title: RNA-seq of CNE-2 CSPG4-knockout cells

city: shanghai

first: wang

last: zhitong

address: No. 138, Fenyang Road, Xuhui District

department: Otorhinolaryngology

institute: Eye & ENT Hospital

description: Library name: KO_S41

data_processing:
Raw FASTQ reads were evaluated using FastQC for base quality, GC distribution and adapter contamination.
Assembly: Human reference genome: GRCh38 (hg38)
Supplementary files format and content: Normalized expression matrices are provided in tab-delimited .txt format.

source_name: Nasopharynx

extract_protocol:
Total RNA was extracted using TRIzol reagent following manufacturer instructions. RNA integrity and concentration were measured using Bioanalyzer or TapeStation. Samples with RIN ≥ 7 were used for library preparation.
RNA-seq libraries were generated from poly(A)-selected or rRNA-depleted total RNA using a stranded library construction kit according to manufacturer guidelines. Libraries were barcoded, quantified, pooled, and sequenced on an Illumina HiSeq 2500 platform (paired-end, 150 bp).

value: Nasopharynx

value: Nasopharyngeal carcinoma epithelial cells


title: TMBPF_10_donor2_R2_P2

status: Public on Jan 06 2026

type: SRA

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description: Library name: s142

library_source: transcriptomic

data_processing:
Reads were demultiplexed from the BCL files and processed into FASTQ files using  DRAGEN analysis v1.3.0 on the Illumina Basespace Sequence Hub (Illumina, Inc., San Diego, CA, USA). Processing and quality control of the FASTQ files, differential expression analysis, and exploratory statistical analyses were performed using the R-ODAF_Health_Canada pipeline (https://github.com/R-ODAF/R-ODAF_Health_Canada; accessed December 2024), which manages workflows using snakemake v8.0 (Mölder et al., 2021) and relies on scripts in R (v.4.3.2). The preprocessing steps use fastp v0.23.2 for trimming (Chen et al., 2018), STAR v2.7.8a (Dobin et al., 2013) to perform alignment of raw reads to the reference sequence, and the qCount function of the QuasR R package (v1.30.0; Gaidatzis et al., 2015) to extract the feature counts from the aligned reads (BAM files) using features specified in a GTF file. A samples-by-probes count matrix was produced.
Assembly: Probe sequence set provided by biospyder based on Human Whole Transcriptome kit v2.1
Supplementary files format and content: Tab-delimited table containing read counts per TempO-Seq probe

molecule: total RNA

organism: Homo sapiens

source_name: Mammary

growth_protocol: HMECs from three biological donors were kept at low passage and not allowed to exceed 80% confluency to preserve epithelial subpopulations and maintained in complete media. Cells were cultured in T75 flasks supplemented Mammary Epithelial Cell Growth Medium containing phenol red at 37°C in a humidified atmosphere (5% CO2).

extract_protocol:
Cells were washed with phosphate-buffered saline and lysed in situ using 2x TempO-Seq lysis buffer diluted with an equal amount of PBS for TempO-Seq library building.
Gene expression was measured using the TempO-Seq Human Whole Transcriptome v2.0 and 2.1 kits (BioSpyder Technologies Inc, Carlsbad, California) as per the manufacturer’s instructions

treatment_protocol: For the experiment, cells (passage 7) were seeded at 20,000 cells per well in 96-well plates in supplemented MEGM without phenol red (Lonza Bioscience). After 48 h, the media were removed and replaced with supplement-free MEGM without phenol red containing chemicals of interest at eight concentrations (0.001, 0.01, 0.1, 0.5, 1, 5, 10, 50 µM) and E2 (0.1 and 1 nM). The experiment included at least six plate-matched solvent controls (0.1% DMSO) and four technical replicates from each donor were exposed for 48 h.

tag: tissue

value: Mammary

tag: cell line

value: Primary

tag: cell type

value: Epithelial

tag: genotype

value: WT

tag: treatment

value: chemical exposure

tag: chemical

value: tetramethyl bisphenol F

tag: dose

tag: donor

tag: batch


title: Mouse retina, WT

city: New York

first: Eugene Yu-Chuan

last: Kang

state: NY

address: 701 W. 168 St, HHSC 2nd floor, 210

country: USA

institute: Columbia University Irving Medical Center

description:
Library name: Sample1
10x Genomics

library_source: transcriptomic single cell

data_processing:
The data was aggregated using the Cell Ranger aggr program. The integrated dataset was first imported into the Rosalind platform (https://www.rosalind.bio/) for dimension reduction and unsupervised clustering using Cell Ranger Graph Based Clustering (10 Genomics). The dataset was then loaded into R (v4.2) and the Seurat package (v5.0).(105) Cell types were annotated using SC-type (v1.0)(106) with cell markers for major retinal cells
Assembly: Mouse  mm9
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: nuclear RNA

organism: Mus musculus

source_name: Retina

extract_protocol:
Mouse retinas were harvested and nucleus extraction was performed using the Miltenyi Nuclei Extraction Buffer (Miltenyi Biotec) according to the manufacturer’s guidelines. Upon isolation, the nuclei were counted using trypan blue and a Countess III Automated Cell Counter (Thermo Fisher Scientific, Waltham, MA, USA).
SnRNA libraries were prepared using the Chromium Single Cell 3' kit (10X Genomics) and sequenced on an Illumina platform using standard protocols. After obtaining the sequencing data, we used Cell Ranger (v8.0) with default parameters to generate a filtered_feature_bc_matrix.h5 file containing cell barcodes and transcript counts for each sample.

value: Retina

value: Retinal cells

tag: age

value: 360 days


title: RNA-seq of CNE-2 CSPG4-deficient cells (PEP6)

state: shanghai

country: China

description: Library name: PEP6_S95


title: MDS-Dx-37

type: genomic

city: Toronto

first: Sagi

last: Abelson

state: ON

address: 661 University Avenue

institute: Ontario Institute for Cancer Research

hyb_protocol: Bisulphite converted DNA was amplified, fragmented, and hybridized to human Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader(HiScan) and standard recommended Illumina scanner settings

data_processing:
Raw IDAT files were preprocessed and normalized using preprocessNoob from the minfi package in R (v4.2.2)
Beta values

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Bone marrow

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to the manufacturer's instructions.

value: Bone marrow

tag: disease

value: MDS

tag: Stage

value: Diagnosis

tag: Sex

value: Male


title: RNA-seq of CNE-2 CSPG4-rescue cells

description: Library name: Res_S94


title: RNA-seq of CNE-2 wild-type cells (CSPG4-WT)

description: Library name: MT_S42


title: TMBPF_1_donor2_R2_P2

description: Library name: s140


title: MDS-Dx-41


title: MDS-Dx-35

value: Female


title: TMBPF_5_donor2_R2_P2

description: Library name: s141


title: WT Skin MC903 4

city: Inchon

first: YunJae

last: Jung

address: 155 Gaetbeol-ro, Yeonsu-gu

department: Microbiology

country: South Korea

institute: College of Medicine, Gachon University

description: Library name: WT-MC903-4

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to rn6 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -e
The reads were prepared for analysis using the Trimmomatic version 0.38 to remove adapter sequences and trim the low-quality bases. Subsequently, the processed reads were aligned to the Rattus norvegicus reference genome (rn6) using HISAT version 2.1.0 by incorporating both HISAT and Bowtie2 for alignment.83 Reference genome sequences and gene annotation data were sourced from the NCBI Genome Assembly and NCBI RefSeq databases. Following alignment, data formatted in SAM was sorted and indexed using SAMtools version 1.9. Then, the StringTie version 2.1.3b tool was used to assemble and quantify the transcripts.84,85 Differential gene expression analysis was performed using edgeR version 3.40.2 with raw count data input.86 The exactTest function within edgeR was used to determine the statistical significance of the differentially expressed genes (DEGs) after adjusting the p-values using the Benjamini–Hochberg method to control the false discovery rate. The DEGs were identified based on the criteria: |fold change| ≥ 2 and p < 0.05.
Assembly: mm10
Supplementary files format and content: FPKM, TPM values for each Sample

molecule: polyA RNA

source_name: Ear skin tissue

growth_protocol: C57BL/6 mice purchased from Orient Bio (Gyeonggi-do, Korea) were maintained at standard temperature and humidity in a specific pathogen-free environment. All procedures were reviewed and approved by the Center of Animal Care and Use at the Lee Gil Ya Cancer and Diabetes Institute, Gachon University (LCDI-2023-0038, LCDI-2023-0028).

extract_protocol:
RNA from the skin and small intestines of the mice was extracted using QIAzol and purified using an RNeasy mini kit. The purified RNA was processed with DNase I  to remove genomic DNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To induce AD-like inflammation, bilateral ear skin was topically treated with 50 µM of MC903 (calcipotriol; Tocris Biochemicals, Bristol, UK) in 20 µL of 100% ethanol and with 10 µL of 10 mg/mL ovalbumin (OVA; Sigma-Aldrich, St. Louis, MO, USA) in phosphate-buffered saline (PBS) daily for 10 days. Control mice were treated with 20 µL of 100% ethanol followed by 10 µL of 10 mg/mL OVA in PBS. To induce itch flares associated with atopic dermatitis, mice were administered an intradermal injection of 20 µL of 2.5 mg/mL OVA on day 10. Scratching behavior was recorded for 5 min prior to the injection and for 30 min following the challenge.

value: Ear skin tissue

value: 50 µM of MC903


title: MDS-Dx-34


title: SW620_AFZC_02

city: Guangzhou

first: Guangzhao

last: Lyu

state: Guangdong

address: 651 Dongfengdong Rd

department: Colorectal Surgery

institute: Sun Yat-Sen University Cancer Center

description:
Library name: sample8
Column_name_SW620_AFZC_2_in_counts_symbol.txt

data_processing:
The raw sequencing data were processed using a standard RNA-seq analysis pipeline. First, raw reads were subjected to quality control (QC) and adapter trimming using FastQC and Trimmomatic/Cutadapt. Clean reads were then aligned to the reference genome (GRCh38) using HISAT2/STAR. Gene-level expression quantification was performed by counting the number of reads mapped to each gene feature using featureCounts. Differential expression analysis between experimental conditions was conducted using DESeq2/edgeR. Significantly differentially expressed genes were subsequently used for functional enrichment analysis (GO, KEGG).
Assembly: The reference genome used for read alignment and quantification was GRCh38 (Genome Reference Consortium Human Build 38).
Supplementary files format and content: The primary processed data file is a gene expression matrix in tab-delimited text format (.txt). The file contains a header row with sample identifiers and subsequent rows for each gene. Columns typically include: Gene identifier (e.g., GeneID, Gene Symbol) and the raw read counts for that gene in each sample. This matrix serves as the input for downstream differential expression and statistical analysis.

extract_protocol:
Total RNA was extracted from tissues or cells using a standard extraction method. RNA quality control was performed primarily using the Agilent 2100 Bioanalyzer to precisely assess RNA integrity (RIN) and quantity. Only samples passing quality thresholds proceeded to library construction. Detailed metrics are provided in the sample QC report.
Libraries were constructed using the standard (non-strand-specific) protocol. Briefly, polyadenylated mRNA was enriched from total RNA using Oligo(dT) magnetic beads. The enriched mRNA was then fragmented using divalent cations under elevated temperature. First-strand cDNA synthesis was performed using random hexamer primers, followed by second-strand cDNA synthesis. The double-stranded cDNA underwent end repair, A-tailing, adapter ligation, size selection, PCR amplification, and purification to generate the final sequencing library. Library quality was assessed using a Qubit 2.0 Fluorometer for preliminary quantification, an Agilent 2100 Bioanalyzer for insert size distribution, and qPCR for accurate quantification of effective library concentration. Qualified libraries were pooled and sequenced on the Illumina platform using sequencing-by-synthesis (SBS) chemistry.

