title: SKO scRNA-seq

city: Suzhou

first: Xiaoyu

last: Lin

address: No. 100, Chongwen Road, Suzhou Industrial Park

institute: Suzhou Institute of Systems Medicine

description:
Library name: Sample2
10xGenomics

data_processing:
For bioinformatics analysis, results from Illumina sequencing were converted to FASTQ format using bcl2fastq software (version 5.0.1). The scRNA-seq sequencing data were compared to reference genome using CellRanger software, and cellular and individual cellular 3' end transcripts were identified and counted in thesequenced samples (https://support.10xgenomics.com/single-cell-gene expression/software/pipelines/latest/what-is cell-ranger , version 7.0.0).
Assembly: mm10
Supplementary files format and content: Taq-separated value files and matrix files

source_name: MC38 tumor

extract_protocol:
MC38 tumors from SPP1fl/fl and SPP1fl/fl-Lyz2-icre mice were dissected and digested with a solution containing collagenase IV (0.2 mg/ml) and deoxyribonuclease I (10 mg/ml; Sigma- Aldrich). The single- cell suspension was obtained by passing through a 70- mm cell mesh and re-suspending in Hanks’ buffer. Samples were stained for 30 min using an antibody against CD45. 7-AAD was freshly added before cell sorting. CD45+7-AAD- single cells were sorted for library construction of scRNA-seq.
For chromium 10´ Genomics library and sequencing, single-cell suspension was added to the 10´ Chromium chip according to the instructions for the 10´ Genomics Chromium Single-Cell 3' kit (V3), with the expectation of capturing 8,000 cells. cDNA amplification and library construction were performed according to standard protocols. Libraries were sequenced by LC-Bio Technology (Hangzhou, China) on an Illumina NovaSeq 6000 sequencing system (double-end sequencing, 150 bp) at a minimum depth of 20,000 reads per cell.

value: MC38 tumor

value: CD45+ cells


title: Fiaj1_CHR_Rep1

status: Public on Jun 30 2026

type: SRA

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

description:
Library name: Fiaj1_CHR_Rep1
cell_lines_salmon.merged.gene_tpm.tsv.gz

library_source: transcriptomic

data_processing:
Quality control, trimming and mapping of the FASTQ files was performed using the rnaseq pipeline (version 3.12.0), distributed by nf-core [doi: https://zenodo.org/records/7998767]. The pipeline was configured so that each constituent component was under version control and executed within a Singularity container [https://sylabs.io]. The following command was used to execute the pipeline:  nextflow run nf-core/rnaseq -r 3.12.0 --input samplesheet.csv --genome homo_sapiens.GRCh38.release_102 -config config.txt --extra_trimgalore_args '--nextseq 20' --outdir results --deseq2_vst -bg  These parameters generally adhere to the defaults set by the nf-core rnaseq pipeline. That pipeline release used STAR (version 2.7.9a) as the aligner, mapping reads to the human reference genome (GRCh38 / release 102). The specified read trimming parameter (--nextseq 20) were sequencing platform-specific, to account for the Illumina colour chemistry in which high quality calls for guanine nucleotides may actually reflect no signal on a flow cell. The pipeline was also passed a sample list detailing the forward and reverse FASTQ file pairings, along with the sample identities and how any technical and biological replicates should be grouped together. The nf-core rnaseq pipeline produces quantitated expression values for every gene for each sample, reporting raw counts and TPM values. These expression matrices were used in subsequent analyses.
FASTQ files could not be submitted for male HipSci cell lines owing to donor confidentiality regarding chromosome Y sequence information. Instead, BAM files generated by the nf-core atacseq pipeline (described previously) were submitted.  The BAM files were filtered by using samtools v1.21  to   contain only reads mapping to autosomes and chromosome X.
Assembly: GRCh38
Supplementary files format and content: The processed data files list the TPM expression values for each gene, segmented by biological replicate.  These data were produced by the nf-core rnaseq pipeline.

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: All cell lines were cultured under atmospheric oxygen, 5% CO2 and at 37 degrees C in Essential 8 (E8) medium (Thermo Fisher A1517001) on TC-treated 6 well plates (Corning 3506) coated with rh-VTN (Thermo Fisher A14700) at 10 mcg/well in PBS without calcium or magnesium. For CHR lines culture plates were coated with rhL521 (Gibco A29249) at 5mcg per well of a 6 well plate in DPBS with calcium and magnesium (Gibco 14040133) and cells were cultured in Stemflex (ThermoFisher, A3349401) supplemented with 3mcM IWP2 (Cayman Chemicals 13951).

extract_protocol:
700,000 hiPSCs or hESCs were used for RNA extraction for each biological replicate. Cells were washed once with 1ml Dulbecco's Phosphate Buffered Saline (DPBS) and harvested using 500µl Accutase (StemCell Technologies, 07922) for 3 minutes at 37°C. Dissociated cells were then collected with 5ml of corresponding hPSC medium and centrifuged for 3 min at 400 RCF at RT. Supernatant was aspirated and the cells were resuspended in 1ml cold DPBS. RNA extraction from hiPSCs/hESCs was conducted using the Monarch Total RNA Miniprep Kit (NEB T2010S) according to the manufacturer’s protocol, with DNase I treatment used to enzymatically remove residual gDNA. RNA concentration was quantified using Nanodrop and the RNA Integrity Number (RIN) was assessed using the Agilent RNA 6000 Pico Kit (Agilent, 5067-1513) on Agilent 2100 Bioanalyzer (Agilent). A RIN value of >7 was deemed to be of good quality and used for downstream RNA-seq library processing. The isolated RNA was frozen and stored at -80°C until RNA-seq library preparation.
RNA-seq library preparation was performed on the isolated RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module, which isolated mRNA from total RNA (100ng input) by poly(A)-enrichment. RNA-seq libraries were subsequently prepared from the isolated mRNA using the NEBNext Ultra II Directional RNA Library Prep Kit from Illumina, the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L), and the NEBNext Multiplex Oligos from Illumina (Index Primers Set 1, 2, 3 and 4, NEB, E7335S, E7500S, E7710S, E7730S), following the manufacturer’s protocols. The final sequencing-ready libraries were amplified using the protocol’s PCR programme with 12 cycles. Size distribution and yield quantification of the RNA-seq libraries were assessed using an Agilent 2100 Bioanalyzer high sensitivity DNA chip (Agilent 5067–4626).

tag: cell line

tag: cell type

value: human pluripotent stem cells

tag: treatment


title: neurons,cK2c,week18,female,rep2 (501_H3K27ac)

city: Philadelphia

first: Matthew

last: Edwards

state: PA

address: 450 Clinical Research Building

department: Genetics

country: USA

institute: University of Pennsylvania School of Medicine

description: Library name: 501_H3K27ac

library_source: genomic

data_processing:
CUT&Tag profiles for all four histone marks were trimmed using Cutadapt and aligned to the mm10 using bowtie2.  Reads were then centered and extended to represent the full DNA fragment, and were normalized using base-pair normalization with the Deeptools BamCoverage function.
Assembly: mm10
Supplementary files format and content: Bigwig tracks of histone modifications after BPM normalization
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Mus musculus

source_name: Cortex

extract_protocol:
Cut&Tag was used to profile H3K4me3, H3K4me2, H3K4me1 and H3K27ac in eighteen-week-old cortical neurons. The CUT&Tag-direct V.3 protocol31,32 were performed with minor modifications. For each sample, 50,000 GFP⁺/NeuN⁺ excitatory neuron nuclei were bound to Concanavalin-A beads (3.5 µL bead slurry per reaction) and incubated with primary antibodies (1:50 dilution) overnight at 4°C: H3K4me1 (EpiCypher #13-0057), H3K4me2 (EpiCypher #13-0027), H3K4me3 (Active Motif #39159), or H3K27ac (Active Motif #39133). After washing, bead-bound nuclei were incubated with guinea pig anti-rabbit secondary antibody for 30 min at room temperature. Protein A–Tn5 transposome (pAG-Tn5; EpiCypher #15-1117) was added (2.5 µL per reaction) and incubated for 1 hr at room temperature, followed by tagmentation at 37°C for 1 hour.Tagmented chromatin was released by incubation with 0.1% SDS at 58°C for 1 hr and neutralized with 0.67% Triton-X100.
Libraries were amplified using NEBNext High-Fidelity 2× PCR Master Mix (non-hot-start) (NEBNext #M0541L) with unique dual indexes (Buenrostro-style i7/i5 indexing) for 11–12 cycles depending on mark abundance. PCR products were cleaned with 1.3× SPRI bead purification, eluted in 13.2 µL, and assessed by Qubit and Bioanalyzer.

tag: tissue

value: Cortex

value: In vivo

value: Excitatory neurons

tag: genotype

value: conditional kmt2c knockout

tag: batch


title: 2_12_19_TWM2_F_TTAACT_R1

city: Brookings

first: Anne

last: Fennell

state: SD

address: Raven Precision Ag Building Box 2100A

department: Agronomy, Horticulture & Plant Science

institute: South Dakota State University

description:
Library name: 12685_5751_144676_HW3JMBGXJ_NSF023_C02_2_12_19_TWM2_F_TTAACT_R1
Total RNA single illumina

data_processing:
1. Quality Control of Raw Reads- Raw RNA-seq reads were assessed for quality using FastQC, and summary reports across all samples were generated using MultiQC.
2. Adapter Trimming and Filtering- Adapter sequences and low-quality bases were removed using Trimmomatic. Since the data consisted of single-end reads, the TruSeq2 single-end adapter file was used during trimming.
3. Reference Genome Preparation- The Vitis vinifera 12Xv2 reference genome assembly and V2.20 GFF3 annotation file were downloaded and prepared for downstream analysis.
4. Genome Index Generation - Genome indices were generated using STAR to facilitate efficient alignment of RNA-seq reads.
5. Read Alignment - Trimmed reads were aligned to the Vitis vinifera reference genome using STAR, producing BAM alignment files for each sample.
Assembly: 6. Gene Expression Quantification- Gene-level read counts were generated using featureCounts  with the V2.20 GFF3 annotation file, retaining gene IDs for downstream expression analysis.
Supplementary files format and content: The processed data file consists of a tab-delimited text matrix file generated by featureCounts. The matrix contains raw, un-normalized digital gene-level counts, where rows correspond to specific unique Gene IDs derived from the Vitis vinifera 12Xv2 (V2.20 GFF3) reference annotation, and columns represent the individual biological samples (replicates) mapped using single-end RNA-seq reads. No normalized values (such as FPKM or TPM) are included in this specific file.

molecule: total RNA

organism: Vitis hybrid cultivar

source_name: Bud

growth_protocol: Standard commercial vineyard management, Tuckers Walk, Garretson SD.

extract_protocol:
Total RNA was extracted from grapevine bud tissue using a modified CTAB protocol or standard commercial RNA isolation kit optimized for woody plant tissues. RNA quality and quantity were assessed using an Agilent Bioanalyzer or NanoDrop spectrophotometer to ensure high-quality material prior to library preparation.
Sequencing libraries were constructed using the Illumina TruSeq RNA Library Prep Kit following the manufacturer's standard protocols. Poly-A selected mRNA was fragmented, converted to cDNA, ligated with TruSeq adapters, and PCR amplified to generate single-end sequencing libraries.

treatment_protocol: Controled chilling (4ºC) in dark.  Field natural chilling temperatures.

value: Bud

value: Field Chilling

value: total RNA

value: single


title: Micro-C of Fbn2_lowCTCF cell line, replicate 4

first: James

middle: Martin

last: Jusuf

state: MA

address: Building 56 Room 787B, 32 Vassar Street

department: Biological Engineering

institute: Massachusetts Institute of Technology

description:
Library name: Fbn2_lowCTCF_rep4
Cell line containing TetO and Anchor3 arrays for fluorescent labeling of the Fbn2 loop on chr18 with CTCF tagged with mAID (leaky depletion)

data_processing:
Base calls for NovaSeq output were obtained using bcl2fastq (v2.20.0.422).
Paired-end reads were aligned to the mm39 reference genome or modified versions of mm39 using bwa-mem2 (v2.2.1). The modified genomes contained the synthetic DNA sequences inserted at the anchors of the Fbn2, Npr3, or synTAD loops.
Aligned paired-end reads were then parsed with pairtools (v1.0.3) parse with --add-columns mapq --walks-policy all --min-mapq 30.
When aligning to the modified genomes only, a custom pipeline was implemented to recover multiply mapping reads in the synthetic regions by randomly assigining them to unique positions.
Parsed reads were filtered for PCR duplicates and unmapped/mutiply mapping reads with pairtools dedup with --max-mismatch 1.
For all samples, trans reads were downsampled in order to ensure that trans reads constituted a fixed 5% of total reads.
These filtered reads were subsequently converted to .cool format with cooler (v.0.9.3) cload pairs and subsequently to .mcool format with cooler zoomify with --balance --balance-args '--ignore-dist 20000'
Assembly: mm39
Supplementary files format and content: mcool files contain all valid Micro-C pairs stored in HDF5 format with multiple resolutions
Supplementary files format and content: mESC_merged_54B_mm39.mcool contains all valid Micro-C pairs of untreated mESC cells from this study, Hansen et al. 2019, Hsieh et al. 2020, Hsieh et al. 2022, Narducci & Hansen 2025, and Paldi et al. 2026.

