title: BEKO low density, replicate 2

description:
Library name: Sample 3
Column name in BEKO_RNA_tpm.txt: TPM_3

value: WT


title: RNAseq TCPS_16-1_S3

status: Public on Jul 14 2026

type: SRA

city: Manchester

first: Carlos

last: Lopez Garcia

state: Greater Manchester

address: Paterson Building, Wilmslow Rd

department: TLCB

country: United Kingdom

institute: CRUK-MI

description: Library name: CLG7_03_TCPS_16-1_S3

library_source: transcriptomic

data_processing:
Data were aligned to both GRCh38 and GRCm38 independently using STAR-aligner (RNA; version 2.5.1b) or B37 and mm10 with BWA (DNA; version 0.7.17).
Xenofilter (version 1.6) was used to split data from human and mouse aligned data.
RNA counts quantified using FeatureCounts (rsubread version 2.8.2)
Somatic mutations extracted from WES using Mutect2 (GATK version 4.40) -- comparing tumour to parental (PI) samples.
Assembly: GRCh38/B37
Supplementary files format and content: i) Gene counts for all samples used within comparisons [including those from PMID: 40185723].
Supplementary files format and content: ii) Sample annotations defining metadata and sequencing run origin.

molecule: polyA RNA

organism: Homo sapiens

source_name: Lung

extract_protocol:
PDX mice were generated as described within methods.
RNA-seq libraries perared using Quant-seq protocol (Lexogen); WES libraries were preares using Twits exome 2.0 protocol.

tag: tissue

value: Lung

tag: cell line

value: Bronchial epithelial cells

tag: cell type

value: Xenograft

tag: genotype

value: TC+PS


title: LAbrini_CO_B3

city: Tartu

first: Kaspar

last: Valgepea

state: Tartumaa

address: Nooruse 1

department: Institute of Bioengineering

country: Estonia

institute: University of Tartu

description: Library name: Sample 3

data_processing:
The quality of NextSeq raw reads was verified using MultiQC (Ewels et al., 2016) and adapter sequences were trimmed using the Cutadapt package (version 2.10; Martin 2011)
Sequencing reads were aligned and mapped to the genome of C. autoethanogenum LAbrini (GenBank CP110420.1) using the Rsubread package (version 2.4.2; Liao et al., 2019).
Genomic features were assigned using the featureCounts functions within Rsubread
Raw library sizes were normalized and transcript abundances in reads per kilobase of transcript per million mapped reads (RPKM) were estimated from feature counts and gene lengths using edgeR (version 3.32.1; Robison et al., 2010).
Assembly: CP110420.1
Supplementary files format and content: RPKM value tab-delimited text files

molecule: total RNA

organism: Clostridium autoethanogenum

source_name: bacterial

growth_protocol: Clostridium autoethanogenum strains were grown on syngas or CO in chemically defined medium anaerobically at 37C and a pH of 5 in chemostats at dilution rate ~1 day-1

extract_protocol:
Frozen pellets were thawed and total RNA was extracted using cellular lysis in RNase-free acid-washed glass beads (Merck) and RNeasy mini kit (Qiagen) with off-column DNase treatment followed by enrichment and purification using RNA Clean & ConcentratorTM (Zymo Research). Ribosomal RNA was removed with QIAseq® FastSelect™ Kit (335925; Qiagen).
Stranded mRNA libraries were prepared with QIAseq® Stranded RNA Lib Kit (180743; Qiagen). Constructed mRNA libraries were prepared for sequencing using the NextSeq 2000 P1 300 cycles sequencing kit (Illumina).

treatment_protocol: Culture was pelleted by rapid centrifugation (5,000 × g for 3 min at 4C) followed by resuspension in 5 mL of RNAlater (Qiagen). Samples were stored at 4C overnight, centrifuged (4000 × g for 10 min at 4C) and the pellets stored at -80C.

value: bacterial

tag: sample group


title: LS8 cells, Control, H3K27Ac (ChIP)

city: Davie

first: Maiko

last: Suzuki

state: Florida

address: 3300 S. University Drive

department: College of Dental Medicine

country: USA

institute: Nova Southeastern University

description: Library name: AcH3K27_C_S1_R1.fastq

library_source: genomic

data_processing:
Sequencing was performed on the Nextseq500 (Illumina) using the High Output v2.5 kit, with a 75-cycle single-read protocol.
BCL files generated via the Nextseq500 were converted to FASTQ files for the downstream analysis. The FASTQ files had quality scores above 35 on a scale of 1 to 40, with 20 to 30 million reads obtained per sample.
Assembly: mm9
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Mus musculus

source_name: Cell line

extract_protocol:
Cells were fixed with 1% formaldehyde for the crosslinking was stopped by adding glycine. Cells were subsequently lysed, and the isolated chromatin was sheared in the kit-provided lysis buffer via sonication (30 s ON, 30 s OFF, 30 cycles) using a Bioruptor®® Pico (Diagenode).
ChIP-seq librarieswere prepared using the TruSeq ChIP Library PreparationKit (Illumina, San Diego, CA, USA). The prepared library was examined via a bioanalyzer and Qubit (Thermo Fisher Scientific) to test library quality and quantity, respectively.

value: Cell line

value: Mouse ameloblast-like cells

tag: treatment


title: BEKO low density, replicate 1

city: Stockholm

first: Taras

last: Kreslavsky

address: Karolinska University Hospital L8:03, Visionsgatan 18

country: Sweden

institute: Karolinska Institutet

description:
Library name: Sample 1
Column name in BEKO_RNA_tpm.txt: TPM_1

data_processing:
Analysis was performed as described previously (Glaros et al, 2021).  The data sets were analyzed using the R package DESeq2 version 1.2.10 (Love et al, 2014). Sample normalizations and dispersion estimations were conducted using the default DESeq2 settings. Transcripts per million (TPM) were calculated from RNA-seq data, as described (Wagner et al, 2012).
Assembly: MM9
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

source_name: BEKO

extract_protocol:
RNA was isolated using ZYMO Quick-RNA Microprep Kit.
Eukaryotic Strand-Specific Transcriptome Library was constructed by Novogene.

value: BEKO

value: thymic lymphoma cells


title: BEKO high density, replicate 1

description:
Library name: Sample 2
Column name in BEKO_RNA_tpm.txt: TPM_2


title: LAbrini_CO_B2

description: Library name: Sample 2


title: CN_HSF1_Input

city: Dallas

first: Lahiri

last: Konada

state: TX

address: 5225 Fleetwood Oaks Ave, Apt 527

department: Pshychiatry

institute: UTSW Medical center

data_processing:
Raw FASTQ sequencing reads were analyzed for quality control using FastQC, trimmed using Trimmomatic, and aligned to the mm10 reference genome (GRCm38.p6 assembly) using BWA-MEM.
BAM files were marked and filtered for duplicate reads using Sambamba and Samtools, respectively.
Peaks were called using MACS2 from biological duplicates and pseudo-replicates where each ChIP sample was normalized to single control input DNA.
MACS2-generated bedGraph files were converted to bigWig files using Kent Utils for individual replicates and pooled replicates
IDR (irreproducible discovery rate thresholding was performed on MACS2 peak calls using an IDR threshold of 0.05.
Assembly: mm10
Supplementary files format and content: BED - IDR thresholded peaks
Supplementary files format and content: Bigwig - signal tracks

source_name: Brain

growth_protocol: Dissociated cortical neurons from E16 Swiss-Webster mice (Charles River) were plated at a density of 5 million cells/plate in 10 cm plates. The plates were pre-coated with poly-D-lysine (0.5 mg/ml) overnight at 37°C, followed by washing twice with dH2O. Neurons were maintained in neurobasal media (GIBCO) supplemented with L-glutamine, penicillin/streptomycin, and B27. N-Methyl-D-Aspartc acid(NMDA, 50µM, Sigma E1383) was dissolved in water. Cells were treated with NMDA for 10 minutes followed by 20 min recoery prior to collection