value: colon cancer

value: AFZC


title: WT Skin MC903 3

description: Library name: WT-MC903-3


title: WT Skin MC903 2

description: Library name: WT-MC903-2


title: TMBPF_0-5_donor2_R2_P2

description: Library name: s139

value: Mammary

value: Primary


title: NegativeControl_R1_P1

description: Library name: s79

organism: synthetic construct

value: Epithelial

value: technical control

value: lysis buffer


title: WT Skin MC903 1

description: Library name: WT-MC903-1

value: WT


title: SW620_AFZC_01

description:
Library name: sample7
Column_name_SW620_AFZC_1_in_counts_symbol.txt


title: SW620_5FU_02

description:
Library name: sample6
Column_name_SW620_5FU_2_in_counts_symbol.txt


title: WT Skin con 4

description: Library name: WT-Con-4

value: control


title: WT Skin con 5

description: Library name: WT-Con-5


title: MDS-Dx-33


title: TMBPF_0-1_donor2_R2_P2

description: Library name: s138

value: chemical exposure

value: tetramethyl bisphenol F


title: DMSO_0-1_donor2_R7_P2

description: Library name: s136

value: vehicle control

value: dimethyl sulfoxide


title: MDS-Dx-32

value: Bone marrow

value: MDS

value: Diagnosis


title: SW620_5FU_01

description:
Library name: sample5
Column_name_SW620_5FU_1_in_counts_symbol.txt


title: TMBPF_0-01_donor2_R2_P2

description: Library name: s137


title: MDS-Dx-31

value: Male


title: WT Skin con 2

description: Library name: WT-Con-2

value: Ear skin tissue


title: MDS-Dx-29

value: Female


title: HCT116_AFZC_02

description:
Library name: sample4
Column_name_HCT116_AFZC_2_in_counts_symbol.txt

value: colon cancer

value: AFZC


title: HCT116_5FU_02

description:
Library name: sample2
Column_name_HCT116_5FU_2_in_counts_symbol.txt


title: HCT116_AFZC_01

description:
Library name: sample3
Column_name_HCT116_AFZC_1_in_counts_symbol.txt


title: MDS-Dx-30


title: BPAF_5_donor2_R2_P2

description: Library name: s134

value: Mammary

value: Primary

value: Epithelial

value: bisphenol AF


title: BPAF_0-5_donor2_R2_P2

description: Library name: s132

value: WT


title: MDS-Dx-28


title: WT Skin con 1

description: Library name: WT-Con-1

value: control


title: BPAF_1_donor2_R2_P2

description: Library name: s133

value: chemical exposure


title: MDS-Dx-26


title: ex2

city: Atlanta

first: Patricia

middle: J

last: Ward

state: Georgia

address: 201 Dowman Drive

institute: Emory University

description: Library name: D11

data_processing:
Raw reads were cleaned for low quality sequences and reads with adapters were removed using the novogene analysis pipeline.
Cleaned reads were aligned using HISAT v2.2 to the GRCm38.p3 reference genome.
Aligned reads were quantified using Illumina Dragen v3.7.5.
Assembly: GRCm38.p3
Supplementary files format and content: tab delimited text file with read counts for each gene

source_name: extensor digitorum longus

extract_protocol:
RNA was harvested using Rneasy Fibrous Tissue Mini Kit (Qiagen)
RNA libraries for RNA-seq were prepared using Illumina TruSeq following manufacturer's protocols.

treatment_protocol: Surgical lumbar sympathectomy was performed on sympathectomized mice. Exercise protocol was given on a treadmill for 1 hour a day over 17 days.

value: extensor digitorum longus

value: exercised


title: HCT116_5FU_01

description:
Library name: sample1
Column_name_HCT116_5FU_1_in_counts_symbol.txt


title: WT Skin con 3

description: Library name: WT-Con-3


title: BPAF_0-1_donor2_R2_P2

description: Library name: s131


title: ex1

description: Library name: D10


title: HTX33_ILV3_3

city: tianjin

first: cancan

last: Dong

address: No. 32, West Seventh Road, Tianjin Airport Economic Zone

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

description:
Library name: HTX33_ILV3_3
Overexpressed Ilv3 engineered strain

data_processing:
Reads were aligned to P. pastoris reference genome using HISAT2 and TopHat2 . Gene expression was quantified with FPKM. Differential expression analysis was performed with DESeq2.
Assembly: GCF_000027005.1
Supplementary files format and content: csv files include FPKM values for each sample

organism: Komagataella pastoris

source_name: yeast cells

growth_protocol: P. pastoris strains were grown in basic salt medium containing 0.5% methanol. Cells were harvested at exponential phase for RNA extraction.

extract_protocol:
Total RNA was extracted from tissue samples, and its concentration and purity were measured using a Nanodrop 2000. RNA integrity was assessed by agarose gel electrophoresis, and the RQN value was determined using an Agilent 5300 system. For each library construction, the RNA requirements were as follows: total amount 1 μg, concentration 30 ng/μL, RQN > 6.5, and OD260/280 ratio between 1.8 and 2.2
RNA-seq transcriptome library was prepared following Illumina ® Stranded mRNA Prep, Ligation (SanDiego, CA) using 1μg of total RNA.

tag: strain

value: yeast cells

value: Ilv3 overexpression

value: methanol induction


title: HTX33_ILV3_2

description:
Library name: HTX33_ILV3_2
Overexpressed Ilv3 engineered strain


title: MDS-Dx-25

value: Bone marrow

value: MDS

value: Diagnosis

value: Male


title: unex2

description: Library name: C8

value: unexercised


title: BPAF_0-01_donor2_R2_P2

description: Library name: s130

value: Mammary


title: BPAF_10_donor2_R2_P2

description: Library name: s135

value: Primary


title: MDS-Dx-22

value: Female


title: unex1

description: Library name: C7


title: HTX33_ILV3_1

description:
Library name: HTX33_ILV3_1
Overexpressed Ilv3 engineered strain


title: BPAF_0-001_donor2_R2_P2

description: Library name: s129

value: Epithelial

value: bisphenol AF


title: MDS-Dx-20


title: BPA_50_donor2_R2_P2

description: Library name: s128

value: WT

value: bisphenol A


title: MDS-Dx-21


title: sympx+ex2

description: Library name: B6

value: extensor digitorum longus


title: sympx+ex1

description: Library name: B5


title: BPA_10_donor2_R2_P2

description: Library name: s127

value: chemical exposure


title: sympx+unex2

description: Library name: A2


title: MDS-Dx-19


title: BPA_5_donor2_R2_P2

description: Library name: s126


title: MDS-Dx-18


title: BPA_1_donor2_R2_P2

description: Library name: s125


title: HTX-33_WT_1, control

description:
Library name: HTX-33_1
WT

value: yeast cells


title: sympx+unex1

description: Library name: A1


title: scRNA-seq of EGFP+ lung macrophages in BLM-treated mouse

city: Tokyo

first: Kohsuke

last: Shirakawa

address: 35 Shinanomachi, Shinjuku-ku

department: Cardiology

country: Japan

institute: Keio University School of Medicine

description: Library name: Spp1-EGFP+ IMs

data_processing:
Raw sequencing reads (Read1: 28 bp, Read2: 91 bp) were trimmed and processed using the Cell Ranger pipeline, including alignment to the mouse reference genome, gene expression quantification, cell barcode calling, and clustering. The resulting processed data files, including barcode, matrix, and gene annotation files, were generated for downstream analysis.
Assembly: Mouse reference genome GRCm38 (GENCODE M25)
Supplementary files format and content: Processed data files include the sparse gene expression matrix (matrix.mtx), the list of genes (genes.tsv or features.tsv), and corresponding cell barcodes (barcodes.tsv) generated by the Cell Ranger pipeline. These files represent filtered gene-cell count matrices used for downstream single-cell RNA-seq analysis.

source_name: lung

extract_protocol:
Spp1-EGFP+SiglecF-CD11b+ interstitial macrophages (IMs) were sorted from Spp1egfp/+ mice using a BD FACSAria III with an 85 μm nozzle. Sorted cells were manually counted and mixed prior to library preparation.
Approximately 10,000 sorted cells with 80–90% viability were used for gel bead-in-emulsion (GEM) generation on a Chromium Controller (10× Genomics). Reverse transcription and cDNA amplification were performed using Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10× Genomics) according to the manufacturer’s instructions. Libraries were quantified by Qubit dsDNA assay and TapeStation analysis.

value: lung

value: Spp1-EGFP+ SiglecF- CD11b+ interstitial macrophages


title: Cd31 enriched, hyperoxia at P3

city: San Fransisco

first: Cristina

last: Alvira

state: CA

address: 555 Mission Bay Blvd South

institute: University of California, San Fransisco

description: Library name: Cd31_Hyox_P3

data_processing:
Sequencing reads were aligned to the Grcm39 mouse genome using Cellranger (v9.0.0). SoupX was used to remove ambient RNA signal.  Gene expression count tables were turned into anndata objects and processed using scanpy when not otherwise specified. Cells that had more than five median absolute deviations of either unique genes or UMIs detected were removed. Cells that had more than three median absolute deviations of percent mitochondrial or ribosomal UMIs were removed. Scrublet was used to automatically detect and remove doublets. Counts were normalized and log transformed16. PCA was run prior to embedding and clustering. The Leiden algorithm was used for clustering, and Uniform Manifold Approximation and Projection for embedding. Lineage identity was assigned using canonical markers: Cdh5 (endothelial); Epcam (epithelial); Ptprc (immune); and Col1a1 (mesenchymal). Cell typing was performed after each lineage was re-clustered and embedded as detailed above. Cell types were assigned a second time after regressing out cell cycle genes
Assembly: GRCm39
Supplementary files format and content: Tab seperated value files and matrix files containing raw UMI counts, cell metadata, and gene metadata

extract_protocol:
Lungs were perfused with HBSS, excised, finely minced, pooled, and digested in Liberase TM (0.2mg/mL) plus DNaseI (0.01mg/mL) for 10min at 37.5 in a bacteriological shaker. The suspension was triturated 15 times. Liberase was inactivated using 2mM EDTA and cold FBS prior to pelleting the cell suspension. Cells were treated with 1X RBC Lysis for 5min then passed over a 30μm cell strainer before microbead enrichment (SmartStrainer, Miltenyi). Enrichment by magnetic associated cell sorting (MACS)- Immune cells were depleted using anti-CD45 coated Dynabeads (Invitrogen). The supernatant was pelleted, counted, and resuspended with blocking buffer (anti-mouse CD16/CD32 and anti-rat IgG; 1:100) for 10min. Mouse anti-BST1–APC (PVEC marker, Biolegend) and rat anti-CD31–biotin (pan-EC marker, BD Pharminogen) antibodies were added to the cells (2μg/10M cells) and incubated on a HulaMixer for 20 minutes. To ensure sufficient PVEC for our analysis, following the manufacturer’s protocol, cells were first enriched for BST1 using the MACS anti-APC microbeads and then the flow through was enriched for CD31 using anti-biotin microbeads (Miltenyi MACS).
Chromium GEMX 3’ v4 gene expression- Following the manufacturers protocol, enriched populations were then adjusted to 1500 cell/μL to obtain the 20,000 cell target input for gel bead emulsion formation (10X Genomics). Samples that met QC standards (Bioanalyzer, Stanford Protein and Nucleic Acid core) were used for barcoding, library construction and sequenced by NovoSeq Χ at a depth of 1B paired reads per sample (NovoGene Corporation Inc.).

treatment_protocol: 80 % oxygen post birth

value: All lung cell types, enriched for endothelial cells

value: Hyperoxia


title: SRCAPcd IAA RNA 2

city: Lausanne

first: David

middle: Michael

last: Suter

address: EPFL SV-IN Station 19

department: Institute of Bioengineering

country: Switzerland

institute: École polytechnique fédérale de Lausanne

data_processing:
RNA-seq reads were aligned to the mm10 genome using STAR, allowing only uniquely mapped reads. Reads not aligning to chr1-19, chrX, or, chrY were removed using SAMTools 1.10 and duplicates were removed using Picard. Reads in refGene exons or introns were counted using featureCount from Rsubread. Counts were normalized and differentially expressed transcripts determined using DeSeq2.
Assembly: mm10
Supplementary files format and content: Matrix of raw intronic and exonic counts
Supplementary files format and content: Table with Deseq2-normalized counts and results of differential expression analysis on intronic reads

source_name: SYAT

growth_protocol: CGR8 mouse ES cells and SYAT mESC were routinely cultured at 37 °C and 5% CO2 on cell culture-treated dishes coated with 0.1% gelatin using the following culture medium: GMEM supplemented with 10% ES-cell qualified fetal bovine serum, 1% nonessential amino acids, 2mM L-glutamine,  2mM sodium pyruvate, 100μM 2-mercaptoethanol, 1% penicillin and streptomycin, in-house produced leukemia inhibitory factor (LIF), CHIR99021 at 3 μM and PD184352 at 0.8 μM. Cells were passaged by trypsinization every two to three days. Three days before all experiments, mESC medium was changed to Serum LIF medium: GMEM supplemented with 10% ES-cell qualified fetal bovine serum, nonessential amino acids, 2 mM L-glutamine, sodium pyruvate, 100 μM 2-mercaptoethanol, penicillin and streptomycin, in-house produced leukemia inhibitory factor (LIF). SYAT cells were cultured routinely with 200nM Auxinole (Control condition) to avoid basal degradation of SRCAP. For SRCAP degradation, SYAT cells were treated for 1, 2, 4, 6 or 8 h with 500µM Indole-3-Acetic Acid (IAA). For induction of wtSRCAP or cdSRCAP expression, 1µg/mL Doxycycline was added for 24 h prior cell collection.