growth_protocol: Fbn2, Fbn2_lowCTCF, and synTAD cell line: Cells were cultured on plates pre-coated with 0.1% gelatin solution (Sigma-Aldrich, G1890) in KnockOut Dulbecco's Modified Eagle Medium (Thermo Fisher, 10829018) supplemented with 15% fetal bovine serum (HyClone, SH30396.03),  2 mM GlutaMAX (Thermo Fisher, 35050061), 1% MEM Non-Essential Amino Acid Solution (Thermo Fisher, 11140050), 0.1 mM 2-mercaptoethanol (Sigma-Aldrich, M3148), 1000 U/mL leukemia inhibitory factor (home-made [Hansen et al 2017]), 10 μM MEK inhibitor (Tocris, PD0325901), 3 μM GSK3 inhibitor (Sigma-Aldrich, SML1046), and 100 μg/ml Penicillin-Streptomycin (Thermo Fisher, 15140122) in 5% CO2 at 37 °C. In addition, synTAD cells were grown with GSK-3484862 (TargetMol, cat. no. T11469) at a 2 µM concentration at all times. Npr3 cell line: Cells were cultured on plates pre-coated with 0.1% gelatin solution (Sigma-Aldrich, G2500) in Glasgow Minimum Essential Medium (Sigma-Aldrich, G5154) supplemented with 15% fetal calf serum (Eurobio Abcys), 1% L-Glutamine (Thermo Fisher, 25030024), 1% Sodium Pyruvate MEM (Thermo Fisher, 11360039), 1% MEM Non-Essential Amino Acids (Thermo Fisher, 11140035), 0.1 mM 2-mercaptoethanol (Thermo Fisher, 31350010), 20 U/mL leukemia inhibitory factor (Miltenyi Biotec, premium grade), 1 µM MEK inhibitor (Axon, 1408), and 3 µM GSK3 inhibitor (Axon, 1386) in 8% CO2 at 37 °C.

extract_protocol:
Cells were fixed with 3 mM DSG for 35 minutes, followed by an additional 10 minutes with 1% formaldehyde. Following quenching, nuclei were prepared from fixed cells. Chromatin was digested in situ using MNase, DNA 3' ends were chewed back and biotinylated, and then free DNA ends were proximity ligated. Unligated ends were digested, and chromatin crosslinks were reversed. DNA was purified by the DNA Clean and Concentrator kit (Zymo), and size selected for dinucleosomal fragments on an agarose gel. Following end polishing of DNA fragments, a streptavidin pulldown was used to enrich for ligated dinucleosomal fragments.
Size selected DNA fragments bound to streptavidin coated beads were used to prepare Micro-C libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), using NEBNext Multiplex Oligos for Illumina for indexing samples. Libraries were amplified with 7 PCR cycles on the thermocycler using KAPA HiFi HotStart ReadyMix (Roche) and purified using AMPure XP beads (Beckman Coulter). Purified libraries were quantified using qPCR and pooled in a 1:1 ratio. Following qPCR quantification, the library pool was submitted for sequencing.

treatment_protocol: Micro-C was performed on cells in untreated condition.

value: Embryonic stem cells


title: propionic acid, biol rep4

city: Guangzhou

first: Lan

last: Yang

state: Guangdong

address: 1838 North Guangzhou Street

department: Department of Plastic and Aesthetic Surgery

country: China

institute: Nanfang Hospital of Southern Medical University

data_processing:
Illumina Casava software was used for basecalling
Cutadapt sofftware was used for data filtering. Data filtering steps required at least 10 bp Overlap,and 20% base false rate was permitted
HISAT2 software 2.1.0 with the parameter of -rna-strandness rf --fr was used for reads alignment
Assembly: mm10
Supplementary files format and content: The processed data file (.xls) includes FPKM values for every gene and every sample

source_name: skin

growth_protocol: C57BL/6 mice (6 weeks of age, female) were housed in SPF environment at room temperature 22 °C with a 12:12 h light/dark cycle and were provided with rodent chow and water

extract_protocol:
Total RNA was extracted using the TRIzol reagent. 1 μg of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit following manufacturer’s instructions

treatment_protocol: The mice were topically applied 5 nmol of MC903 on the back skin for 10 consecutive days. After 1 h of MC903 treatment, control or propionic acid (1 mM) was topically applied on the skin of these mice. At day 11, the skin lesions were harvested for RNA-seq

value: skin

value: wild type

value: propionic acid


title: Feec2_untreated_Rep2

description:
Library name: Feec2_untreated_Rep2
cell_lines_salmon.merged.gene_tpm.tsv.gz


title: Micro-C of Fbn2_lowCTCF cell line, replicate 3

description:
Library name: Fbn2_lowCTCF_rep3
Cell line containing TetO and Anchor3 arrays for fluorescent labeling of the Fbn2 loop on chr18 with CTCF tagged with mAID (leaky depletion)


title: neurons,cK2c,week18,female,rep1 (175_H3K4me3)

description: Library name: 175_H3K4me3


title: propionic acid, biol rep3


title: Feec2_untreated_Rep1

description:
Library name: Feec2_untreated_Rep1
cell_lines_salmon.merged.gene_tpm.tsv.gz


title: Micro-C of Fbn2_lowCTCF cell line, replicate 2

description:
Library name: Fbn2_lowCTCF_rep2
Cell line containing TetO and Anchor3 arrays for fluorescent labeling of the Fbn2 loop on chr18 with CTCF tagged with mAID (leaky depletion)


title: neurons,cK2c,week18,female,rep1 (175_H3K4me2)

description: Library name: 175_H3K4me2


title: Burb1_untreated_Rep2

description:
Library name: Burb1_untreated_Rep2
cell_lines_salmon.merged.gene_tpm.tsv.gz


title: propionic acid, biol rep1


title: Burb1_untreated_Rep1

description:
Library name: Burb1_untreated_Rep1
cell_lines_salmon.merged.gene_tpm.tsv.gz


title: neurons,cK2c,week18,female,rep1 (175_H3K27ac)

description: Library name: 175_H3K27ac


title: C57BL/6J (Input)

city: Mississauga

first: Iva

last: Zovkic

state: ON

address: 3359 Missisauga Road, DV1015 (Zovkic Lab)

department: Psychological and Brain Sciences

country: Canada

institute: University of Toronto Mississauga

description: Library name: Sample 9

data_processing:
Adaptors were trimmed with trimmomatic (v0.39).
Trimmed reads were mapped to GrCM38/mm10 using Bowtie 2 (v2.5.1). Aligned reads were filtered and deduplicated with samtools (v1.12) to keep only uniquely paired reads with a quality score over 20.
Peaks were called by comparing the ChIP samples against the merged input using MACS3 (v3.0.1) with a q-value cutoff of 0.1.
bigWig files were generated using deepTools (v3.5.6).
Assembly: mm10
Supplementary files format and content: bigWig
Adaptors trimmed using soft-clipping in Rsubread
Reads aligned using Rsubread in R (version 2.12.3, R version 4.2.3)
Aligned reads counted using featureCounts in Rsubread library (version 2.12.3) (genes with count sum <20 across all samples removed prior to analysis)
Differential expression analysis performed in DESeq2 in R using padj<0.05
Assembly: mm39
Supplementary files format and content: bigWig

source_name: Hippocampus

extract_protocol:
Whole bilateral hippocampi from 10-12 week old male C57BL/6 mice were homogenized in 1xPBS containing 1x Protease Inhibitor Cocktail (1xPIC; Cell Signaling #5871) and crosslinked in 1% formaldehyde for 5min at RT, then quenched with 125mM glycine for 5min at RT and spun at 2000g for 3min at 4ºC. Pellets were washed 3x with 200uL ice-cold PBS containing PIC, then resuspended in 1mL ice-cold LB1 (50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) containing PIC and rotated for 10min at 4ºC. Nuclei were collected by centrifugation at 2000g for 5mins at 4ºC, washed by rotating for 5 min at 4ºC in 200uL TM2 (10mM Tris-HCl pH 8.0, 2mM MgCl2) containing PIC, then resuspended in 200uL TM2 and warmed for 5mins at 37ºC before adding 1mM CaCl2.
ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit following manufacturer's protocol. Input samples were merged before library preparation.
Total RNA was extracted from AAV-shRNA infected dorsal hippocampal tissue using Qiagen RNeasy kit. Eluate was sent to CD Genomics (Shirley, NY) for polyA selection and library prep
Library preparation performed at CD Genomics (Shirley, NY)

value: Hippocampus

value: WT


title: control, biol rep4

value: control


title: Burb1_CHR_Rep2

description:
Library name: Burb1_CHR_Rep2
cell_lines_salmon.merged.gene_tpm.tsv.gz


title: C57BL/6J, macroH2A1.2 (ChIP), rep4

description: Library name: Sample 8


title: neurons,WT,week18,female,rep3 (505_H3K4me2)

description: Library name: 505_H3K4me2

value: wild-type


title: control, biol rep3


title: neurons,WT,week18,female,rep3 (505_H3K4me3)

description: Library name: 505_H3K4me3


title: Burb1_CHR_Rep1

description:
Library name: Burb1_CHR_Rep1
cell_lines_salmon.merged.gene_tpm.tsv.gz

value: human pluripotent stem cells


title: Sojd3_untreated_Rep2

description:
Library name: Sojd3_untreated_Rep2
cell_lines_salmon.merged.gene_tpm.tsv.gz


title: control, biol rep2


title: neurons,WT,week18,female,rep3 (505_H3K4me1)

description: Library name: 505_H3K4me1

value: Cortex


title: C57BL/6J, macroH2A1.2 (ChIP), rep2

description: Library name: Sample 6


title: control, biol rep1


title: neurons,WT,week18,female,rep3 (505_H3K27ac)

description: Library name: 505_H3K27ac

value: In vivo


title: Sojd3_untreated_Rep1

description:
Library name: Sojd3_untreated_Rep1
cell_lines_salmon.merged.gene_tpm.tsv.gz


title: C57BL/6J, macroH2A1.2 (ChIP), rep1

description: Library name: Sample 5


title: stomach, Arid1a mutant, ATAC, rep1

city: TORONTO

first: Adrian

middle: Kwan Ho

last: Loe

address: 686 Bay Street

institute: The Hospital for Sick Children

description: 10x Genomics

library_source: genomic single cell

data_processing:
cellranger-arc-2.0.1
Assembly: GRCm39/mm39
Supplementary files format and content: CellRanger output files: mRNA_barcodes.tsv.gz, mRNA_features.tsv.gz, mRNA_matrix.mtx.gz
Supplementary files format and content: CellRanger output file: ATAC_fragment.tsv.gz
Supplementary files format and content: Text files include UMAP embedding
Supplementary files format and content: Text files include metadata

source_name: stomach

extract_protocol:
Single cells were encapsulated in GEMS using the 10X Chromium controller with the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 4 rxns PN-1000285
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (CG000338 Rev C)

value: stomach

value: High dose tamoxifen, 35 days

tag: library type

value: ATAC


title: Sojd3_CHR_Rep2

description:
Library name: Sojd3_CHR_Rep2
cell_lines_salmon.merged.gene_tpm.tsv.gz


title: C57BL/6J, macroH2A1.1 (ChIP), rep4

description: Library name: Sample 4


title: neurons,WT,week18,female,rep2 (504_H3K4me2)

description: Library name: 504_H3K4me2

value: Excitatory neurons


title: Sojd3_CHR_Rep1

description:
Library name: Sojd3_CHR_Rep1
cell_lines_salmon.merged.gene_tpm.tsv.gz


title: stomach, Arid1a mutant, GEX, rep1

description: 10x Genomics

library_source: transcriptomic single cell

molecule: nuclear RNA

value: mRNA


title: neurons,cK2c,week18,female,rep3 (9776_H3K4me2)