extract_protocol:
HSF1 ChIP was performed for two biological replicates using a ChIP assay kit (MilliporeSigma) as described by the manufacturer. Briefly, DIV13 primary cortical neurons (~15M cells per replicate) were crosslinked with 1% formaldehyde for 10 minutes at 37°C, washed twice with ice-cold PBS, scraped, and resuspended in SDS lysis buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS, protease and phosphatase inhibitor cocktail). Cells were sonicated to shear DNA to 200-500 bp using a bioruptor (Diagenode; high power, 30 seconds on/30 seconds off for 40 cycles). Samples were then centrifuged at 13,000 RPM for 10 minutes at 4°C to remove cellular debris, and the supernatant was diluted up to 2 mL in ChIP dilution buffer (16.7 mM Tris-HCl pH 8, 167 mM NaCl, 1.2 mM EDTA, 1.1% Triton X-100, 0.01% SDS). Prior to immunoprecipitation, 1% of each sample transferred to a clean tube to be used for input normalization. Samples were then incubated with anti-HSF1 antibody (1:200, CST, #12972S) overnight at 4°C followed by incubation with ChIP-grade protein A/G magnetic beads (Thermo) for 3 hours at 4°C. Antibody-conjugated beads were washed with low salt buffer (20 mM Tris-HCl pH 8, 1% Triton-X-100, 2 mM EDTA, 0.1% SDS, 150 mM NaCl), high salt buffer (20 mM Tris-HCl pH 8, 1% Triton-X-100, 2 mM EDTA, 0.1% SDS, 500 mM NaCl), LiCl buffer (10 mM Tris-HCl pH 8, 1% IGEPAL-CA630, 1% deoxycholic acid (sodium salt), 1 mM EDTA, 0.25 M LiCl), and twice with TE buffer (50 mM Tris-HCl pH 8, 1 mM EDTA) for 5 minutes each with agitation at room temperature. Immunoprecipitated HSF1-DNA complexes were eluted from the magnetic beads in 500 µl ChIP elution buffer (1% SDS, 0.1 M NaHCO3). DNA-protein crosslinks for immunoprecipitated samples and input DNA were reversed via incubation with an additional 20 mM NaCl for 4 hours at 37°C and residual protein was digested with Proteinase K (NEB) for 1 hour at 45°C. DNA was precipitated using phenol/chloroform isolation and ethanol precipitation, washed with 70% ethanol, and resuspended in 50 µl TE buffer.
Samples were prepared for sequencing using a paired-end library preparation kit compatible with Illumina sequencing instruments (KAPA biosciences) according to the manufacturer’s instructions. Following library amplification, DNA fragment size was assessed via Tapestation (Agilent) to ensure a final library size of 350-450 bp. DNA concentration was quantified by fluorometry (dsDNA high sensitivity Qubit assay, Thermo) to ensure equal DNA concentration for each replicate before replicates were pooled and sequenced on an Illumina NextSeq 500 instrument using V2.5 reagents to an average depth of 25-35 million reads per replicate.

treatment_protocol: DIV13 primary cortical neurons were bath stimulated with 50 micromolar NMDA for 10 minutes followed by washout and recovery in drug-free media for 20 minutes prior to collection

value: Brain

value: Primary

value: Mouse cortical neurons


title: CN_HSF1_NMDA_ChIP_2

value: NMDA


title: RNAseq TCKS_ALI_S1

description: Library name: CLG7_01_TCKS_ALI_S1

value: ALI

value: TC+KS


title: RNAseq TCK_7-2_S2

description: Library name: CLG7_02_TCK_7-2_S2

value: TC+K


title: CN_HSF1_NMDA_ChIP_1

value: WT


title: Lung primary fibroblasts, WT, male 3

city: Rochester

first: Francesco

last: Morandini

state: NY

address: 402 Hutchison Hall

institute: University of Rochester

data_processing:
Trimming: TrimGalore!
Alignment: STAR --outFilterMultimapNmax 100 --winAnchorMultimapNmax 200 --outFilterMismatchNoverLmax 0.04
Counting: TEcounts
Assembly: GRCm39
Supplementary files format and content: TEcounts .cntTable

source_name: lung primary fibroblasts

growth_protocol: All cell lines were grown in humidified incubators at 5% CO2 and 5% O2 at 37 degrees Celsius. Primary lung cells were cultured in Dulbecco’s modified Eagle’s medium nutrient mixture F12 with 15% FBS and 1X antibiotic-antimycotic. Cell lines are regularly tested for mycoplasma contamination.

extract_protocol:
RNA was purified from pulverized tissue utilizing RNA PureLink Mini Kit (Thermo).
Ribodepletion

value: lung primary fibroblasts

tag: Sex

value: male


title: Human esophageal squamous cell carcinoma cells (KEAP1null-KYSE450), replicate 3

city: Camden

first: Xiaoxin

middle: Luke

last: Chen

state: NJ

address: 403 Haddon Avenue

institute: Coriell Institute for Medical Research

description: Library name: Sample 6

data_processing:
The data quality was assessed with FastQC (version 0.11.5), low-quality reads were removed, and remaining adapter sequences were hard clipped with cutadapt (version 1.12) whenever applicable. The quality filtered reads were aligned with STAR (version 2.6.90c) to human reference genome (hg38) with its respective RefSeq annotation, at last, the expression levels of genes were obtained with FeatureCounts (version 1.5.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text files for each Sample

growth_protocol: The cells were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum, 50 U/ml penicillin, and 50 µg/ml streptomycin at 37°C in 5% CO2/95% air.

extract_protocol:
Total RNA was extracted from human esophageal squamous cell carcinoma cells (KYSE450 and KEAP1null-KYSE450) using RNeasy Kit (Qiagen; Valencia, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

value: no


title: LAbrini_CO_B1

description: Library name: Sample 1


title: wt_11_biol_rep_3

city: Paris

first: Pedro Pablo

last: HERNANDEZ CERDA

address: 11-13 rue Pierre et Marie Curie, BDD building

country: France

institute: Institut Curie

description: Library name: D1752T58

data_processing:
Institut Curie - Nextflow raw-qc analysis pipeline
Assembly: danRer11
Supplementary files format and content: A csv file containing raw read counts, with each column representing a sample

organism: Danio rerio

source_name: Gut

extract_protocol:
10-15 guts per replicate were dissected and RNA was extracted using the Single Cell RNA Purification Kit (Norgen, #51800) following the manufacturer’s instructions. RNA integrity and concentration were analyzed on the Agilent 4200 Tapestation system using the High Sensitivity RNA ScreenTape Analysis kit (Agilent, #5067-5579). cDNA quality was checked on the Agilent 2100 Bioanalyzer using the Agilent High Sensitivity DNA Kit (Agilent #5067-4626). After quality control, libraries were sequenced with 100-bp paired-end (PE100) reads on the NovaSeq 6000 (Illumina) sequencer. Raw data were checked for quality using FastQC (v0.11.8) and aligned to the reference genome for Danio rerio danRer11 from the Genome Reference Consortium.
RNA sequencing libraries were prepared from 500 ng to 1 μg of total RNA using the Illumina TruSeq Stranded mRNA Library Preparation Kit

value: Gut

value: wt


title: Lung primary fibroblasts, WT, male 2


title: Human esophageal squamous cell carcinoma cells (KEAP1null-KYSE450), replicate 2

description: Library name: Sample 5


title: wt_10_biol_rep_2

description: Library name: D1752T57


title: Lung primary fibroblasts, WT, male 1


title: CN_HSF1_CON_ChIP_2


title: Human esophageal squamous cell carcinoma cells (KEAP1null-KYSE450), replicate 1

description: Library name: Sample 4


title: Lung primary fibroblasts, WT, female 2

value: female


title: CN_HSF1_CON_ChIP_1


title: Human esophageal squamous cell carcinoma cells (KYSE450), replicate 3

description: Library name: Sample 3


title: RNA-seq_in_Control WT_3

first: Ram

last: Madabhushi

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

data_processing:
Raw FASTQ files were analyzed using FastQC (v0.11.2) and FastQ Screen (v0.4.4) Reads were quality-trimmed using fastq-mcf (ea-utils/1.1.2-806) The trimmed reads were mapped to the mm10 assembly (University of California at Santa Cruz, version from iGenomes) using STAR (v2.5.3a) The RNA counts generated from FeatureCounts (subread v1.4.6) and were TMM normalized.
Assembly: mm10

source_name: Mouse Cortical Neurons

extract_protocol:
QIAgen Rneasy
RNA HyperPrep kit (KAPA biosystems)