extract_protocol:
500,000 mES cells were treated with indicated treatment prior to cell collection. Cell pellets were resuspended in 500 μL Nuclear RNA lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mMMgCl2, 1% BSA, 0.1% Tween, 1 mM DTT, 0.5U/μl Protector RNase Inhibitor, 0.1% NP-40, 0.01% Digitonin and incubated 5 min on ice. Then 500 μl Nuclear RNA wash buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween, 1 mM DTT, 0.5U/μl Protector RNase Inhibitor) were added before spinning down cells at 300g 4°C for 5 min. Two more washes with Nuclear RNA wash buffer were performed before proceeding to RNA extraction using the Rneasy Plus Micro Kit following manufacturer instructions with the addition of an on-column DNAse digestion.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

treatment_protocol: SRCAP degradation was induced by 2,4,6 or 8-hour treatment with 500µM IAA. wtSRCAP or cdSRCAP overexpression was induced by a 24-hour Doxycyline treatment (1µg/mL)

value: SYAT

value: mESC

value: Dox 24h + IAA 4h


title: MDS-Dx-17

value: Bone marrow

value: MDS

value: Diagnosis


title: HTX-33_WT_3, control

description:
Library name: HTX-33_3
WT

value: methanol induction


title: MDS-Dx-14

value: Female


title: BPA_0-5_donor2_R2_P2

description: Library name: s124

value: Mammary

value: Primary

value: Epithelial

value: WT


title: MDS-Dx-16


title: Cd31 enriched, normoxia at P3

description: Library name: Cd31_Nox_P3

value: Normoxia


title: BPA_0-1_donor2_R2_P2

description: Library name: s123

value: chemical exposure

value: bisphenol A


title: SRCAPcd NT RNA 2

value: Dox 24h


title: Bst1 enriched, hyperoxia at P3

description: Library name: Bst1_Hyox_P3

value: lung

value: All lung cell types, enriched for venous endothelial cells

value: Hyperoxia


title: MDS-Dx-13

value: Male


title: Bst1 enriched, normoxia at P3

description: Library name: Bst1_Nox_P3


title: BPA_0-01_donor2_R2_P2

description: Library name: s122


title: SRCAPwt NT RNA 2

value: SYAT

value: mESC


title: SRCAPcd IAA RNA 1

value: Dox 24h + IAA 4h


title: HTX-33_WT_2, control

description:
Library name: HTX-33_2
WT

value: yeast cells

value: methanol induction


title: SRCAPwt IAA RNA 2


title: MDS-Dx-12

value: Bone marrow

value: MDS

value: Diagnosis


title: BPA_0-001_donor2_R2_P2

description: Library name: s121

value: Mammary

value: Primary

value: Epithelial

value: WT


title: TMBPF_50_donor1_R2_P2

description: Library name: s119

value: chemical exposure

value: tetramethyl bisphenol F


title: Rat, cardiomyocytes, Sham2, anti-ERRβ (IP)

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

description:
Library name: Sham2-Esrrb
CUT&Tag of anti-ERRβ (IP) from Sham-2

library_source: genomic

data_processing:
For CUT&Tag data. Raw fastq files were aligned to the Rn7 by bowtie2. The reference genome Escherichia_coli_K_12_MG1655 were applied for spike-In parameters. Sam files were converted into bam and bed files by samtools. Bed files then converted to bedgraph files by bedtools and adjusted by spike-In parameters. For visualization, bigwig files were generated using wigToBigWig from bedgraph. Read distribution was visualized on the IGV. Macs2 facilitated peakcalling with bam files converted from adjusted bedgraph files. For more extensive information on CUT&Tag parameters, refer to the Steven Henikoff process. Peaks identified by macs2 were filtered with the cutoff set as P value ≤ 0.05and homer motif enrichment analysis was performed to treat these peaks with the findMotifsGenome.pl (-len 8 -mask) function.
Assembly: Rn7
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

organism: Rattus norvegicus

source_name: heart

growth_protocol: All animal experiments were approved by the Animal Care and Use Committee of Zhejiang University (Protocol No. 20150119-013) and conducted in accordance with institutional guidelines. Male Sprague-Dawley rats (8-10 weeks old, 200-240 g) were purchased from the Zhejiang Academy of Medical Sciences and housed under controlled conditions with free access to food and water.

extract_protocol:
Excised hearts were rinsed in ice-cold 1× PBS to remove residual blood and adipose tissue, and the myocardium was minced into ~1 mm³ pieces on ice. For each preparation, 0.1-0.3 g of minced tissue was transferred into 3 mL pre-chilled Buffer A and homogenized in a glass Dounce homogenizer using a loose-clearance pestle. When indicated to suppress RNase activity, 1 mL citrate solution was added during homogenization. The tissue suspension was triturated once with the loose pestle, incubated on ice for 5 min, and further triturated 5–10 strokes. After an additional 5 min on ice, the sample was triturated 3–5 strokes with the loose pestle and then 5 strokes with the tight-clearance pestle. The homogenate was filtered through a 100 µm cell strainer, and the strainer was rinsed sequentially with 1 mL and 750 µL Buffer A to maximize nuclei recovery. Triton X-100 was then added to a final concentration of 0.5% (v/v), and the suspension was further homogenized by trituration (20-50 strokes). The lysate was passed through a 35 µm cell strainer and centrifuged at 500g for 5 min at 4°C. The supernatant was discarded, and the pellet was resuspended in 1 mL citrate solution, followed by centrifugation at 500g for 5 min at 4°C. The pellet was subsequently centrifuged at 3,000g for 5 min at 4°C, resuspended in 1 mL Buffer B and centrifuged again, and the resulting pellet was resuspended in 200 µL Buffer B. A final clarification spin was performed at 20,000g for 3 min at 4°C. Nuclei were assessed by trypan blue staining and quantified using a Countess automated cell counter. All procedures were carried out on ice or at 4°C unless otherwise specified.
CUT&Tag (Cleavage Under Targets and Tagmentation) libraries were constructed using the Vazyme CUT&Tag Library Prep Kit for Illumina (Vazyme, Cat# TD903) following the manufacturer’s instructions with minor modifications. Cell Preparation and Bead Binding Briefly, approximately 1 X 105 cells per sample were harvested and washed twice with Wash Buffer. Concanavalin A-coated magnetic beads (Vazyme) were activated and added to the cell suspension, followed by incubation at room temperature for 10 min to allow cell-bead binding. Primary and Secondary Antibody Incubation The bead-bound cells were resuspended in Antibody Binding Buffer containing the specific primary antibody ERRβ and incubated at 4 ℃ overnight with gentle agitation. After washing to remove unbound antibodies, the cells were incubated with a secondary antibody (Goat Anti-Mouse IgG) in Dig-Wash Buffer at room temperature for 1 hour. Tagmentation and DNA Extraction The cell-bead complexes were washed three times to remove residual secondary antibodies and then incubated with pA-Tn5 (protein A-Tn5) adapter complex at room temperature for 1 hour. To activate tagmentation, the samples were resuspended in Tagmentation Buffer and incubated at 37℃ for 1 hour. The reaction was terminated by adding EDTA, SDS, and Proteinase K, followed by incubation at 55℃ for 1 hour to digest proteins and release DNA fragments. Genomic DNA was subsequently extracted via phenol-chloroform or using the DNA Clean Beads provided in the kit. Library Amplification and Purification The extracted DNA was used as a template for PCR amplification to add Illumina-compatible sequencing adapters. The PCR program was set as follows: initial extension at 72℃ for 3 min; denaturation at 95℃ for 3 min; followed by 12 cycles of 98℃ for 10 s and 60℃ for 5 s; and a final extension at 72℃ for 1 min. The resulting libraries were purified using VAHTS DNA Clean Beads (Vazyme, Cat# N411) at a ratio of 2.0 X to remove primer dimers.

treatment_protocol: Aged, male Sprague–Dawley rats (retired breeders) weighing ~ 500 g were anesthetized with 100 mg/kg intraperitoneal sodium pentobarbital and supplemented as needed to maintain a surgical plane. Sham-operated rats underwent the same surgical procedure without LAD ligation.

value: heart

value: cardiomyocytes

value: Sham

tag: antibody

value: anti-ERRβ (IP)


title: MDS-Dx-06

value: Female


title: DMSO_0-1_donor1_R8_P2

description: Library name: s120

value: vehicle control

value: dimethyl sulfoxide


title: Rat, cardiomyocytes, Sham2, anti-ERRβ (Input)

description:
Library name: Sham2-Input
CUT&Tag of anti-ERRβ (Input) from Sham-2

value: input


title: Rat, cardiomyocytes, Sham1, anti-ERRβ (Input)

description:
Library name: Sham1-Input
CUT&Tag of anti-ERRβ (Input) from Sham-1


title: TMBPF_10_donor1_R2_P2

description: Library name: s118


title: SRCAPcd NT RNA 1

value: SYAT

value: mESC

value: Dox 24h


title: MDS-Dx-05

value: Bone marrow

value: MDS

value: Diagnosis

value: Male


title: SRCAPwt NT RNA 1


title: SRCAPwt IAA RNA 1

value: Dox 24h + IAA 4h


title: MDS-Dx-04


title: TMBPF_5_donor1_R2_P2

description: Library name: s117

value: Mammary

value: Primary

value: Epithelial

value: WT

value: chemical exposure

value: tetramethyl bisphenol F


title: MDS-Dx-03

value: Female


title: TMBPF_0-5_donor1_R2_P2

description: Library name: s115


title: MDS-Dx-01


title: SYAT IAA LG1 2

value: IAA 500uM 1h


title: Methanothermobacter marburgensis transcriptome under 5000 nM Ni (replicate 3)

city: Hachioji

first: Shunsuke

last: Nomura

state: Tokyo

department: Microbial Protein Structure Group

institute: Max Planck Institute for Terrestrial Microbiology

description:
Library name: Ni5000_3
M. marburgensis cultured under 5000 nM nickel; replicate 3 for transcriptomic analysis

data_processing:
Adapter trimming and quality filtering were performed to remove low-quality reads. Clean paired-end reads were aligned to the M. marburgensis reference genome (NCBI RefSeq: NC_014408.1) using a standard short-read aligner. Gene expression levels were quantified by counting reads mapped to each gene, normalized for sequencing depth and gene length using DESeq2.
Assembly: NC_014408.1 (Methanothermobacter marburgensis DSM 2133)
Supplementary files format and content: The processed data file contains DESeq2-normalized gene expression counts for all samples across different nickel concentrations and biological replicates. Rows represent annotated genes identified by NCBI RefSeq locus tags. Columns represent individual samples, with headers matching the sample names listed in the metadata. Values are normalized counts suitable for differential expression analysis.

organism: Methanothermobacter marburgensis

source_name: archaeal culture

growth_protocol: Methanothermobacter marburgensis DSM2133 was cultivated anaerobically in defined medium at 65 °C under continuous gas flow (80% H₂, 20% CO₂, 0.2% H₂S). The medium was stirred at ~300 rpm and fed by peristaltic pump under slight N₂ pressure.

extract_protocol:
Cells were harvested anaerobically by centrifugation at 13,000 × g for 15 min at 4 °C, frozen, and used for RNA extraction. Total RNA was isolated using TRIzol and purified with RNeasy columns.
Total RNA quality and quantity were verified using Nanodrop, Agilent 2100 Bioanalyzer, and agarose gel electrophoresis. Ribosomal RNA was depleted to enrich for mRNA. Strand-specific cDNA libraries were constructed using Novogene’s standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 platform with 150 bp paired-end reads.

treatment_protocol: Nickel concentration was adjusted to either 50 nM (limiting) or 5000 nM (sufficient) by adding NiCl₂ to the medium. Cells were grown under these conditions for transcriptomic comparison.