description: Library name: 9776_H3K4me2

value: conditional kmt2c knockout


title: stomach, day35, ATAC, rep1

description: 10x Genomics

value: wildtype


title: Micro-C of synTAD cell line, replicate 1

description:
Library name: synTAD_G2_rep1
Cell line containing 3xCTCF sites forming synthetic loop (synTAD) on chr2 and flanking synBsr1 and Anchor3 arrays for fluorescent labeling

value: Embryonic stem cells


title: C57BL/6J, macroH2A1.1 (ChIP), rep3

description: Library name: Sample 3


title: Foxa1_ChIP_rep1

city: Basel

first: Prisca

last: Liberali

address: Klingelbergstrasse 48

department: D-BSSE

country: Switzerland

institute: ETHZ

description: Library name: Foxa1_ChIP_rep1

data_processing:
Illumina RTA 3.4.4 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. All analyses, unless stated otherwise, were performed within R (version 4.3.2) and Bioconductor (version 3.18) (14). ChIP-seq read pairs were aligned to the GRCm38/mm10 mouse genome assembly using the qAlign function from the QuasR package (Gaidatzis et al., Bioinformatics 2015) with default parameters.
BigWig files with alignment fragment coverage along the genome were generated from the bam files using bedtools version 2.30, by first extracting a bed file with fragment coordinates (bedtools bamtobed), calculating genome coverage in a bedGraph file (bedtools genomecov) and then converting it to BigWig format using bedGraphToBigWig from KentTools version 442.
Assembly: GRCm38/mm10
Supplementary files format and content: bigwig files with alignment fragment coverage along the genome

source_name: mouse small intestinal organoids

growth_protocol: Organoids were generated from isolated crypts of mice, as previously described (Sato et al.,Nature 2009). Maintenance of organoid cultures was performed in ENR medium (advanced DMEM/F-12 with 15mM HEPES (STEM CELL Technologies) supplemented with 100 μg/ml Penicillin and Streptomycin, 1×Glutamax (Thermo Fisher Scientific), 1×B27 (Thermo Fisher Scientific), 1xN2 (Thermo Fisher Scientific), 1mM N-acetylcysteine (Sigma), 500ng/ml R-Spondin (kind gift from Novartis), 100 ng/ml Noggin (PeproTech) and 100 ng/ml murine EGF (R&D Systems)).

extract_protocol:
A total of 10⁷ cells were crosslinked for 8 minutes at room temperature in 10 mL PBS supplemented with 1% formaldehyde (Sigma, F8775). The reaction was quenched by adding glycine to a final concentration of 0.125 mM. Cells were pelleted by centrifugation at 500 × g for 3 minutes at 4°C, washed once with PBS, pelleted again, flash-frozen in liquid nitrogen, and stored until further processing.
30µL of a 1:1 mixture of Protein A/G Dynabeads (Invitrogen, 10002D and 10004D) was pre-coupled with 3 µL of FOXA1 antibody (ab170933) for 1 hour at room temperature, followed by three washes with 1× ChIP buffer and stored on ice until use. The cells were lysed in 10 mL of buffer A (50 mM HEPES pH 8.0, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) on ice for 10 minutes. After centrifugation, the pellet was resuspended in 5 mL of buffer B (10 mM Tris pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl) and incubated on ice for 5 minutes. Nuclei were pelleted by centrifugation at 500 × g for 3 minutes at 4°C, resuspended in 150 µL of buffer C (50 mM Tris pH 8.0, 5 mM EDTA, 1% SDS, 100 mM NaCl), and incubated on ice for 10 minutes. TE buffer (1.3 mL) was then added, and chromatin was sheared in 15 mL tubes using a Bioruptor Pico device for two sessions of 10 cycles (30 seconds ON / 30 seconds OFF). After shearing, 160 µL of 10× ChIP buffer (0.1% SDS, 10% Triton X-100, 12 mM EDTA, 167 mM Tris-HCl pH 8.0, 1.67 M NaCl) was added. The chromatin was transferred to fresh tubes and centrifuged at 13,000 × g for 10 minutes at 4°C. Per sample, 30 µL of 1:1 pre-coupled beads were added to the chromatin, and the mixture was incubated with rotation for 4 hours at 4°C. The ChIP samples were washed four times with LSB (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate), twice with HSB (same as LSB but with 500 mM NaCl), twice with LiSB (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE+ buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 50 mM NaCl). During the final wash, beads were transferred to fresh tubes, and the wash buffer was completely removed. DNA was eluted twice from the beads using 75 µL of elution buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 150 mM NaCl, 1% SDS) by incubation at 65˚C with shaking. The eluates were pooled, and 2 µL of RNase A (20 µg/µL) was added, followed by incubation for 1 hour at 37°C. Input samples were adjusted to a total volume of 150 µL with elution buffer and processed in the same manner as ChIP samples. Proteinase K (2 µL, 20 mg/mL) was added, and samples were incubated for 2 hours at 55°C and then for 6 hours at 65°C. Afterward, 9 µL of 5 M NaCl, 30 µL of AMPure XP beads, and 190 µL of isopropanol were added. Samples were vigorously mixed, incubated at room temperature for 10 minutes, and the beads were collected on a magnetic rack. The beads were washed twice with 80% ethanol, and DNA was eluted in 30 µL of 10 mM Tris-HCl pH 8.0 for 5 minutes at 37°C. For library preparation, 25 µL of ChIP DNA or 50 ng of input DNA was used with the NEBNext Ultra II Library Prep Kit for Illumina (NEB), following the manufacturer’s protocol but with reactions scaled down to half-volume. Libraries were sequenced on the NovaSeq 6000 platform (Illumina) with paired-end reads (2x 56 bp).

value: mouse small intestinal organoids

tag: strain

value: intestinal epithelial cells

value: Lgr5::DTR-EGFP (Genentech, de Sauvage laboratory)

tag: chip antibody

value: FOXA1 antibody ab170933


title: neurons,WT,week18,female,rep2 (504_H3K4me1)

description: Library name: 504_H3K4me1


title: HUES8_iCas9_untreated_Rep2

description:
Library name: HUES8_iCas9_untreated_Rep2
cell_lines_salmon.merged.gene_tpm.tsv.gz


title: stomach, day35, GEX, rep1

description: 10x Genomics


title: HUES8_iCas9_untreated_Rep1

description:
Library name: HUES8_iCas9_untreated_Rep1
cell_lines_salmon.merged.gene_tpm.tsv.gz


title: C57BL/6J, macroH2A1.1 (ChIP), rep1

description: Library name: Sample 1

value: Hippocampus

value: WT


title: Hehd1_untreated_Rep2

description:
Library name: Hehd1_untreated_Rep2
cell_lines_salmon.merged.gene_tpm.tsv.gz

value: human pluripotent stem cells


title: neurons,WT,week18,female,rep1 (500_H3K4me2)

description: Library name: 500_H3K4me2

value: Cortex

value: wild-type


title: stomach, day7, ATAC, rep1

description: 10x Genomics

value: stomach

value: High dose tamoxifen, 7 days


title: MC38 (kd) tumor 4

city: Chicago

first: Lu

last: Gao

state: IL

institute: University of Chicago

description: Library name: kd4

data_processing:
Raw sequence reads were quality checked using FastQC software. Cutadapt software was used to trim poor-quality bases (<20) and Illumina universal adapter sequences from raw reads before alignment
Reads were then aligned to mm10 reference genome using the STAR aligner.
Picard tools were used to mark duplicate sequences as an additional quality control step. Raw gene expression counts were summarized with FeatureCounts.
Sample quality metrics and raw read counts were imported into R for further processing. The DESeq2 R package was used to estimate library size factors, normalize counts and perform differential expression analyses.
Assembly: mm10
Supplementary files format and content: rds file includes raw counts for each sample

source_name: xenograft tumor

growth_protocol: Cells were grown in DMEM + 10% FBS

extract_protocol:
RNAs were extracted with TRIZOL reagent.
Libraries were made using Roche KAPA RNA HyperPrep Kit

treatment_protocol: Cells were subcutaneously injected to C57BL/6 mice to induce tumor xenografts.

value: xenograft tumor

value: Colon cancer cell

value: Acss2 kd

value: subcutaneous xenograft


title: Hehd1_untreated_Rep1

description:
Library name: Hehd1_untreated_Rep1
cell_lines_salmon.merged.gene_tpm.tsv.gz


title: MC38 (kd) tumor 3

description: Library name: kd3


title: neurons,WT,week18,female,rep1 (500_H3K4me1)

description: Library name: 500_H3K4me1

value: In vivo

value: Excitatory neurons


title: Hehd1_CHR_Rep2

description:
Library name: Hehd1_CHR_Rep2
cell_lines_salmon.merged.gene_tpm.tsv.gz


title: MC38 (kd) tumor 2

description: Library name: kd2


title: MC38 (kd) tumor 1

description: Library name: kd1


title: neurons,WT,week18,female,rep1 (500_H3K27ac)

description: Library name: 500_H3K27ac


title: stomach, normal, ATAC, rep1

description: 10x Genomics

value: wildtype

value: no treatment

value: ATAC


title: stomach, normal, GEX, rep1

description: 10x Genomics

value: mRNA


title: neurons,cK2c,week6,female,rep6

description: Library name: 1773

data_processing:
Read quality was assessed with FastQC (v0.11.7). Adapter sequences were trimmed with cutadapt (v5.0; Martin, 2011) in paired-end mode (minimum length 1; Nextera or Illumina adapters according to the library). Trimmed reads were aligned to the mouse genome (mm10) with STAR33 (v2.7.9a) using the Ensembl gene annotation (sjdbOverhang 99), retaining only uniquely mapped reads (outFilterMultimapNmax 1) with at most three mismatches (outFilterMismatchNmax 3). Alignments were sorted and indexed with SAMtools34 (v1.9). Gene-level counts were generated with featureCounts35 (Subread v2.0.3) against the same Ensembl annotation, counting properly paired fragments (-p -B -C) at a minimum mapping quality of 10 (-Q 10) on the reverse strand (-s 2). Fragments were summarized over transcript features (-t transcript) and aggregated by gene (-g gene_id), so that intronic reads from nuclear RNA were retained.
Assembly: mm10
Supplementary files format and content: Featurecount matricies (.txt) obtained as described in data processing

extract_protocol:
RNA was extracted from sorted nuclei using the AllPrep DNA/RNA Kit (Qiagen #80204) according to manufacturer instructions with modifications to preserve nuclear RNA. RLT buffer was freshly supplemented with β-mercaptoethanol (Bio-rad #1610710) and lysates were passed through AllPrep DNA columns and then mixed 1:1 with 70% ethanol before binding to RNeasy columns on a vacuum manifold. Columns were washed with RW1 and RPE, dried by centrifugation, and RNA was eluted in RNase-free water. DNase treatment (37 µL DNase mix, 25 min, RT) was followed by ethanol precipitation with glycogen and sodium acetate.
Nuclear RNA-seq libraries were generated using the illumina Standard Total RNA Prep, Ligation with Ribo-Zero Plus kit (Illumina # 20040529) and were indexed using the IDT for Illumina RNA UD Indexes Set A (Illumina # 20091655). Indexed Libraries were amplified by 12 cycles of PCR, followed by 1× AMPure XP cleanup. Libraries were quantified by Qubit fluorometry and size-checked using the Agilent High Sensitivity DNA Bioanalyzer assay.

value: conditional kmt2c knockout

tag: age

tag: Sex

value: female


title: H9_untreated_Rep2

description:
Library name: H9_untreated_Rep2
cell_lines_salmon.merged.gene_tpm.tsv.gz

value: human pluripotent stem cells


title: neurons,cK2c,week6,female,rep5

description: Library name: 1767

value: Cortex


title: Male, DCT(early), replicate 7

city: Baltimore

first: Hyun Jun

last: Jung

state: MD

address: 720 Rutland Ave, Ross Research Building 1165B

department: Medicine (Nephrology)

institute: Johns Hopkins University School of Medicine

data_processing:
Two technical repliates of each biological replicate were concatenated into one replicate for further downstream data processing.
Counts and were generated by quantifying sequence reads on transcripts from Gencode GRCm38.p6 using salmon (0.14.10).
Assembly: Gencode (GRCm38.p6)
Supplementary files format and content: tab-delimited text files include raw gene counts for each gene

source_name: Kidney

growth_protocol: Mice were fed with a normal diet with free access to water.

extract_protocol:
Microdissection of the tubules were performed at 9-11 am. The microdissected tubules were washed in PBS three times and lyzed in Trizon solution. Total RNA was extracted using Direct-zol RNA Microprep kit (ZYMO RESEARCH).
For library preparation, cDNA was synthesized using SMART-Seq HT Kit (Clontech) and Nextera XT DNA Library Preparation Kit (Illumina).

