


title: Group1b

value: HL-60 Cell


title: UUATAC-seq datasets of Zebrafish_Muscle

description: single-nucleus ATAC profile of Zebrafish_Muscle

source_name: Muscle

value: Muscle

value: AB

value: 16 weeks


title: 5AF atrial fibrillation

value: peripheral blood

value: pBMC


title: Tacrolimus KIRI rep1

description:
Library name: sample1
TC-1-FPKM

value: single batch


title: Tacrolimus KIRI rep2

description:
Library name: sample2
TC-2-FPKM


title: Control, mouse dermal fibroblasts -1

description:
Library name: WT1
PE150 mode

value: Primary dermal fibroblasts

value: Primary cells


title: CLPs-3 from fetal liver of WT mice

description:
Library name: Sample 3
CLPs from fetal liver of WT mice

value: fetal liver

value: lymphocytes

value: 6-8 weeks old

value: B6 WT

value: no


title: UUATAC-seq datasets of Zebrafish_Liver

description: single-nucleus ATAC profile of Zebrafish_Liver

source_name: Liver

value: Liver

value: Wild-type


title: CLPs-2 from fetal liver of WT mice

description:
Library name: Sample 2
CLPs from fetal liver of WT mice


title: 4HS healthy control

value: healthy control


title: 18S reads obtained from sample SS32 (Run 3 - Replicate 3)

city: Pisa

first: Giulio

last: Petroni

address: Via A. Volta n°4/6

department: Department of Biology

institute: University of Pisa

description:
Library name: SS32_18S
Full-length 18S rRNA gene sequencing

data_processing:
Primer-trimmed sequences delivered by CD Genomics (Shirley, NY, USA) were put through the DADA2 pipeline in R: quality filtering, dereplication, denoising and chimera removal
The resulting ASV table and sequences were imported in QIIME2 (2022.2) for taxonomic classification using a Naive Bayes classifier trained on the reference database EUKARYOME (v1.9)
Supplementary files format and content: dna-sequences.fasta: text file containing the ASV IDs and sequences
Supplementary files format and content: feature_table.tsv: TSV text file containing the ASV abundances in each sample
Supplementary files format and content: taxonomy.tsv: TSV text file containing the taxonomic classification of the ASVs

organism: activated sludge metagenome

source_name: mixed microbial community

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Kit (QIAGEN, Hilden, Germany)
PacBio Full-Length Amplicon Library Preparation using the SMRTbell Prep Kit 3.0 protocol

value: mixed microbial community


title: CLPs-1 from fetal liver of WT mice

description:
Library name: Sample 1
CLPs from fetal liver of WT mice


title: UUATAC-seq datasets of Zebrafish_IntestinePancreas

description: single-nucleus ATAC profile of Zebrafish_IntestinePancreas

source_name: Intestine and pancreas

value: Intestine and pancreas


title: 4AF atrial fibrillation

value: atrial fibrillation


title: UUATAC-seq datasets of Zebrafish_Testis

description: single-nucleus ATAC profile of Zebrafish_Testis

source_name: Testis

value: Testis

value: AB

value: 16 weeks


title: 18S reads obtained from sample SS22 (Run 3 - Replicate 2)

description:
Library name: SS22_18S
Full-length 18S rRNA gene sequencing


title: 3HS healthy control

value: peripheral blood

value: pBMC


title: αLPs from bone marrow of WT mice

description:
Library name: Sample 2
xiaoshu-bone marrow αLPs

data_processing:
The raw gene expression data were converted to Seurat data using the Seurat (v4.0) R toolkit.
Low quality cells with unique feature counts < 200 or > 4500 and > 20% mitochondrial counts were removed by quality control.
αLPs from the FL (8884 cells) or BM (7067 cells) populations were retained for subsequent analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bone marrow

extract_protocol:
To obtain Lin−CD45+CD127+Flt3−α4β7+CD25− αLPs subsets from fetal liver and bone marrow of WT B6  mice, the  mononuclear cells (MNCs) were incubated with anti-CD45 mAbs for 30 min at 4°C. Subsequently, MNCs were incubated with anti-PE beads for 60 min at 4°C. Nextly, MNCs were incubated with the indicated antibodies for 30 min at 4°C. 7AAD was added to the MNCs suspension, which was subsequently sorted using a FACSAria Fusion (BD Biosciences, San Diego, USA). The purity of the sorted cell populations was >  90%. Purified live cells were labelled with 0.4% Trypan blue to determine their viability (> 90% before processing for scRNA-seq).
Single-cell barcode scRNA-seq libraries were generated using the Chromium Single Cell 3’ Library (v2 chemistry; Nugen) according to the manufacturer’s standard protocol. The libraries were sequenced on a NovaSeq 6000 (Illumina). Gene-barcode matrices were generated by counting UMIs and filtering non-cell-associated barcodes.