value: archaeal culture

value: wild type

value: 5000 nM nickel


title: TMBPF_1_donor1_R2_P2

description: Library name: s116


title: MDS-Dx-10


title: SYAT unt LG1 2

value: SYAT

value: mESC

value: Control


title: SYAT IAA EG1 2


title: Methanothermobacter marburgensis transcriptome under 5000 nM Ni (replicate 1)

description:
Library name: Ni5000_1
M. marburgensis cultured under 5000 nM nickel; replicate 1 for transcriptomic analysis


title: TMBPF_0-1_donor1_R2_P2

description: Library name: s114


title: Rat, cardiomyocytes, Sham1, anti-ERRβ (IP)

description:
Library name: Sham1-Esrrb
CUT&Tag of anti-ERRβ (IP) from Sham-1

value: heart

value: cardiomyocytes

value: Sham

value: anti-ERRβ (IP)


title: Methanothermobacter marburgensis transcriptome under 5000 nM Ni (replicate 2)

description:
Library name: Ni5000_2
M. marburgensis cultured under 5000 nM nickel; replicate 2 for transcriptomic analysis


title: Patient_14_Rm2

data_processing:
Raw IDAT files were preprocessed and normalized using preprocessNoob from the minfi package in R (v4.2.2)
processed value definition: Beta values

source_name: Peripheral blood

value: Peripheral blood

tag: disease status

tag: age at diagnosis

value: female


title: SYAT IAA LG1 1


title: TMBPF_0-01_donor1_R2_P2

description: Library name: s113

tag: tissue

value: Mammary

value: Primary

value: Epithelial

value: WT


title: Patient_14_Dx

value: Diagnosis


title: Patient_14_Rm1


title: Methanothermobacter marburgensis transcriptome under 50 nM Ni (replicate 2)

description:
Library name: Ni50_2
M. marburgensis cultured under 50 nM nickel; replicate 2 for transcriptomic analysis

value: archaeal culture

value: 50 nM nickel


title: Methanothermobacter marburgensis transcriptome under 50 nM Ni (replicate 3)

description:
Library name: Ni50_3
M. marburgensis cultured under 50 nM nickel; replicate 3 for transcriptomic analysis

value: wild type


title: SYAT unt EG1 2

tag: cell line

value: SYAT


title: DMSO_0-1_donor1_R7_P2

description: Library name: s112

tag: cell type

value: vehicle control

value: dimethyl sulfoxide


title: Patient_13_Rm2

value: male


title: SYAT unt LG1 1

value: mESC

value: Control


title: human week 20 slide 2 (Wk20s2)

type: RNA

city: Philadelphia

first: Alex

last: Hughes

state: PA

address: 390 Towne Building 220 S. 33rd Street

institute: University of Pennsylvania

description:
Xenium Analyzer
FFPE spatial sequencing

hyb_protocol: Xenium Prime barcoding assay steps

scan_protocol: Xenium Prime barcoding assay steps

data_processing:
For each cycle and image plane, the onboard pipeline detected fluorescent puncta, decoded them into gene identities, and assigned a per-transcript basecalling quality ‘Q score’. Cell boundaries were computed by morphology-based segmentation of DAPI images using a neural-network model, enabling assignment of decoded transcripts to individual cells.
data files format and content:
analysis_summary.html: Analysis summary
analysis.zarr.zip: Secondary analysis outputs, such as clustering results
cell_boundaries.csv.gz: Cell spatial boundaries
cell_boundaries.parquet: Cell spatial boundaries
cell_feature_matrix.h5: Cell × feature (gene/transcript) counts for transcripts passing Q20
cell_feature_matrix.zarr.zip: Cell × feature (gene/transcript) counts for transcripts passing Q20
barcodes.tsv.gz: List of barcode sequences. Should be placed in sub-directory called “cell_feature_matrix”
features.tsv.gz: List of pre-designed panel genes and custom add-on genes, negative controls, unassigned codewords, and deprecated codewords. Should be placed in sub-directory called “cell_feature_matrix”.
matrix.mtx.gz: Cell × feature (gene/transcript) counts for transcripts passing Q20 in MEX format. Should be placed in sub-directory called “cell_feature_matrix”
cells.csv.gz: Cell summary file
cells.parquet: Cell summary file
cells.zarr.zip: Segmentation masks and spatial boundaries for nuclei and cells
experiment.xenium: Manifest file with metadata & relative paths. Can be opened in Xenium Explorer for data browsing.
gene_panel.json: Pre-designed/custom gene panel list
metrics_summary.csv: Summary of gene expression metrics
morphology_focus_0000.ome.tif: 2D autofocus projection image for the nuclei DAPI/other stain images. Should be placed in sub-directory called “morphology_focus”
morphology_focus_0001.ome.tif: 2D autofocus projection image for the nuclei DAPI/other stain images. Should be placed in sub-directory called “morphology_focus”
morphology_focus_0002.ome.tif:2D autofocus projection image for the nuclei DAPI/other stain images. Should be placed in sub-directory called “morphology_focus”
morphology_focus_0003.ome.tif: 2D autofocus projection image for the nuclei DAPI/other stain images. Should be placed in sub-directory called “morphology_focus”
morphology.ome.tif: 3D Z-stack of the DAPI image
nucleus_boundaries.csv.gz: Nucleus spatial boundaries
nucleus_boundaries.parquet: Nucleus spatial boundaries

source_name: Spatial Transcriptomics

label_protocol: Xenium Prime barcoding assay steps were then performed, comprising priming hybridization, RNase treatment and polishing, probe hybridization, ligation, amplification, cell segmentation staining (ATP1A1/CD45/ECAD for cell boundaries; 18S rRNA and aSMA/Vimentin for cell interior), autofluorescence quenching, and DAPI staining. Barcode decoding was then performed through automated iterative cycles of fluorescent probe hybridization, imaging, and probe removal on the Xenium Analyzer instrument.

extract_protocol: Formalin-fixed tissues were paraffin embedded, and 5 µm sections were cut with a cryostat

value: human fetal kidney

tag: genotype

value: wild-type


title: BPAF_10_donor1_R2_P2

description: Library name: s111

tag: treatment

value: chemical exposure

value: bisphenol AF


title: SYAT IAA EG1 1

value: IAA 500uM 1h


title: Patient_13_Rm1

value: Peripheral blood


title: SYAT unt EG1 1


title: BPAF_5_donor1_R2_P2

description: Library name: s110

value: Mammary

value: Primary

value: Epithelial

value: WT

tag: chemical


title: Methanothermobacter marburgensis transcriptome under 50 nM Ni (replicate 1)

description:
Library name: Ni50_1
M. marburgensis cultured under 50 nM nickel; replicate 1 for transcriptomic analysis

value: archaeal culture

value: wild type

value: 50 nM nickel


title: human week 20 slide 1 (Wk20s1)

description:
Xenium Analyzer
FFPE spatial sequencing


title: CGR8 NT 2


title: Patient_12_Rm2


title: BPAF_0-1_donor1_R2_P2

description: Library name: s107

tag: dose


title: BPAF_0-5_donor1_R2_P2

description: Library name: s108

tag: donor


title: Patient_12_Rm1


title: Patient_12_Dx

value: Diagnosis


title: human week 17 slide 1, part 2 (Wk17s1_2)

description:
Xenium Analyzer
FFPE spatial sequencing


title: CGR8 IAA4h 1

value: IAA 500uM 4h


title: CGR8 IAA4h 2

value: mESC


title: BPAF_0-01_donor1_R2_P2

description: Library name: s106

tag: batch


title: SYAT IAA8h 2

value: SYAT

value: IAA 500uM 8h


title: BPAF_1_donor1_R2_P2

description: Library name: s109


title: human week 17 slide 2 (Wk17s2)

description:
Xenium Analyzer
FFPE spatial sequencing

value: human fetal kidney

value: wild-type


title: BPA_50_donor1_R2_P2

description: Library name: s104

value: chemical exposure

value: bisphenol A


title: human week 17 slide 1, part 1 (Wk17s1_1)

description:
Xenium Analyzer
FFPE spatial sequencing


title: Patient_13_Dx

value: Peripheral blood

value: male


title: mouse E18 slide 1 (E18s1)

description:
Xenium Analyzer
FFPE spatial sequencing

value: CD1 mouse fetal kidney


title: Patient_11_Rm1


title: mouse E18 slide 2 (E18s2)

description:
Xenium Analyzer
FFPE spatial sequencing


title: SYAT IAA6h 2

value: IAA 500uM 6h


title: BPA_10_donor1_R2_P2

description: Library name: s103

value: Mammary

value: Primary

value: Epithelial

value: WT


title: Patient_10_Rm2


title: Patient_11_Dx

value: Diagnosis


title: BPA_5_donor1_R2_P2

description: Library name: s102


title: Patient_11_Rm2


title: BPAF_0-001_donor1_R2_P2

description: Library name: s105

value: bisphenol AF


title: mouse E17 slide 1 (E17s1)

description:
Xenium Analyzer
FFPE spatial sequencing


title: BPA_1_donor1_R2_P2

description: Library name: s101


title: mouse E17 slide 2 (E17s2)

description:
Xenium Analyzer
FFPE spatial sequencing


title: Patient_10_Rm1


title: SYAT IAA2h 2

value: mESC

value: IAA 500uM 2h


title: CGR8 NT 1

value: Control


title: Patient_10_Dx


title: SYAT unt 2

value: SYAT


title: SYAT IAA8h 1

value: IAA 500uM 8h


title: BPA_0-5_donor1_R2_P2

description: Library name: s100

value: chemical exposure


title: Patient_9_Rm2


title: BPA_0-1_donor1_R2_P2

description: Library name: s99

value: bisphenol A


title: mouse E15 slide 2 (E15s2)

description:
Xenium Analyzer
FFPE spatial sequencing

value: wild-type


title: mouse E15 slide 1 (E15s1)

description:
Xenium Analyzer
FFPE spatial sequencing


title: NHP D, 28 DPI

city: Galveston

first: Jacquelyn

last: Turcinovic

state: TX

address: Galveston National Laboratory, 301 University Blvd.

department: Microbiology and Immunology

institute: University of Texas Medical Branch

description: Library name: sample36

data_processing:
Raw FASTQ files were aligned to the combined M. fascicularis (Ensembl 102 v5.0) and BOMV (OK633884.1) genomes using STAR aligner v2.7.11b.
Transcript-aligning reads were quantified with Rsubread featureCounts v2.20.0.
Sequencing batch effect was regressed using SVA ComBat-seq v3.54.0.
Postexposure samples were binned by day (DPI) and compared to baseline (-8 DPI) using DESeq2 v1.46.0.
Assembly: M. fascicularis (Ensembl 102 v5.0) and BOMV (OK633884.1)
Supplementary files format and content: counts.tsv is the raw count matrix output from featureCounts

organism: Macaca fascicularis

source_name: Blood

extract_protocol:
Total RNA extracted from TRIzol LS using chloroform phase separation according to the manufacturer's specifications. RNA cleanup was performed via QIAGEN RNeasy cleanup columns, and DNA was digested on-column during cleanup.
Globin and ribosomal RNA were removed via the NEBNext Globin and rRNA Depletion Kit, and sequencing libraries were prepared with the NEBNext Ultra II RNA Library Prep Kit.

value: Blood

value: A


title: SYAT IAA6h 1

value: IAA 500uM 6h


title: Patient_9_Rm1

value: Peripheral blood

value: male


title: SYAT IAA4h 1

value: IAA 500uM 4h


title: NHP B, 28 DPI

description: Library name: sample34


title: NHP C, 28 DPI

description: Library name: sample35


title: SYAT IAA4h 2


title: BPA_0-001_donor1_R2_P2

description: Library name: s97

value: Mammary

value: Primary

value: Epithelial

value: WT


title: Patient_8_Rm2


title: SYAT IAA2h 1

value: mESC

value: IAA 500uM 2h


title: NHP D, 21 DPI

description: Library name: sample32


title: DMSO_0-1_donor3_R6_P1

description: Library name: s94

value: vehicle control

value: dimethyl sulfoxide


title: NHP A, 28 DPI

description: Library name: sample33


title: BPA_0-01_donor1_R2_P2

description: Library name: s98

value: chemical exposure


title: DMSO_0-1_donor3_R5_P1

description: Library name: s93


title: SYAT unt 1

value: SYAT

value: Control


title: Patient_8_Rm1


title: DMSO_0-1_donor2_R6_P1

description: Library name: s92


title: NHP B, 21 DPI

description: Library name: sample30

value: Blood


title: Patient_8_Dx

value: Diagnosis


title: NHP A, 21 DPI

description: Library name: sample29

value: A


title: SYAT unt 2 DNAme

data_processing:
Libraries were mapped using bwa-meth from Bwa (from Brent Pedersen, https://github.com/brentp/bwa-meth). CpG methylation was then calculated using MethylDackel (https://github.com/dpryan79/MethylDackel) before analysis of Differential methylation using MethylKit
Assembly: mm10
Supplementary files format and content: Bedgraph file containing percentage of methylated cytosines in CpG computed using MethylDackel

growth_protocol: SYAT mESC were routinely cultured at 37 °C and 5% CO2 on cell culture-treated dishes coated with 0.1% gelatin using the following culture medium: GMEM supplemented with 10% ES-cell qualified fetal bovine serum, 1% nonessential amino acids, 2mM L-glutamine,  2mM sodium pyruvate, 100μM 2-mercaptoethanol, 1% penicillin and streptomycin, in-house produced leukemia inhibitory factor (LIF), CHIR99021 at 3 μM and PD184352 at 0.8 μM. Cells were passaged by trypsinization every two to three days. Three days before all experiments, mESC medium was changed to Serum LIF medium: GMEM supplemented with 10% ES-cell qualified fetal bovine serum, nonessential amino acids, 2 mM L-glutamine, sodium pyruvate, 100 μM 2-mercaptoethanol, penicillin and streptomycin, in-house produced leukemia inhibitory factor (LIF). SYAT cells were cultured routinely with 200nM Auxinole (Control condition) to avoid basal degradation of SRCAP. For SRCAP degradation, SYAT cells were treated for 4 h with 500µM Indole-3-Acetic Acid (IAA).