value: Mouse Cortical Neurons

value: CON


title: Lung primary fibroblasts, WT, female 1


title: wt_3_biol_rep_1

description: Library name: D1752T56


title: Human esophageal squamous cell carcinoma cells (KYSE450), replicate 2

description: Library name: Sample 2


title: cut_wt_11_biol_rep_3

description: Library name: D1752T55


title: RNA-seq_in_Control WT_2


title: cut_wt_10_biol_rep_2

description: Library name: D1752T54


title: Lung primary fibroblasts, cGAS KO, male 3

value: cGAS KO


title: RNA-seq_in_Control WT_1


title: cut_wt__biol_rep_1

description: Library name: D1752T53


title: Human esophageal squamous cell carcinoma cells (KYSE450), replicate 1

description: Library name: Sample 1


title: Lung primary fibroblasts, cGAS KO, male 2


title: CN,TOP2Bcc-seq_Input_sample_2

data_processing:
Raw FASTQ sequencing reads were analyzed for quality control using FastQC, trimmed using Trimmomatic, and aligned to the mm10 reference genome (GRCm38.p6 assembly) using BWA-MEM.
BAM files were marked and filtered for duplicate reads using Sambamba and Samtools, respectively.
MACS2-generated bedGraph files were converted to bigWig files using Kent Utils for individual replicates and pooled replicates
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

growth_protocol: Dissociated cortical neurons from E16 Swiss-Webster mice (Charles River) were plated at a density of 5 million cells/plate in 10 cm plates. The plates were pre-coated with poly-D-lysine (0.5 mg/ml) overnight at 37°C, followed by washing twice with dH2O. Neurons were maintained in neurobasal media (GIBCO) supplemented with L-glutamine, penicillin/streptomycin, and B27. Etoposide (ETP, 50µM, Sigma E1383) was dissolved in DMSO. Cells were treated by adding drug directly to the culture media 30 minutes prior to collection

extract_protocol:
TOP2Bccs were isolated from sonicated lysates containing covalently bound proteins via native TOP2B ChIP. Prior to immunoprecipitation, 1% of each sample transferred to a clean tube to be used for input normalization. Samples were then incubated with anti-TOP2B antibody (1:50, H-8, sc-25330, RRID:AB_628384) overnight at 4°C followed by incubation with ChIP-grade protein A/G magnetic beads (Thermo) for 3 hours at 4°C. Antibody-conjugated beads were washed with low salt buffer (20 mM Tris-HCl pH 8, 1% Triton-X-100, 2 mM EDTA, 0.1% SDS, 150 mM NaCl), high salt buffer (20 mM Tris-HCl pH 8, 1% Triton-X-100, 2 mM EDTA, 0.1% SDS, 500 mM NaCl), LiCl buffer (10 mM Tris-HCl pH 8, 1% IGEPAL-CA630, 1% deoxycholic acid (sodium salt), 1 mM EDTA, 0.25 M LiCl), and twice with TE buffer (50 mM Tris-HCl pH 8, 1 mM EDTA) for 5 minutes each with agitation at room temperature. Immunoprecipitated TOP2B-DNA complexes were eluted from the magnetic beads in 500 µl ChIP elution buffer (1% SDS, 0.1 M NaHCO3) and purified along with input DNA via phenol-chloroform extraction and ethanol precipitation. Precipitated DNA was washed with 70% ethanol and resuspended in TE buffer.
To prepare libraries for sequencing, immunoprecipitated DNA was first end-repaired, A-tailed, and ligated with paired-end, Illumina barcoded adapters (KAPA biosciences) according to the manufacturer’s instructions. Attempts to amplify libraries for sequencing after this step alone proved unsuccessful, implying the successful isolation of TOP2Bccs. Following the first round of adapter ligation, the 5’strand was digested with l exonuclease (NEB). The resulting 3’strand was used as a temple for 10 rounds of primer extension (cycling conditions: 95°C for 3 min, ten rounds of linear amplification (95°C for 1 min, 57°C for 1 min and 72 °C for 3 min), 95°C for 1 min, hold at 4°C) using primers against the ligated adapter in a solution containing 1X HiFi Phusion buffer (NEB), 0.8 mM dNTPs, 2 U Phusion DNA polymerase (NEB) and 40 nM of P7 extension primer (CAAGCAGAAGACGGCATACGA*G; *denotes phosphorothioate linkage). The resulting single-stranded products were purified using 0.8X Ampure XP beads (Beckman), eluted in 35 µl TE dH2O, and concentrated to a volume of 18 µl using a vacuum centrifuge (Eppendorf). The purified products were appended with ribo-G in 1X terminal deoxynucleotidyl transferase buffer (NEB), 20 U terminal deoxynucleotidyl transferase enzyme (NEB), and 4 mM of rGTP at 37 °C for 15 min followed by 0.8X Ampure XP bead clean-up and elution as before. The single-stranded, ribo-tailed products were ligated to double-stranded adapters with CCC overhang (oligo 1, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTCCC; oligo 2, (Phosphate)GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG) as described previously2. Ligated products were used as templates for standard paired-end library amplification (KAPA biosciences) with an additional extension step prior to linear amplification to create double-stranded DNA templates (cycling conditions: 60°C for 3 min, 98°C for 30 sec, eleven cycles of amplification (98°C for 10 s, 65°C for 30 s, and 60°C for 30 s), 60°C for 5 min and hold at 4°C). The final PCR products were purified using 0.8X Ampure XP beads, eluted in 40 µl EB (Qiagen). DNA fragment size was assessed via Tapestation (Agilent) and additional Ampure XP bead clean-up steps were performed to obtain a final library size of 350-450 bp. DNA concentration was quantified by fluorometry (dsDNA high sensitivity Qubit assay, Thermo) to ensure equal DNA concentration for each replicate before replicates were pooled and sequenced on an Illumina NextSeq 500 instrument using V2.5 reagents to an average depth of 25-35 million reads per replicate.

treatment_protocol: Etoposide (ETP, 50µM, Sigma E1383) for 30 mins

value: Etoposide (ETP, 50microM) for 30 mins


title: Female Normoxia Control Nx12

city: LONDON

first: CHIEN-NIEN

last: CHEN

address: Du Cane Road

department: National Heart and Lung Institute

institute: Imperial College London

description: Library name: FG24014_36

data_processing:
Raw paired-end 150 bp FASTQ files (Illumina PE150, ~10 million reads, ~3 Gb per sample) were processed by the sequencing facility to generate gene-level read count matrices in TSV format. Differential expression analysis was performed using the DESeq2 R package (version 1.24.0). Counts were internally normalized using DESeq2’s median-of-ratios method for statistical analysis and PCA.
Assembly: Rattus norvegicus GCA_000002265.1 Rn_Celera (Sprague Dawley)
Supplementary files format and content: Raw counts for each sample are provided in the submitted processed data.

organism: Rattus norvegicus

growth_protocol: A humanized Slc39a12 knock-in rat (huSlc39a12) was developed on the Sprague Dawley background using CRISPR-Cas9 technology (Horizon Discovery), such that the rat gene was replaced by the human form to enable evaluation of the therapeutic efficacy of humanised anti-ZIP12 antibodies

extract_protocol:
RNA was harvested using Qiagen miRNeasy mini
RNA libraries were for RNA-seq were prepared using Illumina RNA-seq libraries (150-750 bp inserts), including TapeStation QC.

treatment_protocol: Adult age-matched male and female rats (body weight 200-240 g) were randomly allocated to groups. Rats of hhe ypoxtic groups were exposed to normobaric FiO2 = 10% for two weeks. ZIP12 antibodies APL-9796/IgG control 10 mg/kg, i.p, were given with first dose started 48 hours before exposure to hypoxia and then administered every 3 days during hypoxia exposure for 2 weeks until the end-point hemodynamic measurements and tissue collection.