value: Kidney

value: distal convoluted tubule cell

value: C57BL/6-Tg (Pvalb-tdTomato)15Gfng/J


title: H9_untreated_Rep1

description:
Library name: H9_untreated_Rep1
cell_lines_salmon.merged.gene_tpm.tsv.gz


title: MC38 (wt) tumor 2

description: Library name: wt2

value: xenograft tumor

value: Acss2 wt


title: Male, DCT(early), replicate 6


title: neurons,cK2c,week6,female,rep4

description: Library name: 1765


title: H1_untreated_Rep2

description:
Library name: H1_untreated_Rep2
cell_lines_salmon.merged.gene_tpm.tsv.gz


title: MC38 (wt) tumor 1

description: Library name: wt1

value: Colon cancer cell


title: Male, DCT(early), replicate 5


title: neurons,cK2c,week6,female,rep3

description: Library name: 7185


title: H1_untreated_Rep1

description:
Library name: H1_untreated_Rep1
cell_lines_salmon.merged.gene_tpm.tsv.gz


title: TFE4 KO PU1 rep2

city: SAINT LOUIS

first: Hao

last: Hu

state: MO

address: 4370 Duncan Ave

department: Neurology

institute: Washington University School of Medicine

description: Library name: SR008313_TFE4_KO_PU1_11

data_processing:
10x Genomics CellRanger software version 9.0.1 was used for sequence alignment and gene counting
Assembly: mm10
Supplementary files format and content: Compressed folders of tab-separated values files and matrix files

source_name: hippocampus

extract_protocol:
For single nucleus RNA-sequencing (snRNA-seq), mouse brains were collected dissected to isolate the hippocampal regions. The brain slices were mechanically minced with surgical scissors in cold lysis buffer containing 10 mM Tris buffer (pH 7.4), 5 mM MgCl2, 25 mM KCl, 1 mM DTT, 5X EDTA-free protease inhibitor (Millipore Sigma, Cat# 11873580001), 0.02 U/µL RNase-In RNase inhibitor (Promega, Cat# N2518), and 0.02 U/µL SUPERase-In RNase Inhibitor (ThermoFisher Scientific, Cat# AM2696) in nuclease-free water. The suspension was then homogenized on ice using a glass dounce homogenizer (15 loose and 15 tight strokes). The homogenate was filtered through a pre-wet 40-µm cell strainer (Fisher Scientific, Cat# MT4040) and rinsed with cold wash buffer containing PBS, 0.1% BSA, RNase-In, and SUPERase-In. Nuclei were purified with Anti-Nucleus MicroBeads (Miltenyi Biotec, Cat# 130-132-997) per the manufacturer’s protocol. The samples were further sorted with AF647-anti-NeuN (to isolate neuronal nuclei; Cat# ab190565) AT 1:1000 (v:v) and PE-anti-PU.1 (to isolate microglia nuclei; Cat# 57800S) at 1:50 (v:v).
After sorting, nuclei quality and yield were confirmed using a Cellometer K2 fluorescent cell counter with AO/PI staining, and libraries were immediately prepared using Chromium GEM-X Single Cell 3' Kit v4 (10x Genomics) according to manufacturer’s instructions. All snRNA-seq libraries were sequenced using Illumina NovaSeq X targeting 50,000 reads/nuclei through GTAC @ MGI at Washington University in St. Louis.

value: hippocampus

value: TFE4 Irf8d32


title: Deyz2_untreated_Rep2

description:
Library name: Deyz2_untreated_Rep2
cell_lines_salmon.merged.gene_tpm.tsv.gz


title: TFE4 KO DN rep2

description: Library name: SR008313_TFE4_KO_DN_12


title: Male, DCT(early), replicate 3


title: neurons,cK2c,week6,female,rep1

description: Library name: 4322

value: In vivo

value: Excitatory neurons


title: TFE4 WT PU1

description: Library name: SR008099_TFE4_WT_PU1_8

value: TFE4 WT


title: Deyz2_untreated_Rep1

description:
Library name: Deyz2_untreated_Rep1
cell_lines_salmon.merged.gene_tpm.tsv.gz


title: Male, DCT(early), replicate 2


title: neurons,WT,week6,female,rep6

description: Library name: 1920

value: wild-type


title: Cuhk2_untreated_Rep2

description:
Library name: Cuhk2_untreated_Rep2
cell_lines_salmon.merged.gene_tpm.tsv.gz


title: TFE4 WT NeuN

description: Library name: SR008099_TFE4_WT_NeuN_7


title: Male, DCT(early), replicate 1


title: neurons,WT,week6,female,rep5

description: Library name: 1766


title: Cuhk2_untreated_Rep1

description:
Library name: Cuhk2_untreated_Rep1
cell_lines_salmon.merged.gene_tpm.tsv.gz


title: TFE4 WT DN

description: Library name: SR008099_TFE4_WT_DN_9


title: Female, DCT(early), replicate 6


title: neurons,WT,week6,female,rep4

description: Library name: 1764


title: Sojd3-untreated_H3K4me3_REP2

description:
Library name: Sojd_H3K4me3_REP2
cut_and_tag_H3K4me3_peaks.tsv.gz

data_processing:
Quality control, trimming and mapping of the FASTQ files was performed using the cutandrun pipeline (version 3.2.1), distributed by nf-core [doi: 10.5281/zenodo.2634132]. The pipeline was configured so that each constituent component was under version control and executed within a Singularity container [https://sylabs.io].  The following command was used to execute the pipeline:  nextflow run nf-core/cutandrun -r 3.2.1 --input samplesheet.csv --genome homo_sapiens.GRCh38.release_102 -config config.config --blacklist ENCFF356LFX.txt --normalisation_mode CPM --use_control false --skip_heatmaps --outdir results -bg  These parameters generally adhered to the defaults set by the nf-core cutandrun pipeline.  Reads were mapped to the human reference genome (GRCh38 / release 102), but reads mapping to regions blacklisted by the ENCODE project [https://www.encodeproject.org/files/ENCFF356LFX/] were removed. The pipeline was also passed a sample list detailing the forward and reverse FASTQ file pairings, along with the sample identities, antibodies used, and how technical and biological replicates should be grouped together. The pipeline used the software SEACR (version 1.3)102 to identify peaks i.e genomic regions with a localised high abundance of mapped reads. SEACR was run using the default settings for the cutandrun pipeline, but no IgG control was provided.
Consensus peaks were identified separately for the H3K4me3 and the H3K27me3 antibodies. Peaks present in at least 2 of any of the biological replicates were considered as “consensus peaks” and retained.  Since the start and end positions of peaks rarely match to the exact base position between samples, overlapping peak regions from different biological replicates were merged together.
The number of reads mapping to each peak was quantitated using the genome browser and analysis software SeqMonk (version 1.48.1) [https://www.bioinformatics.babraham.ac.uk/projects/seqmonk]. To achieve this, the aligned reads BAM files generated by the nf-core cutandrun pipeline were imported into SeqMonk, along with a text-format list detailing peak genomic locations. By using the “Feature Probe Generator” and “Read Count Quantitation” SeqMonk functions, an “Annotated Probe Report” was created listing the raw read counts for each peak. A separate file was also created using this method, but instead it reported the log2-transformed normalised data (counts per million reads) for each peak.
FASTQ files could not be submitted for male HipSci cell lines owing to donor confidentiality regarding chromosome Y sequence information. Instead, BAM files generated by the nf-core atacseq pipeline (described previously) were submitted.  The BAM files were filtered by using samtools v1.21  to   contain only reads mapping to autosomes and chromosome X.
Assembly: GRCh38
Supplementary files format and content: The processed data files list the coordinates of the peak regions and the associated log2-transformed read count (per million reads) mapping to each peak, as quantitated by the genome browser and analysis software SeqMonk.
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was carried out using EpiCypher CUTANA™ CUT&Tag Protocol v 1.7. 120,000 cells per CUT&Tag experiment were harvested for nuclei extraction. The cell suspension was centrifuged for 3 minutes at 300 RCF at RT. The cell pellet was resuspended in 100 µl/sample of cold nuclei extraction buffer (20 mM HEPES–KOH, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol, 0.5 mM Spermidine (Sigma-Aldrich, 05292), 1x Roche cOmpleteTM, Mini, EDTA-free Protease Inhibitor) and incubated on ice for 10 minutes, followed by centrifugation for 3 minutes at 600 RCF and 4°C. The nuclei pellet was resuspended in nuclei extraction buffer to achieve a final concentration of 1.2 million nuclei/ml and frozen at -80°C until library preparation. Upon thawing of the nuclei suspension, 100µl of the suspension (120,000 nuclei) was aliquoted to be used per CUT&Tag reaction.
Concavalin A (ConA) beads (EpiCypher, 21-1401) were transferred to a 1.5ml Eppendorf tube on a magnetic stand and washed twice with cold bead activation buffer (20 mM HEPES pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). Beads and buffer were added at 11µl and 100µl per sample, respectively, and after washing, the beads were resuspended in a final volume of 11μl of buffer per sample. 10µl of ConA bead slurry was aliquoted into each sample tube of an 8-strip tube containing 100µl nuclei per tube for batch processing. The ConA bead and nuclei mixture was vortexed gently to mix and incubated at RT for 10 minutes. The tubes were placed on a magnetic stand and the supernatant removed. Each nuclei sample was resuspended in 50µl of cold Antibody150 buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x Roche cOmpleteTM, Mini, EDTA-free Protease Inhibitor, 0.01% digitonin (Sigma-Aldrich, D141-100MG), 2mM EDTA) containing primary antibody (anti-H3K27me3 (Active Motif; 39157; dilution 1:50), anti-H3K4me3 (Active Motif; 39160; dilution 1:50), anti-IgG negative control antibody (EpiCypher; 13-0042; dilution 1:50). Samples were then gently mixed and incubated overnight at 4°C on an orbital shaker. The next day, the tubes were placed on a magnet and the supernatant discarded. Each sample was resuspended in 50µl Digitonin150 buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x Roche cOmpleteTM, Mini, EDTA-free Protease Inhibitor, 0.01% digitonin) containing 0.5μg of secondary antibody (anti-rabbit Epicypher; 13-0047) for 1 hr at RT on a nutator. After the incubation, the samples were placed on a magnet and washed twice with Digitonin150 buffer. The samples were then resuspended in 50µl Digitonin300 buffer (20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 1x Roche cOmpleteTM, Mini, EDTA-free Protease Inhibitor, 0.01% digitonin), and 1.25μl of CUTANA pAG-TN5 (EpiCypher, 15-1017) was added. Samples were then gently mixed and incubated for 1hr at RT on a nutator. After the incubation, the samples were placed on a magnet and washed twice with Digitonin300 buffer (20mM HEPES, pH 7.5, 300mM NaCl, 0.5mM Spermidine, 1x Roche cOmpleteTM, Mini, EDTA-free Protease Inhibitor, 0.01% digitonin). The samples were then resuspended in 50 µl of Tagmentation buffer (Digitonin 300 Buffer, 10 mM MgCl2) and incubated for 1hr at 37°C in a thermocycler. Then the sample tubes were placed on a magnet and the supernatant discarded, the samples were then resuspended in 50µl TAPS buffer (10 mM TAPS, pH 8.5, 0.2 mM EDTA). The tubes were returned to the magnet and the supernatant removed, followed by addition of 5µl SDS release buffer (0.5M HEPES-NaOH pH 8.5, 10% SDS). The reaction mixture was vortexed on maximum speed for 10s and briefly centrifuged. The samples were then incubated on the thermocycler for 1hr at 58℃. The SDS was neutralised by the addition of 15µl SDS quench buffer (0.67% Triton-X 100), vortexed at maximum speed for 10s, and centrifuged briefly. The libraries were amplified using KAPA HiFi HotStart ReadyMix (Roche Diagnostics Ltd, KK2602). 25ul KAPA HiFi HotStart ReadyMix per CUT&Tag reaction (mastermix only) was incubated at 95℃ for 3 min and cooled to 22℃ in a thermocycler. 1μl of each of barcoded i5 and i7 primers (5μM stock) and 25µl of the previously heated mastermix was added to the DNA. PCR was conducted using the following programme: extension step at 72°C for 5 min, denaturation at 98°C for 45 s, 13-15 cycles (denaturation at 98°C for 10s and short extension at 60°C for 10s), and final extension at 72°C for 1 min. Amplified libraries were cleaned twice using 1X volume of AMPure XP Beads (Beckman Coulter; A63881) and resuspended in 15μl of 0.1X TE buffer. Size distribution and yield quantification of the CUT&Tag libraries were tested using an Agilent 2100 Bioanalyzer high sensitivity DNA chip (Agilent 5067–4626). Libraries were then multiplexed and sequenced (paired-end 150 bp) on a NovaSeq X Plus Series PE150 (Illumina) to a depth of a minimum 10 million reads per replicate.