extract_protocol:
Genomic DNA was extracted using a DNeasy Blood and Tissue kit  and repurified using a DNA Clean and Concentrator-5 Kit. Next, 200 ng of purified genomic DNA were sonicated for 90s, 10% duty, 140W, 200 cycles on a Covaris E220 focused ultrasonicator and were subsequently processed using NEBNext Enzymatic Methyl-Seq kit following the manufacturer protocol.
Libraries were prepared with NEBNext Ultra II DNA Library Prep Master Mix Set
Enzymatic-Methyl Sequencing

treatment_protocol: SRCAP degradation was induced by a 4-hour treatment with 500µM IAA.


title: SYAT IAA 2 DNAme


title: DMSO_0-1_donor2_R5_P1

description: Library name: s91


title: SYAT unt 1 DNAme


title: Patient_7_Rm1

value: Peripheral blood


title: DMSO_0-1_donor1_R6_P1

description: Library name: s90


title: DMSO_0-1_donor1_R5_P1

description: Library name: s89


title: NHP D, 15 DPI

description: Library name: sample28


title: Patient_7_Dx

value: male


title: TripleNegative_BLM_aOSM_aIL6R_HTO [NGS4659]

city: South San Francisco

first: Jason

middle: Anthony

last: Vander Heiden

address: 1 DNA Way

department: Biological Research AI Development

institute: Genentech

description:
SAM24420083_HTO
hashtag library

data_processing:
FASTQ files were generated using the Cell Ranger v6.0.1 (10X Genomics) bcl2fastq (Illumina) wrapper.
Sequencing reads were assembled and aligned against the GENCODE basic mouse reference using Cell Ranger v6.0.1 (10X Genomics) to generate count matrices.
Assembly: GRCm38
Supplementary files format and content: HDF5 gene count matrices.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit.
Single-cell RNA-seq library preparation was performed using the 10x Genomics Chromium platform with the Single Cell 3’ Library and Gel bead kit following the manufacturer’s user guide.

treatment_protocol: Cells were pelleted right after sorting. Supernatant was discarded and pellet was resuspended in RLT buffer.

value: lung

value: CD45- CD31- EpCAM-

value: bleomycin + anti-IL6R + anti-OSM

tag: time point

value: day 24


title: Patient_9_Dx


title: DMSO_0-1_donor3_R4_P1

description: Library name: s86

data_processing:
Reads were demultiplexed from the BCL files and processed into FASTQ files using  DRAGEN analysis v1.3.0 on the Illumina Basespace Sequence Hub (Illumina, Inc., San Diego, CA, USA). Processing and quality control of the FASTQ files, differential expression analysis, and exploratory statistical analyses were performed using the R-ODAF_Health_Canada pipeline (https://github.com/R-ODAF/R-ODAF_Health_Canada; accessed December 2024), which manages workflows using snakemake v8.0 (Mölder et al., 2021) and relies on scripts in R (v.4.3.2). The preprocessing steps use fastp v0.23.2 for trimming (Chen et al., 2018), STAR v2.7.8a (Dobin et al., 2013) to perform alignment of raw reads to the reference sequence, and the qCount function of the QuasR R package (v1.30.0; Gaidatzis et al., 2015) to extract the feature counts from the aligned reads (BAM files) using features specified in a GTF file. A samples-by-probes count matrix was produced.
Assembly: Probe sequence set provided by biospyder based on Human Whole Transcriptome kit v2.1
Supplementary files format and content: Tab-delimited table containing read counts per TempO-Seq probe

value: Mammary

value: Primary

value: Epithelial

value: WT


title: CD31_EPCAM_BLM_aOSM_aIL6R_HTO [NGS4659]

description:
SAM24420082_HTO
hashtag library

value: CD45- CD31+ EpCAM+


title: NHP C, 15 DPI

description: Library name: sample27


title: DMSO_0-1_donor3_R3_P1

description: Library name: s85

value: vehicle control

value: dimethyl sulfoxide


title: Patient_6_Rm1

value: female


title: DMSO_0-1_donor2_R4_P1

description: Library name: s84


title: NHP B, 15 DPI

description: Library name: sample26

value: Blood


title: Patient_6_Dx

value: Diagnosis


title: NHP D, 10 DPI

description: Library name: sample24

value: B


title: CD45_BLM_aOSM_aIL6R_HTO [NGS4659]

description:
SAM24420081_HTO
hashtag library


title: SYAT IAA 1 DNAme

value: SYAT

value: mESC

value: IAA 500uM 4h


title: Patient_7_Rm2

value: Peripheral blood

value: male


title: Patient_6_Rm2


title: NHP C, 10 DPI

description: Library name: sample23


title: Patient_5_Rm1


title: DMSO_0-1_donor2_R3_P1

description: Library name: s83


title: NHP B, 10 DPI

description: Library name: sample22


title: TripleNegative_BLM_aIL6R_HTO [NGS4659]

description:
SAM24420080_HTO
hashtag library

value: lung

value: CD45- CD31- EpCAM-

value: bleomycin + anti-IL6R

value: day 24


title: CD45_BLM_aIL6R_HTO [NGS4659]

description:
SAM24420078_HTO
hashtag library


title: CD31_EPCAM_BLM_aIL6R_HTO [NGS4659]

description:
SAM24420079_HTO
hashtag library


title: Patient_5_Rm2


title: DMSO_0-1_donor1_R3_P1

description: Library name: s81

value: Mammary

value: Primary

value: Epithelial

value: WT


title: NHP A, 15 DPI

description: Library name: sample25

value: A


title: Patient_5_Dx


title: TripleNegative_BLM_aOSM_HTO [NGS4659]

description:
SAM24420077_HTO
hashtag library

value: bleomycin + anti-OSM


title: DMSO_0-1_donor1_R4_P1

description: Library name: s82

value: vehicle control

value: dimethyl sulfoxide


title: NHP D, 7 DPI

description: Library name: sample20

value: Blood


title: E2_10_donor3_R1_P1

description: Library name: s78

value: chemical exposure


title: Patient_4_Rm2

value: Bone marrow


title: NHP A, 10 DPI

description: Library name: sample21

value: B


title: E2_1_donor3_R1_P1

description: Library name: s77


title: Patient_4_Rl

value: Relapse

value: male


title: Patient_4_Rm1


title: E2_10_donor2_R1_P1

description: Library name: s76


title: NHP C, 7 DPI

description: Library name: sample19


title: NHP B, 7 DPI

description: Library name: sample18


title: TripleNegative_BLM_Control_HTO [NGS4659]

description:
SAM24420074_HTO
hashtag library

value: lung

value: CD45- CD31- EpCAM-

value: bleomycin + isotype control


title: CD45_BLM_aOSM_HTO [NGS4659]

description:
SAM24420075_HTO
hashtag library

value: day 24


title: CD31_EPCAM_BLM_aOSM_HTO [NGS4659]

description:
SAM24420076_HTO
hashtag library

value: CD45- CD31+ EpCAM+


title: CD31_EPCAM_BLM_Control_HTO [NGS4659]

description:
SAM24420073_HTO
hashtag library


title: E2_1_donor2_R1_P1

description: Library name: s75

value: Mammary

value: Primary

value: Epithelial


title: NHP D, 5 DPI

description: Library name: sample16

value: A


title: Patient_4_Dx

value: Diagnosis


title: Patient_3_Rm2

value: female


title: E2_10_donor1_R1_P1

description: Library name: s74

value: WT


title: NHP A, 7 DPI

description: Library name: sample17

value: Blood


title: CD45_BLM_Control_HTO [NGS4659]

description:
SAM24420072_HTO
hashtag library


title: DMSO_0-1_donor3_R2_P1

description: Library name: s72

value: vehicle control

value: dimethyl sulfoxide


title: E2_1_donor1_R1_P1

description: Library name: s73

value: chemical exposure


title: NHP C, 5 DPI

description: Library name: sample15


title: Patient_2_Rm2

value: Bone marrow

value: male


title: TMBPF_50_donor3_R1_P1

description: Library name: s71

value: tetramethyl bisphenol F


title: Patient_2_Rl

value: Relapse


title: Patient_3_Dx


title: CD31_EPCAM_PBS_HTO [NGS4659]

description:
SAM24420070_HTO
hashtag library

value: lung

value: PBS

value: day 24


title: Patient_3_Rm1


title: NHP C, 3 DPI

description: Library name: sample11

value: B


title: TMBPF_10_donor3_R1_P1

description: Library name: s70

value: Mammary

value: Primary

value: Epithelial


title: NHP B, 5 DPI

description: Library name: sample14

value: A


title: TMBPF_5_donor3_R1_P1

description: Library name: s69

value: WT


title: NHP A, 5 DPI

description: Library name: sample13

value: Blood


title: NHP D, 3 DPI

description: Library name: sample12


title: TripleNegative_BLM_aOSM_aIL6R_GEX [NGS4659]

description:
SAM24420083_GEX
gene expression library

value: CD45- CD31- EpCAM-

value: bleomycin + anti-IL6R + anti-OSM


title: CD31_EPCAM_BLM_aOSM_aIL6R_GEX [NGS4659]

description:
SAM24420082_GEX
gene expression library

value: CD45- CD31+ EpCAM+


title: Patient_2_Rm1

value: Bone marrow


title: TMBPF_1_donor3_R1_P1

description: Library name: s68

value: chemical exposure


title: TripleNegative_PBS_HTO [NGS4659]

description:
SAM24420071_HTO
hashtag library


title: Patient_3_Rl

value: female


title: CD45_BLM_aOSM_aIL6R_GEX [NGS4659]

description:
SAM24420081_GEX
gene expression library


title: TMBPF_0-5_donor3_R1_P1

description: Library name: s67

value: tetramethyl bisphenol F


title: NHP B, 3 DPI

description: Library name: sample10


title: Patient_2_Dx

value: Diagnosis

value: male


title: CD45_PBS_HTO [NGS4659]

description:
SAM24420069_HTO
hashtag library

value: lung

value: PBS

value: day 24


title: TripleNegative_BLM_aIL6R_GEX [NGS4659]

description:
SAM24420080_GEX
gene expression library

value: bleomycin + anti-IL6R


title: Patient_1_Rl

value: Relapse


title: TMBPF_0-1_donor3_R1_P1

description: Library name: s66

value: Mammary

value: Primary

value: Epithelial


title: NHP D, 1 DPI

description: Library name: sample08

value: Blood

value: A


title: CD31_EPCAM_BLM_aIL6R_GEX [NGS4659]

description:
SAM24420079_GEX
gene expression library

value: CD45- CD31+ EpCAM+


title: NHP C, 1 DPI

description: Library name: sample07


title: Patient_1_Rm1

value: Bone marrow


title: NHP B, 1 DPI

description: Library name: sample06


title: Patient_1_Rm2


title: DMSO_0-1_donor3_R1_P1

description: Library name: s64

value: WT

value: vehicle control

value: dimethyl sulfoxide


title: TripleNegative_BLM_aOSM_GEX [NGS4659]

description:
SAM24420077_GEX
gene expression library

value: CD45- CD31- EpCAM-

value: bleomycin + anti-OSM


title: Patient_1_Dx

value: Diagnosis

value: male


title: BPAF_5_donor3_R1_P1

description: Library name: s62

value: chemical exposure

value: bisphenol AF


title: NHP A, 1 DPI

description: Library name: sample05


title: CD45_BLM_aIL6R_GEX [NGS4659]