value: Lung

value: Female


title: Human esophageal squamous cell carcinoma cells (NRF2null-KYSE70), replicate 3

description: Library name: Sample 6

extract_protocol:
Total RNA was extracted from human esophageal squamous cell carcinoma cells (KYSE70 and NRF2null-KYSE70) using RNeasy Kit (Qiagen; Valencia, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: CN,TOP2Bcc-seq_Input_sample_1


title: Lung primary fibroblasts, cGAS KO, male 1


title: Lung primary fibroblasts, cGAS KO, female 3


title: Human esophageal squamous cell carcinoma cells (NRF2null-KYSE70), replicate 2

description: Library name: Sample 5


title: CN,TOP2Bcc-seq_ChIP-seq_2


title: Female Normoxia Control Nx11

description: Library name: FG24014_35


title: Female Normoxia Control Nx10

description: Library name: FG24014_34


title: Human esophageal squamous cell carcinoma cells (NRF2null-KYSE70), replicate 1

description: Library name: Sample 4


title: Lung primary fibroblasts, cGAS KO, female 2


title: CN,TOP2Bcc-seq_ChIP-seq_1


title: Human esophageal squamous cell carcinoma cells (KYSE70), replicate 3

description: Library name: Sample 3


title: Female Normoxia Control Nx9

description: Library name: FG24014_33


title: Lung primary fibroblasts, cGAS KO, female 1


title: fastGRO-seq_30_mins_DRB

data_processing:
Read alignment and all subsequent analysis requiring chromosome length files were done using GRCm38.p6 assembly (mm10) reference genome. For GRO-seq data, raw fastq data files of paired-end reads were collected for analysis. The generated fastq files were analyzed for QC using FastQC screen and RSeQC, trimmed using Trimmomatic, and aligned to the mm10 reference genome assembly using BWA-ALN (GRO-seq). A dedicated GRO-seq/Pro-seq pipeline was utilized for generating stranded bigWigs from GRO-seq reads (RunOnBamToBigWig). GRO-seq data were generally processed as described previously. Briefly, transcripts were called using HOMER findpeaks (options: -style groseq -tssFold 6 -bodyFold 5 -pseudoCount 0.5 -minBodySize 500 -maxBodySize 100000) Gro-Seq mode and Corresponding FPKM values were calculated using in analyzeRepeats.pl in either RNA mode (analyzeRepeats.pl rna mm10 -count genes -strand both -rpkm -condenseGenes) or HOMER-called de novo transcripts (analyzeRepeats.pl HOMER-transcripts-file.txt mm10 -count genes).  Pausing index was calculated using analyzeRepeats -count pausing option using -50 to +200 bp for promoter reads, and +200 to +5000bp for gene body reads. Genes with gene length less than 1 kb were excluded for this calculation.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: fast_GRO

source_name: Primary Mouse Cortical Neurons

extract_protocol:
Trizol
RNA HyperPrep kit (KAPA biosystems)

value: Primary Mouse Cortical Neurons

value: DRB


title: Human esophageal squamous cell carcinoma cells (KYSE70), replicate 2

description: Library name: Sample 2


title: HFD_siMARC1_S20

city: Riverside

first: Brendan

last: Gongol

state: Ca

address: 900 University Ave

institute: University of California, Riverside

data_processing:
Following DNA sequencing and read mapping to the mouse GRCm39 genome, reads aligning to coding regions were retained and the number of read counts per gene were calculated.
Assembly: GRCm39
Supplementary files format and content: Excel files include FPKM or values for each sample.

source_name: Liver

extract_protocol:
RNA was extracted using QIAzol reagent followed by a chloroform extraction and an additional purification step using RNeasy mini kit with a DNAse digestion (Qiagen).
For each sample, total RNA was normalized to 100 ng before undergoing library preparation using the Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit per the manufacturer’s instructions. Sample integrity and abundance was assessed using the the Agilent Bioanalyzer and Qubit Fluorometer prior to pooling samples. Samples were sequenced on the Illumina Novaseq 6000 using 2x100 cycles, per manufacturer’s instructions.

value: Liver

tag: strain

value: Male

tag: age

value: 20 wk


title: Female Normoxia Control Nx8

description: Library name: FG24014_32


title: Human esophageal squamous cell carcinoma cells (KYSE70), replicate 1

description: Library name: Sample 1


title: fastGRO-seq_30_mins_ETP

value: WT

value: ETP


title: Female Normoxia Control Nx7

description: Library name: FG24014_31


title: HFD_siMARC1_S19


title: fastGRO-seq_30_mins_CPT

value: CPT


title: HEALTHY CTRL 03 PBMC/buffy coat single-cell RNA-seq

city: Gdansk

first: Krzysztof

last: Pastuszak

state: Pomorskie

address: Debinki 1

department: Translational Oncology

country: Poland

institute: Medical University of Gdansk

description:
Library name: No4_CTRL
Cryopreserved buffy coat/PBMC cells from a healthy donor control. Single-cell RNA-seq library prepared using SCOPE-chip micro-well single-cell RNA-seq. Processed matrix files are sample-prefixed and gzip-compressed for GEO upload uniqueness.

library_source: transcriptomic single cell

data_processing:
Sequencing data were demultiplexed and converted to gzip-compressed FASTQ format. This workbook lists the final GEO-facing FASTQ filenames from the staged server manifest. Ovarian and benign 10x samples include R1/R2 read files and I1/I2 index files across three lanes; Singleron breast and healthy samples include one R1/R2 pair per sample.
UMI count matrices were generated using the GRCh38 human reference genome. Per-sample filtered feature-barcode matrices were retained as processed data.
Low-quality cells were filtered before downstream analysis using thresholds described in the associated manuscript, including minimum read and gene counts and maximum mitochondrial RNA fraction.
Downstream analysis was performed in R. Deposited processed files are the per-sample feature-barcode matrices used as the basis for downstream analysis; derived marker scores and plots are not substituted for the count matrices.
Assembly: GRCh38
Supplementary files format and content: Per-sample 10x/Matrix Market feature-barcode matrices. Each sample is represented by one gzip-compressed matrix triplet: barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz, with sample-prefixed filenames for GEO uniqueness.
Supplementary files format and content: Per-sample Cell Ranger filtered feature-barcode matrices in gzip-compressed 10x format: matrix.mtx.gz (Matrix Market sparse UMI count matrix), features.tsv.gz (gene identifiers and symbols), and barcodes.tsv.gz (cell barcodes). One matrix triplet per sample.

source_name: peripheral blood

growth_protocol: Not applicable. Primary human peripheral blood-derived PBMC/buffy coat fractions were analyzed; no cell line culture or in vitro growth protocol was used.

extract_protocol:
Whole blood was collected into EDTA tubes and processed to obtain the PBMC/buffy coat fraction. Cells were cryopreserved and later thawed for single-cell sequencing. For the 10x-processed ovarian cancer and benign gynecological control samples, thawed cells were transferred with wide-bore tips into warm medium containing 10% FBS, centrifuged, resuspended, and assessed for concentration and viability by trypan blue on a Countess 3 FL counter. Samples with acceptable viability were resuspended in 1x PBS with 0.04% BSA before library preparation. Breast cancer and healthy donor samples were processed from cryopreserved PBMC/buffy coat material by Singleron Biotechnologies.
Ovarian cancer and benign gynecological control samples were prepared using the Chromium Next GEM Single Cell 3' Reagent Kit (10x Genomics) following the manufacturer's protocol. Breast cancer and healthy donor samples were prepared using the Singleron GEXSCOPE SCOPE-chip micro-well single-cell RNA-seq system according to the manufacturer's protocol. Libraries were sequenced as paired-end high-throughput sequencing libraries; instrument models are listed in the sample table.

treatment_protocol: No ex vivo treatment was applied. Blood was collected before downstream single-cell processing.

value: peripheral blood

value: PBMC/buffy coat cell fraction

value: no ex vivo treatment; blood collected prior to processing

tag: batch

tag: disease state

value: healthy control

tag: diagnosis

value: healthy donor control

tag: cancer type

value: not applicable

tag: subtype

value: not provided

tag: Stage

tag: grade

tag: library platform

tag: processing site

value: Singleron Biotechnologies, Germany

tag: source fraction

value: PBMC/buffy coat fraction

tag: original sample id

value: HEALTHY CTRL 03


title: HFD_siMARC1_S18

tag: tissue


title: Female Hypoxia APL-9796 10 mg/kg Hz12

description: Library name: FG24014_30

value: Lung

value: Female

tag: genotype


title: fastGRO-seq_CON

tag: cell type

value: Primary Mouse Cortical Neurons

tag: treatment

value: CON


title: HEALTHY CTRL 02 PBMC/buffy coat single-cell RNA-seq

description:
Library name: No3_CTRL
Cryopreserved buffy coat/PBMC cells from a healthy donor control. Single-cell RNA-seq library prepared using SCOPE-chip micro-well single-cell RNA-seq. Processed matrix files are sample-prefixed and gzip-compressed for GEO upload uniqueness.