treatment_protocol: no treatment


title: Female, DCT(early), replicate 5


title: neurons,WT,week6,female,rep3

description: Library name: 7761


title: TFE4 KO NeuN

description: Library name: SR008099_TFE4_KO_NeuN_10


title: Sojd3-untreated_H3K4me3_REP1

description:
Library name: Sojd_H3K4me3_REP1
cut_and_tag_H3K4me3_peaks.tsv.gz


title: Female, DCT(early), replicate 4


title: mSIorg_96h

description: Library name: mSIorg_96h

data_processing:
Raw sequencing reads were processed using the Alevin module of Salmon (v1.2.0) (Patro et al., 2017; Srivastava et al., 2019). Reads were quantified in paired-end mode (-l ISR) using the 10x Genomics Chromium v3 protocol specification (--chromiumV3). Multiple sequencing lanes per sample were combined at the FASTQ level prior to quantification. Quantification was performed against a spliced–unspliced “gentrome” reference derived from GENCODE mouse release M24 (GRCm38), enabling simultaneous estimation of spliced and intronic counts for RNA velocity–compatible analyses. Gene-level quantification was obtained using a transcript-to-gene mapping file (--tgMap), and feature-level output (spliced/unspliced) was generated using the --dumpFeatures option. Cell barcode whitelisting and UMI deduplication were handled internally by Alevin. Quantification uncertainty was estimated using 50 bootstrap replicates (--numCellBootstraps 50). All runs were executed using 32 threads per sample. Quantification outputs were imported into R using tximeta (v1.12.4) (Love et al., 2020), with inferential replicates discarded (dropInfReps = TRUE). Spliced and unspliced counts were separated using splitSE, and spliced counts were used as the primary assay for downstream analyses. Cell barcodes were prefixed with sample identifiers, sample metadata were appended, and samples were merged into a single SingleCellExperiment object (v1.16.0) containing 54,446 features across 43,684 cells.
Gene annotations were added from GENCODE release M24, including gene biotype, gene symbol, Entrez ID and chromosome. Mitochondrial genes were annotated based on chromosome “chrM” and MitoCarta3.0, and ribosomal protein genes were annotated using GO:0003735 with org.Mm.eg.db (v3.14.0) (Rath et al., 2021). Genes were retained if annotated as protein-coding, immunoglobulin, T cell receptor, mitochondrial rRNA or mitochondrial tRNA genes; all other gene biotypes were removed before downstream analysis. Per-cell and per-feature quality control metrics were calculated using scater (v1.22.0) (McCarthy et al., 2017). Cells were retained if they contained >1,200 detected genes and <22% mitochondrial counts. Library-size normalization was performed using scran (v1.22.1) (Lun et al., 2016). Cells were first grouped into coarse clusters using quickCluster, and deconvolution size factors were estimated with computeSumFactors using min.mean = 0.5. Cells with size factors <0.1 were excluded. Log-normalized expression values were computed with logNormCounts and used for downstream analyses.
To preserve transcriptional heterogeneity and ensure representation of rare cell populations, cells were subsampled using geometric sketching as previously applied in large-scale single-cell analyses (Oost, Kahnwald et al., bioRxiv, 2023). In brief, we used sketchR (v0.1.4), an R interface to the geometric sketching strategy described by Hie et al. (2019). PCA was first computed on log-normalized expression values using 100 components, and representative cells were selected with geosketch using a target sketch size corresponding to approximately 10% of cells, with a minimum of 2,000 cells and capped at the total number of cells. Highly variable genes were identified using modelGeneVar in scran with an FDR threshold of 0.05. Variable genes were identified globally and within each experimental condition, and the union of condition-wise variable genes was used for dimensionality reduction. PCA was computed using 30 components. t-SNE embeddings were generated with snifter/FIt-SNE, and UMAP embeddings were generated using uwot (Linderman et al., 2019; McInnes et al., 2018).
Cell type identities were assigned using marker gene set scoring, graph-based clustering and manual annotation. Curated intestinal marker gene sets were scored separately within culture conditions using swissknife::normGenesetExpression, with non-variable genes used as the background set. Sketched cells were converted to a Seurat object (v4.1.0), and a shared nearest-neighbor graph was constructed in the sketch PCA space using FindNeighbors with k = 20 and 30 principal components (Hao et al., 2021). Cells were clustered using FindClusters across resolutions 0.4–4.0, and resolution 3.5 was used for annotation. Clusters were annotated based on marker gene expression, marker gene set scores and timepoint distribution. One mixed enterocyte cluster was split by timepoint, with 24–48 hour cells annotated as enterocyte reprogramming cells and 60–108 hour cells annotated as mature enterocytes. Cluster labels from sketched cells were transferred to the full dataset by 1-nearest-neighbor classification in sketch PCA space. Final annotations were collapsed into intestinal epithelial cell states, including reprogramming, regenerative, stem/progenitor, secretory and enterocyte-lineage populations.
Assembly: GRCm38/mm10
Supplementary files format and content: barcodes.tsv.gz: gzipped, tab-separated text file with column annotation of the (sparse) alignment count table (genes versus cells). The columns correspond to cell_id (cell identifier), culture medium (intesticult/enr), timepoint (0h, 24h, 36h, 48h, 60h, 72h, 84h, 108h), cell_type (annotated celltype label), TSNE1 (first coordinate for TSNE embedding), TSNE2 (second coordinate for TSNE embedding), UMAP1 (first coordinate for UMAP embedding), UMAP2 (second coordinate for UMAP embedding).
Supplementary files format and content: features.tsv.gz: gzipped, tab-separated text file with row annotation of the (sparse) alignment count table (genes versus cells). The columns correspond to gene symbol, gene_id (ensembl_id), is_variable (logical specifying variable genes used).
Supplementary files format and content: matrix.mtx.gz: gzipped, tab-separated text file with the number of mRNA counts per gene (row) and cell (column), as a sparse matrix in MatrixMarket format.
Supplementary files format and content: matrix_logcounts.mtx.gz: gzipped, tab-separated text file with the log-transformed and normalized expression per gene (row) and cell (column), as a sparse matrix in MatrixMarket format.

growth_protocol: Small intestinal organoids were derived from the duodenum of a 10-week-old male C57BL/6 wild-type mouse as described in Sato et al, Nature 2009. For amplification and maintenance, organoids were cultured in IntestiCult Organoid Growth Medium (STEMCELL Technologies) with 100 μg/ml Penicillin-Streptomycin. Organoid timecourses were started by performing a single-cell dissociation of the maintenance cultures. Specifically, organoids were collected 6 days after passaging and digested with TripLE (Invitrogen) with 10 μM Y-27632 (ROCK inhibitor; STEMCELL Technologies) for 20 min at 37 °C. Dissociated cells were passed through a cell strainer with a pore size of 30 µm and stained with DRAQ7 dye (Invitrogen). Single cells were isolated by fluorescence-activated cell sorting (FACS; SONY MA900 Cell Sorter) by gating for live (DRAQ7-negative) single cells. Cells were seeded into Matrigel (Corining) droplets (1:1 ratio Matrigel:ENR medium) at a density of 600 cell/ul, marking the start of the organoid timecourse. ENR medium consisted of Advanced DMEM/F-12 with 15 mM HEPES (STEM CELL Technologies) supplemented with 100 μg/ml Penicillin and Streptomycin, 1x Glutamax (Thermo Fisher Scientific), 1x B27 (Thermo Fisher Scientific), 1x N2 (Thermo Fisher Scientific), 1 mM N-acetylcysteine (Sigma), 500 ng/ml R-Spondin (kind gift from Novartis), 100 ng/ml Noggin (PeproTech) and 100 ng/ml murine EGF (R&D Systems). For the first 24 hr of the timecourse, ENR was supplemented with 25% Wnt3a-conditioned medium (Wnt3a-CM), 10 μM Y-27632 (ROCK inhibitor, STEMCELL Technologies) and 3 µM of CHIR99021 (STEMCELL Technologies). From 24 to 72 hr, ENR was supplemented with 25% Wnt3a-CM and 10 μM Y-27632 (ROCK inhibitor, STEMCELL Technologies). From 72 to 108 hr, only ENR was added to the organoids. Wnt3a-CM was produced in-house by Wnt3a L-cells (kind gift from Novartis).

extract_protocol:
Organoids were collected at baseline (0h) and at 12-hour intervals throughout the regeneration timecourse (24-108h) for single cell RNA sequencing. For each timepoint, organoids were collected and digested to a single-cell suspension and FACS sorted as described above. For single-cell RNA sequencing library preparation, 13k cells were sorted per collection vial per timepoint.
Single-cell libraries were prepared using the 10x Genomics Chromium Single Cell 3′ Reagent Kit v2 according to the manufacturer’s protocol. Gel bead-in-emulsion (GEM) generation, reverse transcription, cDNA amplification, and library construction were performed following standard procedures. Libraries were sequenced on an Illumina NextSeq 500 platform using a 75-cycle kit with paired-end configuration (Read 1: 26 bp; Read 2: 56 bp; single index: 8 bp). Base calling was performed using Illumina RTA (v2.4.11), and FASTQ files were generated using bcl2fastq2 (v2.17).

value: mouse small intestinal organoids

value: intestinal epithelial cells

value: wildtype


title: Sojd3-untreated_H3K27me3_REP2

description:
Library name: Sojd_H3K27me3_REP2
cut_and_tag_H3K27me3_peaks.tsv.gz

value: human pluripotent stem cells


title: TFE4 KO DN

description: Library name: SR008099_TFE4_KO_DN_12


title: propionic acid, biol rep2

value: skin

value: wild type

value: propionic acid


title: Micro-C of Fbn2_lowCTCF cell line, replicate 1

description:
Library name: Fbn2_lowCTCF_rep1
Cell line containing TetO and Anchor3 arrays for fluorescent labeling of the Fbn2 loop on chr18 with CTCF tagged with mAID (leaky depletion)

value: Embryonic stem cells


title: neurons,WT,week6,female,rep1

description: Library name: 4323

value: Cortex

value: female


title: Sojd3-untreated_H3K27me3_REP1

description:
Library name: Sojd_H3K27me3_REP1
cut_and_tag_H3K27me3_peaks.tsv.gz


title: FE4 WT PU1

description: Library name: SR008099_FE4_WT_PU1_2

value: FE4 WT


title: Female, DCT(early), replicate 2

value: Kidney

value: distal convoluted tubule cell

value: C57BL/6-Tg (Pvalb-tdTomato)15Gfng/J


title: C57BL/6J, macroH2A1.2 (ChIP), rep3

description: Library name: Sample 7

value: Hippocampus

value: WT


title: neurons,cK2c,week6,male,rep4

description: Library name: 7762

value: In vivo

value: Excitatory neurons

value: conditional kmt2c knockout

value: male


title: EA.hy926 cells, PFOA Control, 12 weeks, biological replicate 1

city: Novi Sad

first: Katarina

middle: Dragiša

last: Borković

address: Trg Dositeja Obradovića 3

department: Department for biology and ecology

country: Serbia

institute: University of Novi Sad, Faculty of Sciences

description: Library name: PA_12w_C_1

data_processing:
Raw sequencing reads were subjected to quality control filtering. Reads containing more than 5% ambiguous bases (N), adapter contamination, or more than 20% bases with quality scores below Q15 were removed to generate clean reads.
Sequencing was performed on the DNBSEQ™ platform using paired-end 150 bp reads (PE150).
HISAT was used to align the clean reads to the reference genome (species: Homo sapiens; source: NCBI; reference genome version: GRCh38.p14, https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001405.40/, accessed 18 October 2024), while Bowtie2 was used to align the clean reads to reference genes. The average alignment ratio of the sample comparison genome was 98.74%, whereas the average alignment of the gene set was 85.92%; a total of 18048 genes were detected. The analysis of differentially expressed genes (DEGs) was performed by BGI using the DESeq2 method.
Gene expression quantification and differential expression analysis were performed using DESeq2. Differentially expressed genes were identified using thresholds of FDR < 0.05 and |log2 fold change| ≥ 1.
The reference genome used for alignment was Homo sapiens GRCh38.p14 (NCBI).
Assembly: GRCh38.p14
Supplementary files format and content: CSV files contain normalized read count (NRC) values for all detected genes across biological replicates. Separate files correspond to the 48 h, 6-week, and 12-week exposure experiments.
Supplementary files format and content: Processed data files are CSV tables containing normalized read count (NRC) values for all detected genes across biological replicates from each experimental time point (48 h, 6 weeks, and 12 weeks). Columns correspond to GEO library names and rows correspond to annotated human genes.