description:
SAM24420078_GEX
gene expression library

value: lung

value: bleomycin + anti-IL6R

value: day 24


title: NHP D, -8 DPI

description: Library name: sample04


title: CD31_EPCAM_BLM_aOSM_GEX [NGS4659]

description:
SAM24420076_GEX
gene expression library


title: CD45_BLM_aOSM_GEX [NGS4659]

description:
SAM24420075_GEX
gene expression library


title: NHP A, 3 DPI

description: Library name: sample09

value: B


title: NHP C, -8 DPI

description: Library name: sample03

value: Blood


title: TMBPF_0-01_donor3_R1_P1

description: Library name: s65

value: Mammary

value: Primary

value: Epithelial

value: tetramethyl bisphenol F


title: BPAF_0-5_donor3_R1_P1

description: Library name: s60

value: WT


title: BPAF_1_donor3_R1_P1

description: Library name: s61


title: Patient_62

value: Peripheral blood

tag: age

tag: dnmt3a mutation

value: FALSE

tag: tet2 mutation

tag: clonal hematopoiesis


title: Patient_63

tag: Sex


title: BPAF_0-1_donor3_R1_P1

description: Library name: s59


title: CD31_EPCAM_BLM_Control_GEX [NGS4659]

description:
SAM24420073_GEX
gene expression library

value: CD45- CD31+ EpCAM+

value: bleomycin + isotype control


title: NHP B, -8 DPI

description: Library name: sample02

value: A


title: TripleNegative_BLM_Control_GEX [NGS4659]

description:
SAM24420074_GEX
gene expression library

value: CD45- CD31- EpCAM-


title: Patient_61

value: male

value: TRUE


title: BPAF_10_donor3_R1_P1

description: Library name: s63

value: chemical exposure

value: bisphenol AF


title: Patient_60


title: Patient_64


title: Stromal PSAT1 + IFNT replicate 3

city: Leeds

first: LeedsOmics

last: UoLeeds

state: West Yorkshire

address: Clarendon Way

department: Cross-faculty

country: United Kingdom

institute: University of Leeds

description:
Library name: Bt Stromal PSAT1 + IFNT rep 3
R_S_PSAT1_IFNT_3

data_processing:
To analyze differences in expression, adapter trimming was done by Cutadapt24 and the reads were filtered using fastq_quality_filter as part of FASTX-toolkit with parameters including “-q 20” and “-p 90”. The bovine (Bos taurus) and human (Homo sapiens) reference genome and gene annotation files were retrieved from the Ensembl genome database (release 96)25 and GENCODE (release 31),26 respectively. With the help of the Rsubread package,27 read mapping was performed by means of Subread aligners with only uniquely mapped reads reported in the final alignment and read summarization and quantification was carried out using the featureCounts function. Statistical analysis for differential gene expression was conducted via DESeq228 with the cutoffs of log2FoldChange > 1 (or <−1) and padj < .05.
Assembly: The bovine (Bos taurus) and human (Homo sapiens) reference genome and gene annotation files were retrieved from the Ensembl genome database (release 96) and GENCODE (release 31), respectively
Supplementary files format and content: gene_counts_PoolE.txt = readCounts matrix of the bEECs on a tab-delimited plain text format; gene_counts_PoolS.txt = readCounts matrix of the bESCs on a tab-delimited plain text format; gene_counts_human_CAPG.txt = readCounts matrix of the hEECs on a tab-delimited plain text format;

organism: Bos taurus

source_name: Endometrium

growth_protocol: Primary bovine endometrial cell culture Primary bovine endometrial epithelial cells (bEECs) and primary bovine endometrial stromal cells (bESCs) were isolated by enzymatic digestion from late-luteal phase uterine tracts (n=3). bEECs and bESCs were maintained in complete bovine medium (RPMI 1640 [Gibco, Massachusetts, US], 10% charcoal-stripped FBS [PAA Cell Culture Company, UK], 1% antibiotic antimycotic solution [ABAM, Sigma-Aldrich, Missouri, USA]). bESCs at a concentration of 150,000 cells per well (n=5) and bEECs at a concentration of 300,000 cells per well (n=5) were plated into separate 6-well plates in 2 mL complete bovine medium. All cultures were maintained at 37C/5% CO2 in a humidified incubator. At 70% confluence bEECs and bESCs were treated with one of the following for 24 hr: (1) Media control, (2) Vehicle control (PBS only), (3) 1000 ng/ml rbPDI, 4) 1000ng/mL rbPSAT1, 5) 1000ng/mL rbCAPG, or (6) 1000 ng/ml rbPDI/CAPG/PSAT1 combined with 100 ng/ml roIFNT. Human endometrial cell culture Ishikawa (ECACC 99040201, passage 10) immortalised human endometrial epithelial cells (hEECs) were plated in biological technical triplicate at 300,000 cells per well in a 6 well plate, in 2 mL complete human medium (DMEM/F12 [Gibco, Massachusetts, US], 10% FBS [PAA Cell Culture Company, UK], 1% Glutamine SStreptomycin PPenicillin [Gibco, Massachusetts, US]). The three replicates were from three different flasks of passage 10 cells, which had been split from a single flask of passage 9 Ishikawa cells. All cultures were maintained at 37 C/5% CO2 in a humidified incubator. At 70% confluence hEECs were treated with one of the following for 24 hours: (1) Media control, (2) Vehicle control (PBS only), (3) 1000ng/mL rbCAPG (4) 1000 ng/ml rbPDI, or (5) 1000 ng/ml rbPSAT1.

extract_protocol:
RNA extraction and sequencing Following treatment cells were washed with PBS, lysed in 400µL mirVana lysis solution from mirVana RNA extraction kit (Invitrogen, St. Louis, US) and snap frozen. RNA was extracted from the cell pellets using the MirVana RNA extraction kit (Invitrogen, St. Louis, US) as per manufacturer’s protocol. Genomic DNA removal was carried out using the DNA free kit (Thermo Fisher Scientific, Massachusetts, US) as per the manufacturer’s protocol.
RNA libraries were sequenced at the NGS Facility at the University of Leeds where they were prepared and sequenced as per their standard protocols using the Illumina TruSeq Stranded Total kit according to manufacturer’s guidelines. The RNA libraries were sequenced using the Illumina NextSeq 500 machine (Illumina, California, USA) with a single end 75 bp length read.

value: Endometrium

value: Ishikawa cell line

value: PSAT1 + IFNT


title: NHP A, -8 DPI

description: Library name: sample01

value: Blood


title: BPAF_0-01_donor3_R1_P1

description: Library name: s58

extract_protocol:
Cells were washed with phosphate-buffered saline and lysed in situ using 2x TempO-Seq lysis buffer diluted with an equal amount of PBS for TempO-Seq library building.
Gene expression was measured using the TempO-Seq Human Whole Transcriptome v2.0 and 2.1 kits (BioSpyder Technologies Inc, Carlsbad, California) as per the manufacturer’s instructions

value: Mammary

value: Primary

value: Epithelial


title: CD45_BLM_Control_GEX [NGS4659]

description:
SAM24420072_GEX
gene expression library

value: lung

value: day 24


title: TripleNegative_PBS_GEX [NGS4659]

description:
SAM24420071_GEX
gene expression library

value: PBS


title: BPAF_0-001_donor3_R1_P1

description: Library name: s57

value: WT


title: CD31_EPCAM_PBS_GEX [NGS4659]

description:
SAM24420070_GEX
gene expression library

value: CD45- CD31+ EpCAM+


title: Stromal PSAT1 + IFNT replicate 1

description:
Library name: Bt Stromal PSAT1 + IFNT rep 1
R_S_PSAT1_IFNT_1

value: Stromal


title: BPA_10_donor3_R1_P1

description: Library name: s55

value: bisphenol A


title: BPA_50_donor3_R1_P1

description: Library name: s56


title: Patient_58

value: Peripheral blood

value: male

value: TRUE


title: CD45_PBS_GEX [NGS4659]

description:
SAM24420069_GEX
gene expression library


title: Stromal PSAT1 + IFNT replicate 2

description:
Library name: Bt Stromal PSAT1 + IFNT rep 2
R_S_PSAT1_IFNT_2

value: Endometrium


title: TripleNegative_PBS_GEX [NGS4272]

description:
SAM24411450_GEX
gene expression library

data_processing:
FASTQ files were generated using the Cell Ranger v6.0.1 (10X Genomics) bcl2fastq (Illumina) wrapper.
Sequencing reads were assembled and aligned against the GENCODE basic mouse reference using Cell Ranger v6.0.1 (10X Genomics) to generate count matrices.
Assembly: GRCm38
Supplementary files format and content: HDF5 feature count matrices.

value: CD45- CD31- EpCAM-

value: day 14


title: Patient_57


title: Patient_56

value: FALSE


title: Patient_59


title: BPA_1_donor3_R1_P1

description: Library name: s53

value: Mammary

value: chemical exposure


title: Stromal PSAT1 replicate 2

description:
Library name: Bt Stromal PSAT1 rep 2
R_S_PSAT1_2

value: Primary


title: Patient_55


title: BPA_5_donor3_R1_P1

description: Library name: s54

value: Epithelial


title: CD31_EPCAM_PBS_GEX [NGS4272]

description:
SAM24411449_GEX
gene expression library

value: lung


title: CD45_PBS_GEX [NGS4272]

description:
SAM24411448_GEX
gene expression library

value: PBS


title: Stromal PSAT1 replicate 1

description:
Library name: Bt Stromal PSAT1 rep 1
R_S_PSAT1_1


title: Stromal CAPG + IFNT replicate 3

description:
Library name: Bt Stromal CAPG + IFNT rep 3
R_S_CAPG_IFNT_3

value: CAPG + IFNT


title: BPA_0-5_donor3_R1_P1

description: Library name: s52

value: WT


title: Patient_54


title: Stromal CAPG + IFNT replicate 2

description:
Library name: Bt Stromal CAPG + IFNT rep 2
R_S_CAPG_IFNT_2

value: Stromal


title: BPA_0-1_donor3_R1_P1

description: Library name: s51

value: bisphenol A


title: Patient_53

value: Peripheral blood


title: Patient_52

value: female


title: TripleNegative_BLM_aOSM_aIL6R_GEX [NGS4272]

description:
SAM24411447_GEX
gene expression library

value: bleomycin + anti-IL6R + anti-OSM


title: CD31_EPCAM_BLM_aOSM_aIL6R_GEX [NGS4272]

description:
SAM24411446_GEX
gene expression library

value: CD45- CD31+ EpCAM+


title: CD45_BLM_aOSM_aIL6R_GEX [NGS4272]

description:
SAM24411445_GEX
gene expression library


title: BPA_0-01_donor3_R1_P1

description: Library name: s50


title: Stromal PSAT1 replicate 3

description:
Library name: Bt Stromal PSAT1 rep 3
R_S_PSAT1_3

value: Endometrium


title: BPA_0-001_donor3_R1_P1

description: Library name: s49


title: Patient_50

value: male

value: TRUE


title: Stromal CAPG + IFNT replicate 1

description:
Library name: Bt Stromal CAPG + IFNT rep 1
R_S_CAPG_IFNT_1


title: DMSO_0-1_donor2_R2_P1

description: Library name: s48

value: Mammary

value: vehicle control

value: dimethyl sulfoxide


title: TripleNegative_BLM_aIL6R_GEX [NGS4272]

description:
SAM24411444_GEX
gene expression library

value: CD45- CD31- EpCAM-

value: bleomycin + anti-IL6R

value: day 14


title: CD31_EPCAM_BLM_aIL6R_GEX [NGS4272]

description:
SAM24411443_GEX
gene expression library

value: lung


title: Patient_51

value: FALSE


title: TMBPF_10_donor2_R1_P1

description: Library name: s46

value: Primary

value: Epithelial

value: WT

value: chemical exposure

value: tetramethyl bisphenol F


title: Patient_49

value: Peripheral blood


title: TMBPF_50_donor2_R1_P1

description: Library name: s47


title: Stromal CAPG replicate 2

description:
Library name: Bt Stromal CAPG rep 2
R_S_CAPG_2

value: Endometrium

value: Stromal

value: CAPG


title: TripleNegative_BLM_aOSM_GEX [NGS4272]

description:
SAM24411441_GEX
gene expression library

value: bleomycin + anti-OSM


title: CD45_BLM_aIL6R_GEX [NGS4272]

description:
SAM24411442_GEX
gene expression library


title: TMBPF_5_donor2_R1_P1

description: Library name: s45

value: Mammary


title: Stromal PDI + IFNT replicate 3

description:
Library name: Bt Stromal PDI + IFNT rep 3
R_S_PDI_IFNT_3

value: PDI + IFNT


title: CD31_EPCAM_BLM_aOSM_GEX [NGS4272]