tag: sample group

value: HEALTHY CTRL 02


title: Female Hypoxia APL-9796 10 mg/kg Hz11

description: Library name: FG24014_29

tag: Sex


title: HFD_siMARC1_S17

value: Liver

tag: strain

value: Male

tag: age

value: 20 wk


title: HEALTHY CTRL 01 PBMC/buffy coat single-cell RNA-seq

description:
Library name: No2_CTRL
Cryopreserved buffy coat/PBMC cells from a healthy donor control. Single-cell RNA-seq library prepared using SCOPE-chip micro-well single-cell RNA-seq. Processed matrix files are sample-prefixed and gzip-compressed for GEO upload uniqueness.

value: peripheral blood

value: PBMC/buffy coat cell fraction

tag: batch

tag: disease state

tag: diagnosis

value: HEALTHY CTRL 01


title: TMP-Seq_+_30_mins_DRB_2

data_processing:
Read alignment and all subsequent analysis requiring chromosome length files were done using GRCm38.p6 assembly (mm10) reference genome. For TMP-Seq, raw fastq data files of paired-end reads were collected for analysis. The generated fastq files were analyzed for QC using FastQC screen and RSeQC, trimmed using Trimmomatic, and aligned to the mm10 reference genome assembly using BWA-MEM (TMP-Seq). All BAM files were normalized to samples in which TMP crosslinking was performed following gDNA isolation from neurons to correct for sequencing bias of TMP incorporation, and converted to bigWigs using MACS2.
Assembly: mm10
Library strategy: TMP-seq

extract_protocol:
Phenol chloroform
KAPA HyperPrep Kit

value: WT

value: DRB


title: Female Hypoxia APL-9796 10 mg/kg Hz10

description: Library name: FG24014_28


title: TMP-Seq_+_30_mins_DRB_1


title: HFD_siMARC1_S16


title: BRCA 10 PBMC/buffy coat single-cell RNA-seq

description:
Library name: BC376_TNBC
Cryopreserved buffy coat/PBMC cells from a patient with triple-negative breast cancer. Single-cell RNA-seq library prepared using SCOPE-chip micro-well single-cell RNA-seq. Processed matrix files are sample-prefixed and gzip-compressed for GEO upload uniqueness.

value: no ex vivo treatment; blood collected prior to processing

value: cancer

value: triple-negative breast cancer

value: breast cancer

tag: cancer type

tag: subtype

value: triple-negative

tag: Stage

value: BRCA 10


title: Female Hypoxia APL-9796 10 mg/kg Hz9

description: Library name: FG24014_27

value: Lung

value: Female


title: HFD_siMARC1_S15


title: BRCA 09 PBMC/buffy coat single-cell RNA-seq

description:
Library name: BC366_TNBC
Cryopreserved buffy coat/PBMC cells from a patient with triple-negative breast cancer. Single-cell RNA-seq library prepared using SCOPE-chip micro-well single-cell RNA-seq. Processed matrix files are sample-prefixed and gzip-compressed for GEO upload uniqueness.

tag: grade

tag: library platform

tag: processing site

value: Singleron Biotechnologies, Germany

value: PBMC/buffy coat fraction

value: BRCA 09


title: HFD_siMARC1_S14

tag: tissue

value: Liver

value: Male

value: 20 wk


title: TMP-Seq_+_30_mins_ETP_1

value: Primary Mouse Cortical Neurons

tag: genotype

value: ETP


title: Female Hypoxia APL-9796 10 mg/kg Hz8

description: Library name: FG24014_26


title: BRCA 08 PBMC/buffy coat single-cell RNA-seq

description:
Library name: BC363_TNBC
Cryopreserved buffy coat/PBMC cells from a patient with triple-negative breast cancer. Single-cell RNA-seq library prepared using SCOPE-chip micro-well single-cell RNA-seq. Processed matrix files are sample-prefixed and gzip-compressed for GEO upload uniqueness.

value: peripheral blood

tag: cell type

value: PBMC/buffy coat cell fraction

tag: source fraction

tag: original sample id

value: BRCA 08


title: Female Hypoxia APL-9796 10 mg/kg Hz7

description: Library name: FG24014_25

tag: Sex

tag: treatment


title: TMP-Seq_+_30_mins_ETP_2

value: WT


title: HFD_siMARC1_S13

tag: strain

tag: age


title: TMP-Seq_+_30_mins_CPT_2

value: CPT


title: Female Hypoxia IgG 10 mg/kg Control Hx12

description: Library name: FG24014_24

value: IgG control antibody


title: HFD_siMARC1_S12


title: BRCA 07 PBMC/buffy coat single-cell RNA-seq

description:
Library name: BC354_TNBC
Cryopreserved buffy coat/PBMC cells from a patient with triple-negative breast cancer. Single-cell RNA-seq library prepared using SCOPE-chip micro-well single-cell RNA-seq. Processed matrix files are sample-prefixed and gzip-compressed for GEO upload uniqueness.

value: no ex vivo treatment; blood collected prior to processing

tag: batch

tag: disease state

value: cancer

value: triple-negative breast cancer

tag: sample group

value: breast cancer

value: triple-negative

value: BRCA 07


title: BRCA 06 PBMC/buffy coat single-cell RNA-seq

description:
Library name: BC344_LumB_Her_plus
Cryopreserved buffy coat/PBMC cells from a patient with Luminal B, HER2-positive breast cancer. Single-cell RNA-seq library prepared using SCOPE-chip micro-well single-cell RNA-seq. Processed matrix files are sample-prefixed and gzip-compressed for GEO upload uniqueness.

tag: diagnosis

value: Luminal B, HER2-positive breast cancer

tag: cancer type

tag: subtype

value: Luminal B, HER2-positive

value: Singleron Biotechnologies, Germany

value: PBMC/buffy coat fraction

value: BRCA 06


title: TMP-Seq_+_30_mins_CPT_1

value: Primary Mouse Cortical Neurons


title: Female Hypoxia IgG 10 mg/kg Control Hx11

description: Library name: FG24014_23

value: Lung

value: Female


title: HFD_siMARC1_S11

value: Liver

value: Male

value: 20 wk


title: TMP-Seq_only_2

value: WT

value: CON


title: TMP-Seq_only_1


title: HFD_PBS_S9


title: Female Hypoxia IgG 10 mg/kg Control Hx10

description: Library name: FG24014_22

value: IgG control antibody


title: Female Hypoxia IgG 10 mg/kg Control Hx9

description: Library name: FG24014_21


title: BRCA 04 PBMC/buffy coat single-cell RNA-seq

description:
Library name: BC340_LumB_Her_plus
Cryopreserved buffy coat/PBMC cells from a patient with Luminal B, HER2-positive breast cancer. Single-cell RNA-seq library prepared using SCOPE-chip micro-well single-cell RNA-seq. Processed matrix files are sample-prefixed and gzip-compressed for GEO upload uniqueness.

value: peripheral blood

value: PBMC/buffy coat cell fraction

value: no ex vivo treatment; blood collected prior to processing

value: cancer

value: breast cancer

tag: Stage

tag: grade

tag: library platform

value: BRCA 04


title: HFD_PBS_S8

tag: tissue


title: BRCA 05 PBMC/buffy coat single-cell RNA-seq

description:
Library name: BC343_TNBC
Cryopreserved buffy coat/PBMC cells from a patient with triple-negative breast cancer. Single-cell RNA-seq library prepared using SCOPE-chip micro-well single-cell RNA-seq. Processed matrix files are sample-prefixed and gzip-compressed for GEO upload uniqueness.