growth_protocol: The human macrovascular endothelial cell line EA.hy926 was maintained as a monolayer culture at 37 °C in a humidified atmosphere containing 5% CO2. The complete culture medium consisted of Dulbecco's Modified Eagle's Medium supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin solution, 1.5 g/L NaHCO3, 0.11 g/L sodium pyruvate, 10 mM HEPES buffer, and 4% HAT supplement (5 mM sodium hypoxanthine, 20 µM aminopterin, 0.8 mM thymidine). The medium was refreshed every three to four days, with subculturing performed when the cells reached ~90% confluency. Cells were washed twice with phosphate-buffered saline (PBS) and then trypsinized using 0.25% trypsin-ethylenediaminetetraacetic acid solution for 4 min. Following this, complete culture medium was added, and the cells were centrifuged at 400 × g for 5 min. The resulting suspension was mixed with Trypan blue solution and counted using an automated cell counter. Following counting, cells were seeded in appropriate flasks or assay plates.

extract_protocol:
EA.hy926 cells were exposed either to vehicle control (0.05% DMSO) or to PFOA under short-term (1, 10 and 100 µM) and long-term (1, 10 and 100 nM) exposure conditions. Cells were harvested and lysed directly in TRIzol™ Reagent (Invitrogen). Following treatment, cells were washed with PBS and lysed directly in TRIzol™ Reagent (Invitrogen). Total RNA was isolated according to the TRIzol™ manufacturer's protocol using chloroform extraction and isopropanol precipitation. RNA pellets were washed with 75% ethanol, air-dried, and resuspended in DEPC-treated water. RNA concentration and purity were determined using a BioSpec-Nano spectrophotometer (Shimadzu). RNA quality was further assessed by BGI Europe using an Agilent 4150 Bioanalyzer. All samples exhibited high RNA integrity (RIN > 9) and were considered suitable for RNA sequencing.
High-quality total RNA samples were submitted to BGI Europe (Warsaw, Poland) for library preparation and sequencing. RNA quantity and integrity were evaluated using an Agilent 4150 Bioanalyzer prior to library construction. Sequencing libraries were prepared according to the standard BGI mRNA-seq workflow and sequenced on the DNBSEQ™ platform using paired-end 150 bp reads (PE150).

treatment_protocol: For short-term exposure, EA.hy926 cells were plated in 35-mm dishes (0.6 × 10^6 cells per dish; Nunc™, Thermo Scientific) and exposed to either vehicle (0.05% DMSO; 0 µM PFOA – control group) or three micromolar concentrations of PFOA (1 µM, 10 µM, and 100 µM PFOA – treatment groups) the following day. After 48 h of exposure, the cells were rinsed with PBS, collected in 0.5 mL of TRIzol, and the RNA was extracted afterward. In long-term exposure experiments, EA.hy926 cells originating from each flask after 6 and 12 weeks of continuous exposure to either vehicle (0.05% DMSO; 0 nM PFOA – control group) or three nanomolar concentrations of PFOA (1 nM, 10 nM, and 100 nM PFOA – treatment groups) were collected directly during subculturing on Fridays into clean RNase-, DNase-, and pyrogen-free 1.5 mL microcentrifuge tubes (~1 × 10^6 cells per tube). Cells were centrifuged at 400 × g for 5 min, rinsed with PBS, centrifuged again, and stored in 0.5 mL of TRIzol at –80 °C for subsequent RNA isolation.

value: endothelial cells

value: Control

tag: time

value: 12 weeks


title: Sojd3_CHR_H3K4me3_REP2

description:
Library name: Sojd_CR_H3K4me3_REP2
cut_and_tag_H3K4me3_peaks.tsv.gz

value: human pluripotent stem cells


title: mSIorg_48h

description: Library name: mSIorg_48h

value: mouse small intestinal organoids

value: intestinal epithelial cells

value: wildtype


title: FE4 WT NeuN

description: Library name: SR008099_FE4_WT_NeuN_1

value: hippocampus

value: FE4 WT


title: Female, DCT(early), replicate 1

value: Kidney

value: distal convoluted tubule cell


title: TFE4 KO PU1

description: Library name: SR008099_TFE4_KO_PU1_11

value: TFE4 Irf8d32


title: neurons,cK2c,week6,male,rep3

description: Library name: 7693

value: Cortex


title: Sojd3_CHR_H3K4me3_REP1

description:
Library name: Sojd_CR_H3K4me3_REP1
cut_and_tag_H3K4me3_peaks.tsv.gz


title: Female, DCT(early), furosemide, 96h, replicate 4

growth_protocol: Mice were fed with control diet before furosemide administration.

treatment_protocol: For furosemide treatment, mice were fed with furosemide-containing diet for 12h , 24h, 48h, or 96h. Control diet-fed mice were prepared at each time point.

value: C57BL/6-Tg (Pvalb-tdTomato)15Gfng/J

value: control diet containing furosemide


title: FE4 WT DN

description: Library name: SR008099_FE4_WT_DN_3


title: Sojd3_CHR_H3K27me3_REP2

description:
Library name: Sojd_CR_H3K27me3_REP2
cut_and_tag_H3K27me3_peaks.tsv.gz


title: neurons,cK2c,week6,male,rep2

description: Library name: 7617

value: In vivo

value: Excitatory neurons

value: conditional kmt2c knockout


title: C57BL/6J, macroH2A1.1 (ChIP), rep2

description: Library name: Sample 2

value: Hippocampus

value: WT


title: FE4 KO PU1

description: Library name: SR008099_FE4_KO_PU1_5

value: FE4 Irf8d32


title: neurons,WT,week18,female,rep1 (500_H3K4me3)

description: Library name: 500_H3K4me3

value: wild-type


title: neurons,WT,week18,female,rep2 (504_H3K27ac)

description: Library name: 504_H3K27ac


title: Female, DCT(early), furosemide, 96h, replicate 3


title: neurons,cK2c,week6,male,rep1

description: Library name: 7183

value: male


title: Sojd3_CHR_H3K27me3_REP1

description:
Library name: Sojd_CR_H3K27me3_REP1
cut_and_tag_H3K27me3_peaks.tsv.gz

value: human pluripotent stem cells


title: Female, DCT(early), furosemide, 96h, replicate 2


title: FE4 KO NeuN

description: Library name: SR008099_FE4_KO_NeuN_4

value: hippocampus


title: Hehd1-untreated_H3K4me3_REP2

description:
Library name: Hehd_H3K4me3_REP2
cut_and_tag_H3K4me3_peaks.tsv.gz


title: FE4 KO DN

description: Library name: SR008099_FE4_KO_DN_6


title: neurons,WT,week6,male,rep3

description: Library name: 7692


title: neurons,WT,week6,male,rep2

description: Library name: 7689


title: Female, DCT(early), furosemide, 96h, replicate 1


title: Uterus, Pregnancy day 5 Lcn2f/f control mouse No. 3, scRNA-seq

city: Jinan

first: Wenhao

last: Yu

address: Wenhuaxi road

institute: Shandong University

description:
Library name: NC-D5-3
10× Genomics

data_processing:
The Cell Ranger pipeline (10× genomics) was used to align and analyze the sequencing data.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Uterus

growth_protocol: By mating Lcn2f/f females with Irescre males , Lcn2f/f Irescre e mice were produced.  Lcn2f/f Irescre denotes the knockout of Lcn2 in both endometrial epithelial cells and stromal cells.

extract_protocol:
Uterine samples were collected from Plug-positive mice at days 5. After inhalation anesthesia in mice, Chicago Blue (1% Chicago Blue in Saline, 100 µL/mouse) was intravenously injected into the inner corner of the eye to illustrate the implantation sites on days 5 of pregnancy. Five minutes after being injected with Chicago Blue, the mice were bled and euthanized to separate the uterus to be sequenced.
The Illumina × 10 platform was used to sequence the generated library

value: Uterus


title: Female, DCT(early), furosemide, 48h, replicate 4

value: Kidney


title: neurons,WT,week6,male,rep1

description: Library name: 7613


title: Hehd1-untreated_H3K27me3_REP2

description:
Library name: Hehd_H3K27me3_REP2
cut_and_tag_H3K27me3_peaks.tsv.gz


title: neurons,WT,week6,female,rep2

description: Library name: 7759

value: female


title: Uterus, Pregnancy day 5 Lcn2f/f control mouse No. 2, scRNA-seq

description:
Library name: NC-D5-2
10× Genomics


title: Female, DCT(early), furosemide, 48h, replicate 3

value: distal convoluted tubule cell


title: neurons,cK2c,week18,female,rep6

description: Library name: 9776

value: Cortex


title: Uterus, Pregnancy day 5 Lcn2f/f control mouse No. 1, scRNA-seq

description:
Library name: NC-D5-1
10× Genomics


title: Female, DCT(early), furosemide, 48h, replicate 2

value: C57BL/6-Tg (Pvalb-tdTomato)15Gfng/J


title: neurons,cK2c,week18,female,rep5

description: Library name: 501


title: Hehd1-untreated_H3K27me3_REP1

description:
Library name: Hehd_H3K27me3_REP1
cut_and_tag_H3K27me3_peaks.tsv.gz


title: Hehd1_CHR_H3K4me3_REP2

description:
Library name: Hehd_CR_H3K4me3_REP2
cut_and_tag_H3K4me3_peaks.tsv.gz


title: Female, DCT(early), furosemide, 48h, replicate 1

value: control diet containing furosemide


title: Uterus, Pregnancy day 5 Lcn2f/fIrescre conditional knockout mouse No. 4, scRNA-seq

description:
Library name: IR-D5-4
10× Genomics


title: Hehd1_CHR_H3K4me3_REP1

description:
Library name: Hehd_CR_H3K4me3_REP1
cut_and_tag_H3K4me3_peaks.tsv.gz


title: Uterus, Pregnancy day 5 Lcn2f/fIrescre conditional knockout mouse No. 3, scRNA-seq

description:
Library name: IR-D5-3
10× Genomics


title: Female, DCT(early), furosemide, 24h, replicate 4


title: Hehd1_CHR_H3K27me3_REP2

description:
Library name: Hehd_CR_H3K27me3_REP2
cut_and_tag_H3K27me3_peaks.tsv.gz


title: neurons,cK2c,week18,female,rep3

description: Library name: 9282

value: In vivo


title: Uterus, Pregnancy day 5 Lcn2f/fIrescre conditional knockout mouse No. 2, scRNA-seq

description:
Library name: IR-D5-2
10× Genomics


title: Female, DCT(early), furosemide, 24h, replicate 3


title: neurons,cK2c,week18,female,rep2

description: Library name: 9281

value: Excitatory neurons


title: Hehd1_CHR_H3K27me3_REP1

description:
Library name: Hehd_CR_H3K27me3_REP1
cut_and_tag_H3K27me3_peaks.tsv.gz


title: Uterus, Pregnancy day 5 Lcn2f/fIrescre conditional knockout mouse No. 1, scRNA-seq

description:
Library name: IR-D5-1
10× Genomics


title: Female, DCT(early), furosemide, 24h, replicate 2


title: H9-untreated_H3K4me3_REP2

description:
Library name: H9_H3K4me3_REP2
cut_and_tag_H3K4me3_peaks.tsv.gz


title: BSCI_IL1A_3_MouseMyo_ATACSeq

city: Toronto

first: Jennifer

last: Mitchell

state: Ontario

address: 25 Harbord Street

department: Cell and Systems Biology

institute: University of Toronto

description: Library name: BSCI_IL1A_3_MouseMyometrium_ATACSeq

data_processing:
Adapters were removed, reads were trimmed and aligned using the encode atac-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline)
bedgraphs were generated from aligned files using bamCoverage (part of Deeptools)
Assembly: GRCm38/mm10
Supplementary files format and content: bedgraph

source_name: Myometrium

growth_protocol: Female C57BL/6 mice were naturally bred, with gestational day 1 established as the morning of vaginal plug detection. Mice were maintained in a pathogen-free, humidity-controlled, 12h light, 12h dark cycle facility with free access to food and water.

extract_protocol:
Omni ATAC-seq protocol (Corces, et al. 2007)
Omni ATAC-seq protocol (Corces, et al. 2007)

treatment_protocol: Pregnant C57BL/6 mice were randomly divided into 4 groups: Vehicle, IL1A, BSCI, and IL1A+BSCI. On gestational day (GD)16.5, All mice were anesthetized and, using guided ultrasound, the amniotic sac injected with either saline (vehicle, 20µl) or IL-1α (400ng in 20 µl). These mice also received tail-vein injections of the vehicle (saline) or BSCI (10 mg/kg/day) at GD15.5 and 16.5 to form the four treatment groups. Myometrial tissues were collected on GD 17.5, 24 hours following IL-1α administration.