description:
SAM24411440_GEX
gene expression library

value: CD45- CD31+ EpCAM+


title: TMBPF_1_donor2_R1_P1

description: Library name: s44


title: Patient_48

value: male


title: Patient_46

value: female


title: Stromal CAPG replicate 1

description:
Library name: Bt Stromal CAPG rep 1
R_S_CAPG_1


title: TMBPF_0-5_donor2_R1_P1

description: Library name: s43


title: Stromal PDI + IFNT replicate 1

description:
Library name: Bt Stromal PDI + IFNT rep 1
R_S_PDI_IFNT_1


title: CD45_BLM_aOSM_GEX [NGS4272]

description:
SAM24411439_GEX
gene expression library

value: lung

value: day 14


title: Patient_45

value: FALSE

value: TRUE


title: TMBPF_0-1_donor2_R1_P1

description: Library name: s42

value: Primary

value: Epithelial

value: WT


title: Stromal CAPG replicate 3

description:
Library name: Bt Stromal CAPG rep 3
R_S_CAPG_3


title: Stromal PDI + IFNT replicate 2

description:
Library name: Bt Stromal PDI + IFNT rep 2
R_S_PDI_IFNT_2


title: Patient_44

value: Peripheral blood


title: TripleNegative_BLM_Control_GEX [NGS4272]

description:
SAM24411438_GEX
gene expression library

value: CD45- CD31- EpCAM-

value: bleomycin + isotype control


title: TMBPF_0-01_donor2_R1_P1

description: Library name: s41

value: chemical exposure

value: tetramethyl bisphenol F


title: Stromal PDI replicate 2

description:
Library name: Bt Stromal PDI rep 2
R_S_PDI_2

value: Endometrium

value: Stromal

value: PDI


title: Patient_47

value: male


title: Stromal PDI replicate 3

description:
Library name: Bt Stromal PDI rep 3
R_S_PDI_3


title: Patient_42


title: Patient_41


title: Patient_43


title: BPAF_10_donor2_R1_P1

description: Library name: s39

value: Mammary

value: bisphenol AF


title: CD45_BLM_Control_GEX [NGS4272]

description:
SAM24411436_GEX
gene expression library

value: lung

value: day 14


title: BPAF_5_donor2_R1_P1

description: Library name: s38


title: DMSO_0-1_donor2_R1_P1

description: Library name: s40

value: vehicle control

value: dimethyl sulfoxide


title: Stromal PDI replicate 1

description:
Library name: Bt Stromal PDI rep 1
R_S_PDI_1

value: Primary


title: Bt Stromal IFNT replicate 1

description:
Library name: Bt Stromal IFNT rep 1
R_S_IFNT_1

value: IFNT


title: C15

city: changsha

first: L

middle: L

last: S

address: tongzipo roda  NO 172

department: csu

institute: csu

data_processing:
The raw paired reads were trimmed and quality was controlled by fastp with default parameters. Then clean reads were separately aligned to the reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: mm9
Supplementary files format and content: raw count.xls describes the raw counts of all genes

source_name: skeletal muscle

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according to the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanlyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA samples   (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥8.0, 28S:18S≥1.0, >1μg) was used to construct Sequencing libraries.
The library was constructed using the Illumina TruseqTM RNA sample prep Kit method

value: skeletal muscle

value: control


title: Bt Stromal IFNT replicate 3

description:
Library name: Bt Stromal IFNT rep 3
R_S_IFNT_3


title: Bt Stromal IFNT replicate 2

description:
Library name: Bt Stromal IFNT rep 2
R_S_IFNT_2


title: C9


title: C14


title: BPAF_0-5_donor2_R1_P1

city: Ottawa

first: Matthew

last: Meier

institute: Government of Canada

description: Library name: s36

value: Epithelial

value: WT


title: Patient_40

extract_protocol: Genomic DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to the manufacturer's instructions.

value: Peripheral blood

value: TRUE

value: FALSE


title: Stromal vehicle control replicate 3

description:
Library name: Bt Stromal vehicle control rep 3
R_S_Vehicle_control_3

value: Endometrium

value: Stromal


title: CD31_EPCAM_BLM_Control_GEX [NGS4272]

description:
SAM24411437_GEX
gene expression library

value: CD45- CD31+ EpCAM+

value: bleomycin + isotype control


title: BPAF_1_donor2_R1_P1

description: Library name: s37

value: Mammary

value: chemical exposure

value: bisphenol AF


title: Stromal vehicle control replicate 2

description:
Library name: Bt Stromal vehicle control rep 2
R_S_Vehicle_control_2

value: vehicle control


title: Patient_39

value: male


title: BPAF_0-1_donor2_R1_P1

description: Library name: s35

value: Primary


title: Stromal control replicate 3

description:
Library name: Bt Stromal control rep 3
R_S_Control_3

value: Control


title: BPAF_0-01_donor2_R1_P1

description: Library name: s34


title: Patient_38


title: C8

value: skeletal muscle

value: control


title: A19

value: rosiglitazone


title: Patient_36

value: Peripheral blood


title: BPA_50_donor2_R1_P1

description: Library name: s32

value: Epithelial

value: WT

value: bisphenol A


title: Stromal control replicate 2

description:
Library name: Bt Stromal control rep 2
R_S_Control_2

value: Endometrium

value: Stromal


title: Patient_37

value: TRUE

value: FALSE


title: Stromal control replicate 1

description:
Library name: Bt Stromal control rep 1
R_S_Control_1


title: C3


title: Stromal vehicle control replicate 1

description:
Library name: Bt Stromal vehicle control rep 1
R_S_Vehicle_control_1


title: A25


title: BPAF_0-001_donor2_R1_P1

description: Library name: s33

value: Mammary

value: chemical exposure


title: C13


title: A18


title: Patient_32


title: Patient_35

value: female


title: A14


title: Epithelial PSAT1 + IFNT replicate 3

description:
Library name: Bt Epithelial PSAT1 + IFNT rep 3
R_E_PSAT1_IFNT_3

value: PSAT1 + IFNT


title: BPA_10_donor2_R1_P1

description: Library name: s31

value: Primary


title: A17


title: Patient_34

value: male


title: BPA_5_donor2_R1_P1

description: Library name: s30


title: Epithelial PSAT1 + IFNT replicate 2

description:
Library name: Bt Epithelial PSAT1 + IFNT rep 2
R_E_PSAT1_IFNT_2


title: BPA_0-5_donor2_R1_P1

description: Library name: s28


title: Epithelial PSAT1 replicate 3

description:
Library name: Bt Epithelial PSAT1 rep 3
R_E_PSAT1_3


title: Patient_33


title: BPA_1_donor2_R1_P1

description: Library name: s29


title: Epithelial PSAT1 + IFNT replicate 1

description:
Library name: Bt Epithelial PSAT1 + IFNT rep 1
R_E_PSAT1_IFNT_1


title: Epithelial PSAT1 replicate 2

description:
Library name: Bt Epithelial PSAT1 rep 2
R_E_PSAT1_2


title: Patient_29


title: Patient_28


title: DMSO_0-1_donor1_R2_P1

description: Library name: s24

value: vehicle control

value: dimethyl sulfoxide


title: HCT116,CSF3,rep1

city: Beijing

first: Junfeng

last: Xu

address: Fuxing Road No.28

institute: Senior Department of Gastroenterology, Chinese PLA General Hospital

description:
HCT116 cells with CSF3-1
P18754_1

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing: NOT PROVIDED; REQUESTED

label: biotin

label_protocol: standard protocol

extract_protocol: standard protocol

value: colon


title: Patient_25

city: Toronto

first: Sagi

last: Abelson

institute: Ontario Institute for Cancer Research

value: Peripheral blood


title: HCT116,CSF3,rep2

description:
HCT116 cells with CSF3-2
P18754_2


title: Patient_31


title: BPA_0-01_donor2_R1_P1

address: 251 Sir Frederick Banting Driveway

description: Library name: s26

value: Epithelial


title: BPA_0-1_donor2_R1_P1

description: Library name: s27

value: WT


title: TMBPF_50_donor1_R1_P1

description: Library name: s23

value: tetramethyl bisphenol F


title: BPA_0-001_donor2_R1_P1

description: Library name: s25

value: bisphenol A


title: TMBPF_10_donor1_R1_P1

description: Library name: s22


title: Epithelial CAPG + IFNT replicate 3

description:
Library name: Bt Epithelial CAPG + IFNT rep 3
R_E_CAPG_IFNT_3

value: Endometrium

value: CAPG + IFNT


title: Patient_27

value: TRUE

value: FALSE


title: Epithelial CAPG replicate 3

description:
Library name: Bt Epithelial CAPG rep 3
R_E_CAPG_3

value: CAPG


title: Epithelial CAPG + IFNT replicate 2

description:
Library name: Bt Epithelial CAPG + IFNT rep 2
R_E_CAPG_IFNT_2


title: Epithelial CAPG + IFNT replicate 1

description:
Library name: Bt Epithelial CAPG + IFNT rep 1
R_E_CAPG_IFNT_1


title: HCT116,Ctrl,rep1

description:
HCT116 cells with Ctrl-1
P18751_1

value: control


title: Patient_26

value: female


title: A6

value: skeletal muscle

value: rosiglitazone


title: HCT116,Ctrl,rep3

description:
HCT116 cells with Ctrl-3
P18751_3


title: TMBPF_5_donor1_R1_P1

description: Library name: s21

value: Mammary

value: Primary

value: chemical exposure


title: HCT116,CSF3,rep3

description:
HCT116 cells with CSF3-3
P18754_3

value: colon


title: Epithelial PSAT1 replicate 1

description:
Library name: Bt Epithelial PSAT1 rep 1
R_E_PSAT1_1

value: Epithelial


title: Patient_23

value: Peripheral blood

value: male


title: Patient_24


title: Epithelial CAPG replicate 1

description:
Library name: Bt Epithelial CAPG rep 1
R_E_CAPG_1


title: Ovary, OLD_96h_3

city: Ube

first: Yoichi

last: Mizukami

state: Yamaguchi

department: Science Research Center

institute: Yamaguchi university

description: AB SOLiD System

data_processing:
The obtained sequencing data in the XSQ format was converted to CSFASTA and QUAL format using a XSQ-Tool (Thermo Fisher Scientific) for use with a CLC Genomics Workbench (version 8.01, Qiagen).
The conditions of the trimming were set with quality limit of 0.05, ambiguous trim of 2, removal of 3` terminal nucleotide of 3, discard of short reads of <15, and long read of >1000.
The conditions of the alignment to the mouse reference genome (GRCm38/mm10) were set with mismatch cost of 2, insertion cost of 3, and deletion cost of 3.
Read count normalization were performed using CLC Genomics Workbench.
The fastq files were created using the export tool of CLC Genomics Workbench.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text file includes CPM values for each sample
Library strategy: SuperSAGE

source_name: Ovary

extract_protocol:
Total RNA was extracted from the ovaries using the RNeasy Mini Kit (Qiagen).
The SOLiD™ SAGE™ Kit barcoding adaptor module (Thermo Fisher Scientific) was used to construct libraries of 27-bp tags adjacent to the 3′ends of mRNAs according to the manufacturer’s protocol.
RNA-seq (3′end-tag)

treatment_protocol: Mice were intraperitoneal administered pregnant mare serum gonadotropin (PMSG, 5 IU) and human Chorionic Gonadotropin (hCG, 5 IU) at 48-hour intervals. Ovaries were clollected at indicated time points and stored in RNAlater.

value: Ovary

tag: time

value: 96h after hCG i.p.

tag: strain


title: Epithelial CAPG replicate 2

description:
Library name: Bt Epithelial CAPG rep 2
R_E_CAPG_2

tag: tissue

value: Endometrium


title: Patient_22


title: Ovary, OLD_96h_2

description: AB SOLiD System


title: Epithelial PDI + IFNT replicate 3

description:
Library name: Bt Epithelial PDI + IFNT rep 3
R_E_PDI_IFNT_3

tag: cell line

value: PDI + IFNT


title: TMBPF_1_donor1_R1_P1

description: Library name: s20

tag: cell type

value: WT

value: tetramethyl bisphenol F


title: Patient_30

value: TRUE

value: FALSE


title: TMBPF_0-01_donor1_R1_P1

description: Library name: s17

tag: genotype


title: TMBPF_0-5_donor1_R1_P1

description: Library name: s19

tag: treatment


title: Patient_21


title: BPAF_10_donor1_R1_P1

description: Library name: s15

tag: chemical

value: bisphenol AF


title: Ovary, OLD_72h_1

description: AB SOLiD System

value: 72h after hCG i.p.