tag: cell type

value: triple-negative breast cancer

value: triple-negative

tag: processing site

value: Singleron Biotechnologies, Germany

value: PBMC/buffy coat fraction

value: BRCA 05


title: TMP-Seq_genomic_DNA_2

value: Primary Mouse Cortical Neurons

tag: genotype

value: gDNA


title: BRCA 03 PBMC/buffy coat single-cell RNA-seq

description:
Library name: BC338_LumB_Her_minus
Cryopreserved buffy coat/PBMC cells from a patient with Luminal B, HER2-negative breast cancer. Single-cell RNA-seq library prepared using SCOPE-chip micro-well single-cell RNA-seq. Processed matrix files are sample-prefixed and gzip-compressed for GEO upload uniqueness.

value: Luminal B, HER2-negative breast cancer

value: Luminal B, HER2-negative

tag: source fraction

tag: original sample id

value: BRCA 03


title: Female Hypoxia IgG 10 mg/kg Control Hx8

description: Library name: FG24014_20

value: Lung

tag: Sex

value: Female

tag: treatment

value: IgG control antibody


title: HFD_PBS_S7

value: Liver

tag: strain

value: Male

tag: age

value: 20 wk


title: TMP-Seq_genomic_DNA_1

value: WT


title: HFD_PBS_S6


title: Female Hypoxia IgG 10 mg/kg Control Hx7

description: Library name: FG24014_19


title: BRCA 02 PBMC/buffy coat single-cell RNA-seq

description:
Library name: BC333_TNBC
Cryopreserved buffy coat/PBMC cells from a patient with triple-negative breast cancer. Single-cell RNA-seq library prepared using SCOPE-chip micro-well single-cell RNA-seq. Processed matrix files are sample-prefixed and gzip-compressed for GEO upload uniqueness.

value: peripheral blood

value: PBMC/buffy coat cell fraction

value: no ex vivo treatment; blood collected prior to processing

tag: batch

tag: disease state

value: cancer

value: triple-negative breast cancer

tag: sample group

value: breast cancer

value: BRCA 02


title: HEK293T_T3-8_RNH2A-KO_siRNA_TOP1 replicate 2

city: Atlanta

first: Francesca

last: Storici

state: GA

address: 950 State Street Nw, Krone Engineering Biosystems Building

department: Biological Sciences

institute: Georgia Institute of Technology

description: Library name: FSR19

data_processing:
Ribose-map for ribose-seq, hisat2 and featurecounts for RNA-seq
Assembly: GrCh38
Supplementary files format and content: bedGraph and TPM matrix

source_name: human embryonic kidney

growth_protocol: standard human cell growth protocol

extract_protocol:
Qiagen DNeasy Blood & Tissue Kit (CAT# 69504) for DNA isolation, RNeasy Mini Kit (QIAGEN, Cat#: 74104) with on-column DNase treatment, MethylCode Bisulfite Conversion Kit (#MECOV50, ThermoFisher) ribose-seq for rNMP capture, WGS with KAPA Hyper Prep library preparation, WGBS with Kapa HiFi Uracil Hotstart polymerase enzyme (#KK2801, KAPA Biosystems, Wilmington, MA), RNA-seq with PolyA Selection & NEBNext Ultra II Directional kit
other

treatment_protocol: ribose-seq for rNMP capture, RNA-seq,

value: human embryonic kidney

tag: cell line

value: RNase H2A KO (T3-8)

value: siRNA TOP1 treatment (5+5pmol dosing)


title: BRCA 01 PBMC/buffy coat single-cell RNA-seq

description:
Library name: BC329_LumB_Her_minus
Cryopreserved buffy coat/PBMC cells from a patient with Luminal B, HER2-negative breast cancer. Single-cell RNA-seq library prepared using SCOPE-chip micro-well single-cell RNA-seq. Processed matrix files are sample-prefixed and gzip-compressed for GEO upload uniqueness.

tag: diagnosis

value: Luminal B, HER2-negative breast cancer

tag: cancer type

tag: subtype

value: Luminal B, HER2-negative

tag: Stage

value: Singleron Biotechnologies, Germany

value: PBMC/buffy coat fraction

value: BRCA 01


title: Male Normoxia Control Nx6

description: Library name: FG24014_18

tag: tissue

value: Lung

value: Male


title: HEK293T_T3-8_RNH2A-KO_siRNA_TOP1 replicate 1

description: Library name: FSR18

tag: cell type


title: HFD_PBS_S5

value: Liver

value: 20 wk


title: HFD_PBS_S4


title: HGSOC 12 PBMC/buffy coat single-cell RNA-seq

description:
Library name: SC9_8AS
Cryopreserved buffy coat/PBMC cells from a patient with high-grade serous ovarian carcinoma. Single-cell RNA-seq library prepared using 10x Genomics Chromium Next GEM Single Cell 3'. Processed matrix files are sample-prefixed for GEO upload uniqueness.

value: peripheral blood

value: PBMC/buffy coat cell fraction

value: no ex vivo treatment; blood collected prior to processing

value: high-grade serous ovarian carcinoma

value: high-grade serous ovarian cancer

value: ovarian cancer

value: IIIB

tag: grade

tag: library platform

tag: processing site

value: Institute of Bioorganic Chemistry PAS, Poznan

value: HGSOC 12; SC_OC_090


title: HEK293T_T3-8_RNH2A-KO_siRNA_NC replicate 2

description: Library name: FSR17

value: human embryonic kidney

tag: genotype

value: RNase H2A KO (T3-8)

value: siRNA negative control (5+5pmol dosing)


title: Male Normoxia Control Nx5

description: Library name: FG24014_17

tag: Sex


title: HGSOC 11 PBMC/buffy coat single-cell RNA-seq

description:
Library name: SC9_7AS
Cryopreserved buffy coat/PBMC cells from a patient with high-grade serous ovarian carcinoma. Single-cell RNA-seq library prepared using 10x Genomics Chromium Next GEM Single Cell 3'. Processed matrix files are sample-prefixed for GEO upload uniqueness.

tag: treatment

value: cancer

value: IIIC

tag: source fraction

value: PBMC/buffy coat fraction

tag: original sample id

value: HGSOC 11; SC_OC_089


title: Male Normoxia Control Nx4

description: Library name: FG24014_16

value: Lung

value: Male


title: HFD_PBS_S3

value: Liver

tag: strain

tag: age

value: 20 wk


title: HEK293T_T3-8_RNH2A-KO_siRNA_NC replicate 1

description: Library name: FSR16

tag: cell line


title: HGSOC 10 PBMC/buffy coat single-cell RNA-seq

description:
Library name: SC9_6AS
Cryopreserved buffy coat/PBMC cells from a patient with high-grade serous ovarian carcinoma. Single-cell RNA-seq library prepared using 10x Genomics Chromium Next GEM Single Cell 3'. Processed matrix files are sample-prefixed for GEO upload uniqueness.

value: peripheral blood

value: PBMC/buffy coat cell fraction

value: no ex vivo treatment; blood collected prior to processing

tag: batch

tag: disease state

tag: diagnosis

value: high-grade serous ovarian carcinoma

tag: sample group

value: HGSOC 10; SC_OC_085


title: HFD_PBS_S2

tag: tissue


title: Male Normoxia Control Nx3

description: Library name: FG24014_15


title: HEK293T-RNH2A-KO-T3-8_siTOP1 replicate 3

description: Library name: FS499

library_source: other

molecule: other

tag: cell type

value: siRNA TOP1 treatment (5+5pmol dosing)


title: HGSOC 09 PBMC/buffy coat single-cell RNA-seq

description:
Library name: SC9_5AS
Cryopreserved buffy coat/PBMC cells from a patient with high-grade serous ovarian carcinoma. Single-cell RNA-seq library prepared using 10x Genomics Chromium Next GEM Single Cell 3'. Processed matrix files are sample-prefixed for GEO upload uniqueness.

value: high-grade serous ovarian cancer

tag: cancer type

value: ovarian cancer

tag: subtype

tag: Stage

tag: grade

value: Institute of Bioorganic Chemistry PAS, Poznan

value: HGSOC 09; SC_OC_075


title: Male Normoxia Control Nx2

description: Library name: FG24014_14

tag: Sex

tag: genotype


title: HFD_PBS_S10


title: Male Normoxia Control Nx1

description: Library name: FG24014_13


title: HGSOC 08 PBMC/buffy coat single-cell RNA-seq

description:
Library name: SC8_4AS
Cryopreserved buffy coat/PBMC cells from a patient with high-grade serous ovarian carcinoma. Single-cell RNA-seq library prepared using 10x Genomics Chromium Next GEM Single Cell 3'. Processed matrix files are sample-prefixed for GEO upload uniqueness.