value: bone marrow


title: 18S reads obtained from sample SS12 (Run 3 - Replicate 1)

description:
Library name: SS12_18S
Full-length 18S rRNA gene sequencing


title: UUATAC-seq datasets of Zebrafish_Gill

description: single-nucleus ATAC profile of Zebrafish_Gill

source_name: Gill

value: Gill


title: UUATAC-seq datasets of Zebrafish_Heart

description: single-nucleus ATAC profile of Zebrafish_Heart

source_name: Heart

value: Heart


title: 3AF atrial fibrillation


title: 18S reads obtained from sample S103 (Run 2 - Replicate 3)

description:
Library name: S103_18S
Full-length 18S rRNA gene sequencing


title: 2HS healthy control


title: 18S reads obtained from sample S102 (Run 2 - Replicate 2)

description:
Library name: S102_18S
Full-length 18S rRNA gene sequencing


title: UUATAC-seq datasets of Zebrafish_Brain

description: single-nucleus ATAC profile of Zebrafish_Brain

source_name: Brain

value: Brain


title: Male Homo Cortex, mouse P60

first: Timothy

last: Petros

state: Maryland

address: 35 Convent Drive, Bg 35 Room 3B-1002

institute: NICHD

description:
Library name: P60_Hom_Cortex_male
10x Genomics Multiome

data_processing:
The raw sequencing data were processed using Cell Ranger ARC (v2.0.0) pipeline. The cellranger-arc mkfastq command was used to generate the demultiplexed FASTQ files from BCL files. The sequencing reads were aligned to mouse (GRCm38/mm10) reference genome using cellranger-arc count.  Reads with de-duplicated and valid cell barcodes were used to build gene-by-barcode matrices by cellranger-arc count per genotype.
Assembly: GRCm38/mm10
Supplementary files format and content: cellranger filtered_feature_bc_matrix.h5

source_name: Cortex

extract_protocol:
Embryonic brain dissections: Pregnant dams were anesthetized with an i.p. injection of Euthasol, E13.5 embryos were removed and placed in ice-cold carbogenated artificial cerebral spinal fluid (ACSF, in mM: 87 NaCl, 26 NaHCO3, 2.5 KCl, 1.25 NaH2PO4, 0.5 CaCl2, 7 MgCl2, 10 glucose, 75 sucrose, saturated with 95% O2, 5% CO2, pH 7.4). Embryonic tails were cut for genotyping. MGE and hypothalamus were dissected from individual brains in ice-cold ACSF, transferred to individual 0.5 mL Eppendorf tubes, then flash frozen on dry ice and stored at -80°C. Adult brain dissections:  The somatosensory cortex and hypothalamus were dissected, transferred to 1.5 mL Eppendorf tubes, then flash frozen on dry ice and stored at -80°C. Frozen E13.5 and P60 tissue from Nkx2.1-Cre;H3.3K4M;sun1-GFP mice were mechanically lysed, washed and filtered to generate single nuclei suspensions for the 10x Genomics Multiome assay as previously described. These suspensions were then sorted via flow cytometry to harvest ~100,000 GFP+ nuclei. Nuclei solutions were centrifuged in a bucket centrifuge at 500 g for 5 minutes at 4 degree. Supernatant was removed and nuclei reconstituted in 1x Nuclei buffer at a density of 3,000 nuclei/μL. 5 μL of this solution was then used for the 10x Genomics Single Cell Multiome Assay per manufacturer’s protocol.
Joint libraries for scRNA-seq and scATAC-seq were created using 10X Genomics Single Cell Multiome ATAC + Gene Expression kit (1000285) by following manufacturer’s protocols.

value: Cortex

tag: Sex

value: male

value: Homo

tag: age


title: 1HS healthy control