value: Myometrium


title: Female, DCT(early), furosemide, 24h, replicate 1


title: neurons,WT,week18,female,rep6

description: Library name: 505


title: H9-untreated_H3K4me3_REP1

description:
Library name: H9_H3K4me3_REP1
cut_and_tag_H3K4me3_peaks.tsv.gz


title: Female, DCT(early), furosemide, 12h, replicate 4


title: neurons,WT,week18,female,rep5

description: Library name: 504


title: H9-untreated_H3K27me3_REP2

description:
Library name: H9_H3K27me3_REP2
cut_and_tag_H3K27me3_peaks.tsv.gz


title: BSCI_IL1A_1_MouseMyo_ATACSeq

description: Library name: BSCI_IL1A_1_MouseMyometrium_ATACSeq


title: neurons,WT,week18,female,rep4

description: Library name: 500


title: Female, DCT(early), furosemide, 12h, replicate 3


title: H9-untreated_H3K27me3_REP1

description:
Library name: H9_H3K27me3_REP1
cut_and_tag_H3K27me3_peaks.tsv.gz


title: BSCI_3_MouseMyo_ATACSeq

description: Library name: BSCI_3_MouseMyometrium_ATACSeq


title: neurons,WT,week18,female,rep3

description: Library name: 9777


title: Fiaj1-untreated_H3K4me3_REP2

description:
Library name: Fiaj_H3K4me3_REP2
cut_and_tag_H3K4me3_peaks.tsv.gz


title: BSCI_2_MouseMyo_ATACSeq

description: Library name: BSCI_2_MouseMyometrium_ATACSeq


title: Hehd1-untreated_H3K4me3_REP1

description:
Library name: Hehd_H3K4me3_REP1
cut_and_tag_H3K4me3_peaks.tsv.gz


title: neurons,WT,week18,female,rep2

description: Library name: 9770


title: BSCI_1_MouseMyo_ATACSeq

description: Library name: BSCI_1_MouseMyometrium_ATACSeq


title: Female, DCT(early), furosemide, 12h, replicate 1


title: neurons,WT,week18,female,rep1

description: Library name: 9769


title: Fiaj1-untreated_H3K27me3_REP2

description:
Library name: Fiaj_H3K27me3_REP2
cut_and_tag_H3K27me3_peaks.tsv.gz


title: IL1A_3_MouseMyo_ATACSeq

description: Library name: IL1A_3_MouseMyometrium_ATACSeq

value: IL-1α (400ng in 20 µl saline, GD 16.5)


title: Male, DCT(early), furosemide, 96h, replicate 3


title: Fiaj1-untreated_H3K27me3_REP1

description:
Library name: Fiaj_H3K27me3_REP1
cut_and_tag_H3K27me3_peaks.tsv.gz


title: IL1A_2_MouseMyo_ATACSeq

description: Library name: IL1A_2_MouseMyometrium_ATACSeq


title: neurons,cK2c,week18,female,rep4

description: Library name: 175

value: conditional kmt2c knockout


title: Male, DCT(early), furosemide, 96h, replicate 2


title: LPA4-KO, SNI, rep2

city: izunokuni mifuku

first: takahisa

last: shimoda

state: Shizuoka

country: Japan

institute: Asahi Kasei Pharma

description: Library name: sample14

data_processing:
Sequencing was conducted on the Illumina NovaSeq platform in paired-end mode (150 bp × 2) (performed by Takara Bio, Shiga, Japan).
Raw sequencing reads were subjected to quality control using fastp (v0.22.0).
High-quality reads were aligned to the rat reference genome (mRatBN7.2) using STAR aligner (v2.7.9a).
Gene-level counts and transcripts per million (TPM) were calculated using RSEM (v1.3.1).
Assembly: mRatBN7.2
Supplementary files format and content: CSV (Comma-Separated Values) file includes raw counts for each sample

organism: Rattus norvegicus

source_name: spinal dorsal horn

extract_protocol:
Total RNA was purified using the Monarch Total RNA Miniprep Kit (Catalog # NEB #T2110, New England Biolabs, Ipswich, MA, USA) .
Total RNA was processed for sequencing using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA, USA).

value: spinal dorsal horn


title: Fiaj1-CHR_H3K4me3_REP2

description:
Library name: Fiaj-CR_H3K4me3_REP2
cut_and_tag_H3K4me3_peaks.tsv.gz


title: Male, DCT(early), furosemide, 96h, replicate 1


title: neurons,cK2c,week18,male,rep2

description: Library name: 497


title: Vehicle_3_MouseMyo_ATACSeq

description: Library name: Vehicle_3_MouseMyometrium_ATACSeq

value: Vehicle (20 ul saline)


title: Male, DCT(early), furosemide, 48h, replicate 4


title: Fiaj1-CHR_H3K27me3_REP2

description:
Library name: Fiaj-CR_H3K27me3_REP2
cut_and_tag_H3K27me3_peaks.tsv.gz


title: Vehicle_2_MouseMyo_ATACSeq

description: Library name: Vehicle_2_MouseMyometrium_ATACSeq


title: neurons,cK2c,week18,male,rep1

description: Library name: 174

value: male


title: Male, DCT(early), furosemide, 48h, replicate 3


title: neurons,WT,week18,male,rep4

description: Library name: 9278

value: wild-type


title: Fiaj1-CHR_H3K27me3_REP1

description:
Library name: Fiaj-CR_H3K27me3_REP1
cut_and_tag_H3K27me3_peaks.tsv.gz

value: human pluripotent stem cells


title: Male, DCT(early), furosemide, 48h, replicate 2


title: neurons,WT,week18,male,rep3

description: Library name: 9771


title: Burb1-untreated_H3K4me3_REP2

description:
Library name: Burb_H3K4me3_REP2
cut_and_tag_H3K4me3_peaks.tsv.gz


title: SAMPLES32

city: Yinchuan

first: Wenyi

last: Ren

address: 489 Helanshan West Road, Xixia District, Yinchuan City, Ningxia

department: College of Animal Science and Technology

institute: Ningxia University

description:
Library name: SAMPLES32
W_SA_4

data_processing:
Transcriptome sequencing generated 231.41 Gb clean data across the 32 samples, with at least 5.95 Gb clean data per sample and Q30 values above 96%. Raw reads were quality-filtered using fastp. Adapter sequences, reads without inserts, low-quality 3' bases, reads containing >10% ambiguous bases, and reads shorter than 20 bp after trimming were removed. Clean reads were aligned to the Ovis aries reference genome ARS-UI_Ramb_v2.0, obtained from Ensembl (https://mart.ensembl.org/Ovis_aries_rambouillet/Info/Index), using HISAT2. Mapping rates ranged from 80.08% to 97.88%. Gene and transcript abundance was quantified using RSEM and expressed as transcripts per million.
Assembly: Reference gene source: Ovis_aries; Reference genome version: ARS-UI_Ramb_v2.0; Reference genome source: https://mart.ensembl.org/Ovis_aries_rambouillet/Info/Index
Supplementary files format and content: Comma-Separated Values file

organism: Ovis aries

source_name: Tail fat

extract_protocol:
Hypothalamus, pituitary, liver, and tail adipose tissue samples from four sheep per treatment were used for transcriptome sequencing, yielding 32 RNA-seq libraries in total. Total RNA was extracted using TRIzol reagent. Briefly, tissue samples were ground in liquid nitrogen and lysed in pre-cooled TRIzol reagent. Chloroform was added, and samples were centrifuged at 13000 g for 15 min at 4°C. The aqueous phase was transferred to a new tube, mixed with an equal volume of pre-cooled isopropanol, and incubated at room temperature for 10 min. RNA pellets were collected by centrifugation, washed with 75% ethanol, air-dried for 3-5 min, and dissolved in sterile 0.1% DEPC-treated water.
RNA concentration and purity were assessed using NanoDrop 2000, and RNA integrity was evaluated by agarose gel electrophoresis and an Agilent bioanalyzer. Stranded mRNA libraries were constructed using the Illumina Stranded mRNA Prep, Ligation kit according to the manufacturer's protocol. Briefly, mRNA was enriched using oligo (dT) beads, fragmented, reverse-transcribed into cDNA, end-repaired, A-tailed, ligated to adapters, size-selected, PCR-amplified, and purified. Libraries were quantified using Qubit 4.0 and sequenced on an Illumina NovaSeq 6000 Plus platform.

value: Tail fat


title: Male, DCT(early), furosemide, 48h, replicate 1

value: Kidney


title: neurons,WT,week18,male,rep2

description: Library name: 9768


title: Burb1-untreated_H3K4me3_REP1

description:
Library name: Burb_H3K4me3_REP1
cut_and_tag_H3K4me3_peaks.tsv.gz


title: Male, DCT(early), furosemide, 24h, replicate 4


title: SAMPLES31

description:
Library name: SAMPLES31
W_SA_3


title: neurons,WT,week18,male,rep1

description: Library name: 1219


title: Male, DCT(early), furosemide, 24h, replicate 3


title: neurons,cK2c,week18,female,rep1 (175_H3K4me1)

description: Library name: 175_H3K4me1

data_processing:
CUT&Tag profiles for all four histone marks were trimmed using Cutadapt and aligned to the mm10 using bowtie2.  Reads were then centered and extended to represent the full DNA fragment, and were normalized using base-pair normalization with the Deeptools BamCoverage function.
Assembly: mm10
Supplementary files format and content: Bigwig tracks of histone modifications after BPM normalization
Library strategy: CUT&Tag

extract_protocol:
Cut&Tag was used to profile H3K4me3, H3K4me2, H3K4me1 and H3K27ac in eighteen-week-old cortical neurons. The CUT&Tag-direct V.3 protocol31,32 were performed with minor modifications. For each sample, 50,000 GFP⁺/NeuN⁺ excitatory neuron nuclei were bound to Concanavalin-A beads (3.5 µL bead slurry per reaction) and incubated with primary antibodies (1:50 dilution) overnight at 4°C: H3K4me1 (EpiCypher #13-0057), H3K4me2 (EpiCypher #13-0027), H3K4me3 (Active Motif #39159), or H3K27ac (Active Motif #39133). After washing, bead-bound nuclei were incubated with guinea pig anti-rabbit secondary antibody for 30 min at room temperature. Protein A–Tn5 transposome (pAG-Tn5; EpiCypher #15-1117) was added (2.5 µL per reaction) and incubated for 1 hr at room temperature, followed by tagmentation at 37°C for 1 hour.Tagmented chromatin was released by incubation with 0.1% SDS at 58°C for 1 hr and neutralized with 0.67% Triton-X100.
Libraries were amplified using NEBNext High-Fidelity 2× PCR Master Mix (non-hot-start) (NEBNext #M0541L) with unique dual indexes (Buenrostro-style i7/i5 indexing) for 11–12 cycles depending on mark abundance. PCR products were cleaned with 1.3× SPRI bead purification, eluted in 13.2 µL, and assessed by Qubit and Bioanalyzer.


title: N3

type: RNA

city: zunyi

first: Xiaohua

last: An

state: guizhou

address: No. 149, Dalian Road, Huichuan District

department: Department of Clinical Laboratory

institute: The Third Affiliated Hospital of Zunyi Medical University

description: Cancer tissue group, replicate biosample 3

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent  Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software （version10.7.1.1, Agilent Technologies）using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: The total RNA sample was quantified using the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed with the Agilent Microarray.

treatment_protocol: A total of 27 specimens were collected from patients who underwent radical hysterectomy between June 2021 and February 2022. From these 27 samples, cancer tissues and paired adjacent tissues from 3 cases clinically diagnosed with stage IB2 cervical squamous cell carcinoma were selected for Arraystar LncRNA expression profiling microarray sequencing (provided by Shupu (Shanghai) Biotechnology Co., Ltd.).