tag: treatment

value: cancer

value: IIIB

tag: library platform

tag: processing site

tag: source fraction

value: HGSOC 08; SC_OC_072


title: HFD_PBS_S1

tag: strain

tag: age


title: HEK293T-RNH2A-KO-T3-8_siTOP1 replicate 2

description: Library name: FS483

value: human embryonic kidney

tag: cell line

value: RNase H2A KO (T3-8)


title: HEK293T-RNH2A-KO-T3-8_siTOP1 replicate 1

description: Library name: FS482


title: HGSOC 07 PBMC/buffy coat single-cell RNA-seq

description:
Library name: SC8_3AS
Cryopreserved buffy coat/PBMC cells from a patient with high-grade serous ovarian carcinoma. Single-cell RNA-seq library prepared using 10x Genomics Chromium Next GEM Single Cell 3'. Processed matrix files are sample-prefixed for GEO upload uniqueness.

tag: batch

tag: disease state

tag: diagnosis

value: IIIA

value: PBMC/buffy coat fraction

tag: original sample id

value: HGSOC 07; SC_OC_071


title: Chow_Diet_PBS_S45

tag: tissue

value: Liver

value: Male

value: 20 wk


title: Male Hypoxia APL-9796 10 mg/kg Hz6

description: Library name: FG24014_12

value: Lung


title: HEK293T-RNH2A-KO-T3-8_siNC replicate 2

description: Library name: FS498

tag: cell type

value: siRNA negative control (5+5pmol dosing)


title: HGSOC 06 PBMC/buffy coat single-cell RNA-seq

description:
Library name: SC8_2AS
Cryopreserved buffy coat/PBMC cells from a patient with high-grade serous ovarian carcinoma. Single-cell RNA-seq library prepared using 10x Genomics Chromium Next GEM Single Cell 3'. Processed matrix files are sample-prefixed for GEO upload uniqueness.

value: peripheral blood

value: PBMC/buffy coat cell fraction

value: no ex vivo treatment; blood collected prior to processing

value: high-grade serous ovarian carcinoma

tag: sample group

value: high-grade serous ovarian cancer

tag: cancer type

tag: subtype

tag: Stage

value: IIIC

value: HGSOC 06; SC_OC_070


title: Male Hypoxia APL-9796 10 mg/kg Hz5

description: Library name: FG24014_11

tag: Sex

tag: genotype

tag: treatment


title: HEK293T-RNH2A-KO-T3-8_siNC replicate 1

description: Library name: FS481

value: human embryonic kidney


title: HGSOC 05 PBMC/buffy coat single-cell RNA-seq

description:
Library name: SC8_1AS
Cryopreserved buffy coat/PBMC cells from a patient with high-grade serous ovarian carcinoma. Single-cell RNA-seq library prepared using 10x Genomics Chromium Next GEM Single Cell 3'. Processed matrix files are sample-prefixed for GEO upload uniqueness.

value: cancer

value: ovarian cancer

tag: grade

tag: library platform

tag: processing site

value: Institute of Bioorganic Chemistry PAS, Poznan

tag: source fraction

value: HGSOC 05; SC_OC_068


title: Male Hypoxia APL-9796 10 mg/kg Hz4

description: Library name: FG24014_10


title: Chow_Diet_PBS_S43

value: Liver

tag: strain

tag: age


title: Male Hypoxia APL-9796 10 mg/kg Hz3

description: Library name: FG24014_09

value: Male


title: Chow_Diet_PBS_S44

value: 20 wk


title: BENIGN CTRL 04 PBMC/buffy coat single-cell RNA-seq

description:
Library name: SC16_16AS
Cryopreserved buffy coat/PBMC cells from a non-malignant gynecological control donor. Single-cell RNA-seq library prepared using 10x Genomics Chromium Next GEM Single Cell 3'. Processed matrix files are sample-prefixed for GEO upload uniqueness.

tag: batch

tag: disease state

value: non-malignant control

tag: diagnosis

value: benign ovarian lesion / benign gynecological control

value: benign gynecological control

value: not applicable

value: not provided

value: PBMC/buffy coat fraction

value: BENIGN CTRL 04; SC_OC_098


title: Male Hypoxia APL-9796 10 mg/kg Hz2

description: Library name: FG24014_08

tag: tissue

value: Lung


title: Chow_Diet_PBS_S42


title: Chow_Diet_PBS_S41


title: HGSOC 04 PBMC/buffy coat single-cell RNA-seq

description:
Library name: SC16_15AS
Cryopreserved buffy coat/PBMC cells from a patient with high-grade serous ovarian carcinoma. Single-cell RNA-seq library prepared using 10x Genomics Chromium Next GEM Single Cell 3'. Processed matrix files are sample-prefixed for GEO upload uniqueness.

value: peripheral blood

tag: cell type

value: PBMC/buffy coat cell fraction

value: no ex vivo treatment; blood collected prior to processing

value: high-grade serous ovarian carcinoma

tag: sample group

value: high-grade serous ovarian cancer

value: IIA

tag: original sample id

value: HGSOC 04; SC_OC_097


title: ribose-seq of HEK293T RNase H2 KO (T3-17) genomic DNA with dsF fragmentation, replicate 2

description:
Library name: FS393
To construct ribose-seq libraries with human cell lines, genomic DNA samples were fragmented using NEBNext dsDNA Fragmentase or a combination of restriction enzymes to generate small DNA fragments. Various sets of restriction enzymes were applied to fragment human genomic DNA samples, as indicated in table S1. The used combinations were (i) RE1: [HpyCH4V] + [Hpy116II, Eco53KI, RsaI and StuI]; (ii) RE2: [AleI, AluI and PvuII] + [DraI, HaeIII and SspI]; (iii) RE3: [CviKl-1] + [Mly, MscI and MslI].After fragmentation with restriction enzymes or NEBNext dsDNA Fragmentase, DNA was purified (QIAquick Kit). For Fragmentase-treated samples, NEBNext End Repair Module created blunt ends. Fragments underwent dA-tailing using Klenow Fragment (35 exo-), followed by adapter ligation (T4 DNA ligase, 16C/overnight) and purification. Adapter-ligated DNA was treated with 0.3 M NaOH (55C/2h) to denature strands and cleave rNMP sites, then neutralized (HCl) and purified.ssDNA fragments were circularized using Arabidopsis tRNA ligase, linear DNA removed with T5 Exonuclease, and 2-phosphates eliminated via Tpt1 treatment. Two PCR rounds (6 + 11 cycles) with Q5 polymerase added Illumina indexes, followed by size selection (250700 bp) and normalization. Libraries were sequenced on Illumina NextSeq 500/HiSeq X Ten platforms

data_processing:
Ribose-map for ribose-seq, bowtie2 and featurecounts for RNA-seq, bismark for WGBS, bowtie2 for DNA-seq
Assembly: GrCh38
Supplementary files format and content: bigWig, bedGraph,counts and TPM matrix

extract_protocol:
Qiagen DNeasy Blood & Tissue Kit (CAT# 69504) for DNA isolation, RNeasy Mini Kit (QIAGEN, Cat#: 74104) with on-column DNase treatment, MethylCode Bisulfite Conversion Kit (#MECOV50, ThermoFisher)
ribose-seq for rNMP capture, WGS with KAPA Hyper Prep library preparation,  WGBS with Kapa HiFi Uracil Hotstart polymerase enzyme (#KK2801, KAPA Biosystems, Wilmington, MA), RNA-seq with PolyA Selection & NEBNext Ultra II Directional kit

treatment_protocol: ribose-seq for rNMP capture, RNA-seq, bisulfite-seq and whole genome DNA-seq

value: human embryonic kidney

tag: cell line

value: RNase H2A KO (T3-17)


title: ribose-seq of HEK293T RNase H2 KO (T3-8) genomic DNA with dsF fragmentation, replicate 2