title: Patient_19

value: female


title: TMBPF_0-1_donor1_R1_P1

description: Library name: s18

value: Mammary

value: Primary

tag: dose


title: Epithelial PDI replicate 2

description:
Library name: Bt Epithelial PDI rep 2
R_E_PDI_2

value: PDI


title: Ovary, OLD_72h_3

description: AB SOLiD System


title: Ovary, OLD_72h_2

description: AB SOLiD System


title: Epithelial PDI + IFNT replicate 1

description:
Library name: Bt Epithelial PDI + IFNT rep 1
R_E_PDI_IFNT_1

value: Epithelial


title: Epithelial PDI + IFNT replicate 2

description:
Library name: Bt Epithelial PDI + IFNT rep 2
R_E_PDI_IFNT_2


title: Ovary, OLD_96h_1

description: AB SOLiD System


title: Patient_20

value: Peripheral blood


title: Patient_18

value: male


title: Patient_16


title: BPAF_1_donor1_R1_P1

description: Library name: s13

value: chemical exposure

tag: donor


title: Epithelial PDI replicate 3

description:
Library name: Bt Epithelial PDI rep 3
R_E_PDI_3


title: Patient_17


title: Ovary, OLD_48h_3

description: AB SOLiD System

value: Ovary

value: 48h after hCG i.p.


title: Patient_14


title: BPAF_5_donor1_R1_P1

description: Library name: s14

tag: batch


title: Ovary, OLD_48h_2

description: AB SOLiD System


title: DMSO_0-1_donor1_R1_P1

description: Library name: s16

value: vehicle control

value: dimethyl sulfoxide


title: Patient_15


title: BPAF_0-5_donor1_R1_P1

description: Library name: s12

value: WT


title: Epithelial PDI replicate 1

description:
Library name: Bt Epithelial PDI rep 1
R_E_PDI_1

value: Endometrium


title: Ovary, OLD_48h_1

description: AB SOLiD System


title: Bt Epithelial IFNT replicate 3

description:
Library name: Bt Epithelial IFNT rep 3
R_E_IFNT_3

value: IFNT


title: Bt Epithelial IFNT replicate 2

description:
Library name: Bt Epithelial IFNT rep 2
R_E_IFNT_2


title: BPAF_0-1_donor1_R1_P1

description: Library name: s11

value: bisphenol AF


title: Ovary, OLD_24h_1

description: AB SOLiD System

value: 24h after hCG i.p.


title: BPAF_0-01_donor1_R1_P1

description: Library name: s10


title: BPAF_0-001_donor1_R1_P1

description: Library name: s9


title: Epitheilal vehicle control replicate 3

description:
Library name: Bt Epithelial vehiclel control rep 3
R_E_Vehicle_control_3


title: Patient_13

value: FALSE


title: Ovary, OLD_24h_2

description: AB SOLiD System


title: Ovary, OLD_24h_3

description: AB SOLiD System


title: Patient_11

value: female


title: Patient_12


title: Epitheilal vehicle control replicate 1

description:
Library name: Bt Epithelial vehiclel control rep 1
R_E_Vehicle_control_1

value: Primary


title: Epitheilal vehicle control replicate 2

description:
Library name: Bt Epithelial vehiclel control rep 2
R_E_Vehicle_control_2


title: Patient_10

value: TRUE


title: Ovary, YNG_96h_3

description: AB SOLiD System

value: 96h after hCG i.p.


title: Ovary, YNG_96h_2

description: AB SOLiD System


title: BPA_50_donor1_R1_P1

description: Library name: s8

value: Mammary

value: Epithelial

value: bisphenol A


title: Bt Epithelial IFNT replicate 1

description:
Library name: Bt Epithelial IFNT rep 1
R_E_IFNT_1


title: BPA_10_donor1_R1_P1

description: Library name: s7

value: chemical exposure


title: Patient_9

value: Peripheral blood

value: male


title: Ovary, YNG_96h_1

description: AB SOLiD System

value: Ovary


title: Patient_8


title: Patient_6


title: BPA_5_donor1_R1_P1

description: Library name: s6

value: WT


title: Ovary, YNG_72h_3

description: AB SOLiD System

value: 72h after hCG i.p.


title: Epithelial control replicate 1

description:
Library name: Bt Epithelial control rep 1
R_E_Control_1

value: Endometrium

value: Control


title: Epithelial control replicate 3

description:
Library name: Bt Epithelial control rep 3
R_E_Control_3


title: Ovary, YNG_72h_1

description: AB SOLiD System


title: NegaP03

city: 杭州

first: shuyang

last: cai

state: 浙江省

address: 西湖区余杭塘路866号浙江大学医学院科研楼A615

institute: zhejiang university

description: GFP+ cells in Tg(fli1a:eGFP) zebrafish embryos at 28 hpf with clec16a MO

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: ftp://ftp.ensembl.org/pub/release-107/fasta/danio_rerio/dna/
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Danio rerio

source_name: 28 hpf embryos

extract_protocol:
SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. A modified oligo(dT) primer (the SMART CDS Primer) primes the first-strand synthesis reaction. When SMARTScribeTM Reverse Transcriptase reaches the 5' end of the mRNA, the enzyme's terminal transferase activity adds a few additional nucleotides to the 3' end of the cDNA. The carefully-designed SMARTer Oligonucleotide base-pairs with the non-template nucleotide stretch, creating an extended template to enable SMARTScribe RT continue replicating to the end of the oligonucleotide. The resulting full-length, single-stranded (ss) cDNA contains the complete 5' end of the mRNA, as well as sequences that are complementary to the SMARTer Oligonucleotide. Amplify sscDNA by LD PCR and get enough dscDNA for library construction.
cDNA was fragmented by dsDNA Fragmentase (NEB, M0348S) by incubate at 37°C for 30min. Library construction begins with fragmented cDNA. Blunt-end DNA fragments are generated using a combination of fill-in reactions and exonuclease activity, and size selection is performed with provided sample purification beads. An A-base is then added to the blunt ends of each strand, indexed Y adapters are ligated to the fragments, and the ligated products are amplified with PCR. And then we performed the paired-end sequencing on an Illumina NovaseqTM 6000 at the (LC Sceiences, USA) following the vendor's recommended protocol.

value: 28 hpf embryos

value: GFP+ cells in Tg(fli1a:eGFP)

value: clec16a MO

value: no culture


title: Epithelial control replicate 2

description:
Library name: Bt Epithelial control rep 2
R_E_Control_2

value: Primary


title: Ovary, YNG_48h_3

description: AB SOLiD System

value: 48h after hCG i.p.


title: Ovary, YNG_72h_2

description: AB SOLiD System


title: Patient_7

value: FALSE

value: TRUE


title: HCT116,Ctrl,rep2

description:
HCT116 cells with Ctrl-2
P18751_2

value: colon

value: control


title: Patient_5

value: Peripheral blood


title: BPA_1_donor1_R1_P1

description: Library name: s5

source_name: Mammary

value: Mammary

value: Epithelial

value: chemical exposure

value: bisphenol A


title: BPA_0-01_donor1_R1_P1

description: Library name: s2

value: WT


title: Ovary, YNG_48h_2

description: AB SOLiD System

value: Ovary


title: Ovary, YNG_48h_1

description: AB SOLiD System


title: PRO-seq_02_BRD4-AID_3hAux

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: Library name: S02

library_source: other

data_processing:
Low-quality bases and adapters from 3’ ends were removed using cutadapt requiring a read length of 16–36 bp. Ribosomal RNA reads were also removed.
The remaining reads were aligned using bowtie 2.2.6 with --very-sensitive option91 to a concatenated genome comprised of human hg38 and fly dm6 assemblies. 5’ ends of aligned reads with MAPQ ≥ 30 were retained and assigned to the opposite strand.
Read counts were normalized to total reads aligned to the spike-in genome for the output of bigwig files.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: PRO-Seq

molecule: other

source_name: DLD-1 BDR4-AID

growth_protocol: All cell lines were cultured in DMEM (Corning, #10013CV), supplemented with 10% FBS (Sigma-Aldrich, #F2442), 1% Glutmax (Gibco, #35050061), and 1% PS (Gibco, #15140122), in 37°C incubator with 5% CO2.

extract_protocol:
Briefly, DLD-1 cell nuclei (10 million for BRD4 depletion and 1 million for dBET6 treatment) were mixed with Drosophila S2 spike-in nuclei, which were then used for the nuclear run-on assay.
Libraries were synthesized using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, E7760L). Libraries were sequenced on Illumina NextSeq 500 or NovaSeq 6000.

value: DLD-1 BDR4-AID

value: epithelial


title: NegaP02

address: 西湖区余杭塘路866号浙江大学医学院科研楼A615

value: 28 hpf embryos

value: GFP+ cells in Tg(fli1a:eGFP)

value: clec16a MO


title: Ovary, YNG_24h_3

description: AB SOLiD System

value: 24h after hCG i.p.


title: BPA_0-5_donor1_R1_P1

description: Library name: s4

value: Primary


title: Exp2D2

address: 西湖区余杭塘路866号浙江大学医学院科研楼A615

description: GFP+ cells in Tg(fli1a:eGFP) zebrafish embryos at 28 hpf with control MO

value: control MO

value: no culture


title: Patient_4

address: 661 University Avenue

value: male

value: FALSE


title: Patient_3

value: Peripheral blood

value: TRUE


title: Ovary, YNG_24h_2

description: AB SOLiD System


title: NegaP01

address: 西湖区余杭塘路866号浙江大学医学院科研楼A615


title: BPA_0-001_donor1_R1_P1

description: Library name: s1

value: Mammary

value: Epithelial

value: chemical exposure


title: Exp2D1

address: 西湖区余杭塘路866号浙江大学医学院科研楼A615


title: Patient_2

value: female


title: Exp2D3

address: 西湖区余杭塘路866号浙江大学医学院科研楼A615


title: Patient_1


title: Ovary, YNG_24h_1

description: AB SOLiD System

value: Ovary


title: KO_ZT22b

status: Public on Jan 05 2026

city: Lübeck

first: Leonardo

last: de Assis

address: Marie Curie

country: Germany

institute: University of Lübeck

hyb_protocol: Genome-wide expression analyses utilized Clariom S arrays (Thermo Fisher Scientific) with 100 ng RNA per sample, as per the manufacturer’s recommendations (WT Plus Kit, Thermo Fisher).

scan_protocol: Affymetrix

data_processing: Data analysis was conducted with Transcriptome Analyses Console (Thermo Fisher, version 4.0) with results expressed in log2 values. Microarray data from wild-type mice were obtained from a previous publication (GSE199998). Gene expression data were processed by averaging repeated probes, and lowly expressed genes were filtered out using a log2 expression threshold of less than 3.8, corresponding to the 25th percentile. Only gene names associated with ENSEMBL codes were included in the analysis. After removing duplicates, a total of 14,456 genes were retained for further analysis.

source_name: liver

extract_protocol: Total RNA was extracted following the manufacturer’s instructions using TRIzol (Thermo Fisher, USA).

treatment_protocol: Three- to eight-month-old male ADQ-WT and ADQ-KO mice were group-housed under a 12-hour light, 12-hour dark (LD, ~300 lux in the light phase) cycle at 22 ± 2 °C and a relative humidity of 60 ± 5 % with ad libitum access to standard chow and water. Mice were culled by cervical dislocation at 4-hour intervals, tissues were kept on dry ice and stored at −80 °C.

value: liver

value: Adiponectin global KO

tag: timepoint


title: PRO-seq_01_BRD4-AID_0hAux

description: Library name: S01

source_name: colon

value: colon

value: DLD-1 BDR4-AID

value: epithelial

value: NT


title: BPA_0-1_donor1_R1_P1

description: Library name: s3

value: Primary

value: WT

value: bisphenol A


title: KO_ZT22d

label_protocol: Genome-wide expression analyses utilized Clariom S arrays (Thermo Fisher Scientific) with 100 ng RNA per sample, as per the manufacturer’s recommendations (WT Plus Kit, Thermo Fisher).


title: KO_ZT22a


title: KO_ZT14b


title: KO_ZT10c


title: KO_ZT14d


title: KO_ZT18c


title: KO_ZT18b


title: KO_ZT22c


title: KO_ZT18a


title: KO_ZT6b


title: KO_ZT14c


title: KO_ZT10a


title: KO_ZT6c


title: KO_ZT10d


title: KO_ZT10b