value: Uterus

tag: disease state

value: Cancer tissue


title: Burb1-untreated_H3K27me3_REP1

first: Steven

last: Wingett

institute: MRC Laboratory of Molecular Biology

description:
Library name: Burb_H3K27me3_REP1
cut_and_tag_H3K27me3_peaks.tsv.gz


title: SAMPLES29

description:
Library name: SAMPLES29
W_SA_1


title: Male, DCT(early), furosemide, 24h, replicate 2

value: distal convoluted tubule cell


title: neurons,cK2c,week18,female,rep1

first: Matthew

last: Edwards

institute: University of Pennsylvania School of Medicine

description: Library name: 8839

value: Cortex

value: female


title: N2

description: Cancer tissue group, replicate biosample 2


title: BSCI_IL1A_2_MouseMyo_ATACSeq

description: Library name: BSCI_IL1A_2_MouseMyometrium_ATACSeq


title: Burb1-CHR_H3K4me3_REP2

description:
Library name: Burb-CR_H3K4me3_REP2
cut_and_tag_H3K4me3_peaks.tsv.gz


title: SAMPLES28

description:
Library name: SAMPLES28
W_CON_4


title: Burb1-untreated_H3K27me3_REP2

description:
Library name: Burb_H3K27me3_REP2
cut_and_tag_H3K27me3_peaks.tsv.gz


title: SAMPLES30

description:
Library name: SAMPLES30
W_SA_2


title: Male, DCT(early), furosemide, 24h, replicate 1

value: C57BL/6-Tg (Pvalb-tdTomato)15Gfng/J

value: control diet containing furosemide


title: Burb1-CHR_H3K4me3_REP1

description:
Library name: Burb-CR_H3K4me3_REP1
cut_and_tag_H3K4me3_peaks.tsv.gz


title: SAMPLES27

description:
Library name: SAMPLES27
W_CON_3


title: Female, DCT(early), furosemide, 12h, replicate 2


title: N1

description: Cancer tissue group, replicate biosample 1


title: Male, DCT(early), furosemide, 12h, replicate 4


title: Hehd1_CHR_Rep1

description:
Library name: Hehd1_CHR_Rep1
cell_lines_salmon.merged.gene_tpm.tsv.gz

data_processing:
Quality control, trimming and mapping of the FASTQ files was performed using the rnaseq pipeline (version 3.12.0), distributed by nf-core [doi: https://zenodo.org/records/7998767]. The pipeline was configured so that each constituent component was under version control and executed within a Singularity container [https://sylabs.io]. The following command was used to execute the pipeline:  nextflow run nf-core/rnaseq -r 3.12.0 --input samplesheet.csv --genome homo_sapiens.GRCh38.release_102 -config config.txt --extra_trimgalore_args '--nextseq 20' --outdir results --deseq2_vst -bg  These parameters generally adhere to the defaults set by the nf-core rnaseq pipeline. That pipeline release used STAR (version 2.7.9a) as the aligner, mapping reads to the human reference genome (GRCh38 / release 102). The specified read trimming parameter (--nextseq 20) were sequencing platform-specific, to account for the Illumina colour chemistry in which high quality calls for guanine nucleotides may actually reflect no signal on a flow cell. The pipeline was also passed a sample list detailing the forward and reverse FASTQ file pairings, along with the sample identities and how any technical and biological replicates should be grouped together. The nf-core rnaseq pipeline produces quantitated expression values for every gene for each sample, reporting raw counts and TPM values. These expression matrices were used in subsequent analyses.
FASTQ files could not be submitted for male HipSci cell lines owing to donor confidentiality regarding chromosome Y sequence information. Instead, BAM files generated by the nf-core atacseq pipeline (described previously) were submitted.  The BAM files were filtered by using samtools v1.21  to   contain only reads mapping to autosomes and chromosome X.
Assembly: GRCh38
Supplementary files format and content: The processed data files list the TPM expression values for each gene, segmented by biological replicate.  These data were produced by the nf-core rnaseq pipeline.

extract_protocol:
700,000 hiPSCs or hESCs were used for RNA extraction for each biological replicate. Cells were washed once with 1ml Dulbecco's Phosphate Buffered Saline (DPBS) and harvested using 500µl Accutase (StemCell Technologies, 07922) for 3 minutes at 37°C. Dissociated cells were then collected with 5ml of corresponding hPSC medium and centrifuged for 3 min at 400 RCF at RT. Supernatant was aspirated and the cells were resuspended in 1ml cold DPBS. RNA extraction from hiPSCs/hESCs was conducted using the Monarch Total RNA Miniprep Kit (NEB T2010S) according to the manufacturer’s protocol, with DNase I treatment used to enzymatically remove residual gDNA. RNA concentration was quantified using Nanodrop and the RNA Integrity Number (RIN) was assessed using the Agilent RNA 6000 Pico Kit (Agilent, 5067-1513) on Agilent 2100 Bioanalyzer (Agilent). A RIN value of >7 was deemed to be of good quality and used for downstream RNA-seq library processing. The isolated RNA was frozen and stored at -80°C until RNA-seq library preparation.
RNA-seq library preparation was performed on the isolated RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module, which isolated mRNA from total RNA (100ng input) by poly(A)-enrichment. RNA-seq libraries were subsequently prepared from the isolated mRNA using the NEBNext Ultra II Directional RNA Library Prep Kit from Illumina, the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L), and the NEBNext Multiplex Oligos from Illumina (Index Primers Set 1, 2, 3 and 4, NEB, E7335S, E7500S, E7710S, E7730S), following the manufacturer’s protocols. The final sequencing-ready libraries were amplified using the protocol’s PCR programme with 12 cycles. Size distribution and yield quantification of the RNA-seq libraries were assessed using an Agilent 2100 Bioanalyzer high sensitivity DNA chip (Agilent 5067–4626).


title: Fiaj1-untreated_H3K4me3_REP1

description:
Library name: Fiaj_H3K4me3_REP1
cut_and_tag_H3K4me3_peaks.tsv.gz


title: Burb1-CHR_H3K27me3_REP2

description:
Library name: Burb-CR_H3K27me3_REP2
cut_and_tag_H3K27me3_peaks.tsv.gz


title: C3

description: adjacent to cancer group, replicate biosample 3

value: adjacent to cancer


title: SAMPLES26

description:
Library name: SAMPLES26
W_CON_1


title: Male, DCT(early), furosemide, 96h, replicate 4


title: Male, DCT(early), furosemide, 12h, replicate 3


title: Burb1-CHR_H3K27me3_REP1

description:
Library name: Burb-CR_H3K27me3_REP1
cut_and_tag_H3K27me3_peaks.tsv.gz


title: SAMPLES25

description:
Library name: SAMPLES25
W_CON_2


title: C2

description: adjacent to cancer group, replicate biosample 2


title: Male, DCT(early), furosemide, 12h, replicate 2


title: neurons,cK2c,week18,male,rep4

description: Library name: 9407

value: In vivo

value: Excitatory neurons


title: SAMPLES24

description:
Library name: SAMPLES24
GZ_SA_4

source_name: Liver

value: Liver


title: Male, DCT(early), furosemide, 12h, replicate 1


title: fiaj1, untreated, replicate 2

description: Library name: EM_Fiaj_Rep2

data_processing:
The quality of the raw EM-seq FASTQ reads was assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were subsequently trimmed using Trim Galore v0.6.1.10 (with Cutadapt v4.6) and trimmed reads were reassessed using FastQC.
The adaptor trimmed reads were aligned and mapped to Homo sapiens GRCh38 with Bismark v0.24.2103  with modified trimming parameters optimised for EM-seq. The resulting BAM files were deduplicated and methylation calls were extracted using the Bismark deduplication and methylation extractor tools.
Quantitation of DNA methylation datasets was conducted using SeqMonk. The Bismark-generated methylation call coverage files (.cov files) were imported into SeqMonk. Read positions were generated with CpGs by filtering CpGs with a minimum threshold of 1 read count and grouped into windows containing 100 valid CpGs. The bisulphite methylation feature pipeline in SeqMonk was used to quantitate the CpG windows, with a minimum count of 1 read per CpG position and a minimum of 20 CpGs reads per window. This generated mean percentage methylation values for each window. Differential methylation analysis between incompetent and reset incompetent lines was performed using the EdgeR (for/rev) statistical filter in SeqMonk with a p-value<0.05 cut-off after Benjamimi and Hochberg correction with a minimum methylation difference threshold of 25%.
FASTQ files could not be submitted for male HipSci cell lines owing to donor confidentiality regarding chromosome Y sequence information. Instead, BAM files generated by the nf-core atacseq pipeline (described previously) were submitted.  The BAM files were filtered by using samtools v1.21  to   contain only reads mapping to autosomes and chromosome X.
Assembly: GRCh38
Supplementary files format and content: The processed DNA methylation dataset was generated from enzymatic methyl-sequencing (EM-seq) data following quality control, adapter trimming, alignment to the human reference genome (GRCh38), removal of duplicate reads, and extraction of methylation calls using Bismark v0.24.2 (https://pmc.ncbi.nlm.nih.gov/articles/PMC3102221/). The Bismark-generated methylation call coverage files (.cov files) were imported into SeqMonk (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). Read positions were generated by filtering CpGs with a minimum threshold of 1 read count and grouped into windows containing 100 valid CpGs. The bisulphite methylation feature pipeline in SeqMonk was used to quantitate the CpG windows, with a minimum count of 1 read per CpG position and a minimum of 20 CpGs reads per window. This generated mean percentage methylation values for each window, producing a genome-wide quantitative methylation dataset. Each row represents a genomic window containing 100 CpGs and reports the genomic coordinates and mean percentage.  The genomic locations and the quantitated values for each sample were extracted from the SeqMonk output file.  The values were also rounded to 2 decimal places.
Library strategy: EM-seq

growth_protocol: All cell lines were cultured under atmospheric oxygen, 5% CO2 and at 37 degrees C in Essential 8 (E8) medium (Thermo Fisher A1517001) on TC-treated 6 well plates (Corning 3506) coated with rh-VTN (Thermo Fisher A14700) at 10 mcg/ well in PBS without calcium or magnesium. For CHR lines culture plates were coated with rhL521 (Gibco A29249) at 5mcg per well of a 6 well plate in DPBS with calcium and magnesium (Gibco 14040133) and cells were cultured in Stemflex (ThermoFisher, A3349401) supplemented with 3mcM IWP2 (Cayman Chemicals 13951) for at least 8 passages before the experiment was carried out.

extract_protocol:
hiPSCs or hESCs genomic DNA (gDNA) was extracted from isolated nuclei using the Monarch Spin gDNA Extraction Kit (NEB, #T3010S). gDNA concentration was quantified using a Nanodrop. 200ng of gDNA was fragmented to an average size of ~300bp using a Covaris E220 Sonicator with the following parameters: temperature 7°C, peak incident power 140W, duty factor 10%, cycles per burst 200, treatment time 80s.
The sheared gDNA was then used to prepare EM-seq libraries using the NEBNext Enzymatic Methyl-seq kit (NEB, #E7120S) following the manufacturer’s standard size library protocol. The final sequencing-ready libraries were amplified using the protocol’s PCR programme with 4 cycles. Size distribution and yield quantification of the libraries were tested using an Agilent 2100 Bioanalyzer high sensitivity DNA chip (Agilent 5067–4626). Libraries were then multiplexed and sequenced (paired-end 150 bp) on a NovaSeq X Plus Series PE150 (Illumina) to a depth of a minimum 30 million reads per library.


title: fiaj1, untreated, replicate 1

description: Library name: EM_Fiaj_Rep1


title: lung, heart, spleen, kidney, ovary, brain, eye, skin, and muscle tissues

city: Fuzhou

first: Xuequn

last: Chen

state: Fujian

address: No.1 Qiuyang Road, Shangjie Town, Minhou County,

institute: FJTCM

description: Library name: DF01_2_RNA

data_processing:
Raw RNA-seq reads were first subjected to quality control and adapter/low-quality sequence filtering. Clean reads were aligned to the reference genome using HISAT2. The HISAT2 index was built from the reference genome FASTA file, and paired-end clean reads were mapped to the genome with default parameters except for the specified thread number. The resulting SAM files were converted to BAM format, sorted, and indexed using SAMtools.  Gene-level read counts were generated using featureCounts based on the corresponding gene annotation GTF file. Only reads uniquely assigned to annotated gene features were counted.
Assembly: GCA_054730915.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Anas platyrhynchos

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 SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.


title: C1

description: adjacent to cancer group, replicate biosample 1


title: SAMPLES23

description:
Library name: SAMPLES23
GZ_SA_3


title: Female, DCT(early), control,96h, replicate 4

value: control diet


title: neurons,cK2c,week18,male,rep3

description: Library name: 499

value: conditional kmt2c knockout

value: male


title: blood,stomach, intestine, liver, pancreas

description: Library name: DF01_1_RNA


title: fiaj1, CHR, replicate 2

city: Cambridge

description: Library name: EM_Fiaj_CR_Rep2

value: human pluripotent stem cells


title: SAMPLES22

description:
Library name: SAMPLES22
GZ_SA_2


title: IL1A_1_MouseMyo_ATACSeq

description: Library name: IL1A_1_MouseMyometrium_ATACSeq

value: Myometrium

value: IL-1α (400ng in 20 µl saline, GD 16.5)


title: Female, DCT(early), control,96h, replicate 3

value: Kidney