description:
Library name: FS392
To construct ribose-seq libraries with human cell lines, genomic DNA samples were fragmented using NEBNext dsDNA Fragmentase or a combination of restriction enzymes to generate small DNA fragments. Various sets of restriction enzymes were applied to fragment human genomic DNA samples, as indicated in table S1. The used combinations were (i) RE1: [HpyCH4V] + [Hpy116II, Eco53KI, RsaI and StuI]; (ii) RE2: [AleI, AluI and PvuII] + [DraI, HaeIII and SspI]; (iii) RE3: [CviKl-1] + [Mly, MscI and MslI].After fragmentation with restriction enzymes or NEBNext dsDNA Fragmentase, DNA was purified (QIAquick Kit). For Fragmentase-treated samples, NEBNext End Repair Module created blunt ends. Fragments underwent dA-tailing using Klenow Fragment (35 exo-), followed by adapter ligation (T4 DNA ligase, 16C/overnight) and purification. Adapter-ligated DNA was treated with 0.3 M NaOH (55C/2h) to denature strands and cleave rNMP sites, then neutralized (HCl) and purified.ssDNA fragments were circularized using Arabidopsis tRNA ligase, linear DNA removed with T5 Exonuclease, and 2-phosphates eliminated via Tpt1 treatment. Two PCR rounds (6 + 11 cycles) with Q5 polymerase added Illumina indexes, followed by size selection (250700 bp) and normalization. Libraries were sequenced on Illumina NextSeq 500/HiSeq X Ten platforms

value: RNase H2A KO (T3-8)


title: HGSOC 03 PBMC/buffy coat single-cell RNA-seq

description:
Library name: SC16_14AS
Cryopreserved buffy coat/PBMC cells from a patient with high-grade serous ovarian carcinoma. Single-cell RNA-seq library prepared using 10x Genomics Chromium Next GEM Single Cell 3'. Processed matrix files are sample-prefixed for GEO upload uniqueness.

value: cancer

tag: cancer type

value: ovarian cancer

tag: subtype

tag: Stage

value: IV

value: Institute of Bioorganic Chemistry PAS, Poznan

value: HGSOC 03; SC_OC_095


title: ribose-seq of HEK293T genomic DNA with dsF fragmentation, replicate 2

description:
Library name: FS391
To construct ribose-seq libraries with human cell lines, genomic DNA samples were fragmented using NEBNext dsDNA Fragmentase or a combination of restriction enzymes to generate small DNA fragments. Various sets of restriction enzymes were applied to fragment human genomic DNA samples, as indicated in table S1. The used combinations were (i) RE1: [HpyCH4V] + [Hpy116II, Eco53KI, RsaI and StuI]; (ii) RE2: [AleI, AluI and PvuII] + [DraI, HaeIII and SspI]; (iii) RE3: [CviKl-1] + [Mly, MscI and MslI].After fragmentation with restriction enzymes or NEBNext dsDNA Fragmentase, DNA was purified (QIAquick Kit). For Fragmentase-treated samples, NEBNext End Repair Module created blunt ends. Fragments underwent dA-tailing using Klenow Fragment (35 exo-), followed by adapter ligation (T4 DNA ligase, 16C/overnight) and purification. Adapter-ligated DNA was treated with 0.3 M NaOH (55C/2h) to denature strands and cleave rNMP sites, then neutralized (HCl) and purified.ssDNA fragments were circularized using Arabidopsis tRNA ligase, linear DNA removed with T5 Exonuclease, and 2-phosphates eliminated via Tpt1 treatment. Two PCR rounds (6 + 11 cycles) with Q5 polymerase added Illumina indexes, followed by size selection (250700 bp) and normalization. Libraries were sequenced on Illumina NextSeq 500/HiSeq X Ten platforms

tag: genotype

value: RNase H2A wild-type


title: Male Hypoxia APL-9796 10 mg/kg Hz1

description: Library name: FG24014_07

value: Lung

tag: Sex

value: Male

tag: treatment


title: ribose-seq of HEK293T genomic DNA with RE2 fragmentation

description:
Library name: FS333
To construct ribose-seq libraries with human cell lines, genomic DNA samples were fragmented using NEBNext dsDNA Fragmentase or a combination of restriction enzymes to generate small DNA fragments. Various sets of restriction enzymes were applied to fragment human genomic DNA samples, as indicated in table S1. The used combinations were (i) RE1: [HpyCH4V] + [Hpy116II, Eco53KI, RsaI and StuI]; (ii) RE2: [AleI, AluI and PvuII] + [DraI, HaeIII and SspI]; (iii) RE3: [CviKl-1] + [Mly, MscI and MslI].After fragmentation with restriction enzymes or NEBNext dsDNA Fragmentase, DNA was purified (QIAquick Kit). For Fragmentase-treated samples, NEBNext End Repair Module created blunt ends. Fragments underwent dA-tailing using Klenow Fragment (35 exo-), followed by adapter ligation (T4 DNA ligase, 16C/overnight) and purification. Adapter-ligated DNA was treated with 0.3 M NaOH (55C/2h) to denature strands and cleave rNMP sites, then neutralized (HCl) and purified.ssDNA fragments were circularized using Arabidopsis tRNA ligase, linear DNA removed with T5 Exonuclease, and 2-phosphates eliminated via Tpt1 treatment. Two PCR rounds (6 + 11 cycles) with Q5 polymerase added Illumina indexes, followed by size selection (250700 bp) and normalization. Libraries were sequenced on Illumina NextSeq 500/HiSeq X Ten platforms


city: Cambridge

first: Elena

last: Scarpa

address: Downing Street

department: Physiology Development and Neuroscience

institute: University of Cambridge

description:
Library name: migratory 8
dataset Migratory trunk neural crest at 24 hours post-fertilisation, biological replica 8

data_processing:
Adapter trimming and quality filtering were then performed using fastp (Chen S. 2025. fastp 1.0: An ultra-fast all-round tool for FASTQ data quality control and preprocessing. iMeta 4:e70078. DOI: https://doi.org/10.1002/imt2.70078) with a custom adapter sequence list.
Transcript abundance was quantified using Salmon (Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. 2017. Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference. Nature methods 14:417–419. DOI: https://doi.org/10.1038/nmeth.4197, PMID: 28263959).
A genome-aware Salmon index was generated using the concatenated zebrafish genome and transcriptome assembly (GRCz11) with a k-mer length of 23. Trimmed reads were pseudo-aligned to this index to obtain transcript-level quantifications.
Salmon output was imported into R using the tximport package for downstream analysis.
Assembly: A genome-aware Salmon index was generated using the concatenated zebrafish genome and transcriptome assembly (GRCz11) with a k-mer length of 23
Supplementary files format and content: MigvsPremig_normalised_counts.csv
Supplementary files format and content: comma separated values table of normalised counts

source_name: neural crest

growth_protocol: Embryos expressing Dendra2 were selected for and separated, allowing to age to 16 or 23 hpf (an hour before the desired timepoint). The chorion surrounding the embryos were manually removed with forceps and discarded. The embryos are anaesthetised using tricaine mesylate (Sigma Aldrich, UK) at concentration of 2mg/ml. Anesthetised embryos were directly laterally mounted in 5% carbo-methylcellulose, which additionally contained 0.4mg/ml of tricaine mesylate to ensure total prevention of movement during PC. The embryos were mounted on to a glass-bottomed m-Dish 35mm high (ibidi, USA) compatible with the microscope stage used. Using a Zeiss LSM 880 Microscope, the mounted Dendra2 embryos are imaged in both GFP and RFP channels using Argon 488nm and DPSS561-10 561nm lasers respectively, to determine and mark the location of the targeted NC cell within the trunk of each embryo. For 23-24 hpf embryos, only somites 10-15 were considered. For PC, nuclei of Leader and Follower NC cells were marked using circular regions of interest (ROI), with PM NC marked using a larger free-handed ROI encompassing multiple cells in the dorsal region of the embryo trunk, with 405nm UV Diode 405-30 Laser at 40% laser intensity, pixel dwell 131.07sec for 2 iterations. For each population, 8 embryos were photo-converted where 4 replicates were aimed for. The software used to operate the microscope was Zen (v2.3 SP1).

extract_protocol:
RNA was extracted from the cells  using the SMART-Seq v4 Ultra Low Input Kit (Takara Bio, USA).
Amplified cDNA was purified using Agencourt AMPure XP kit (Beckman Coulter, USA) and validated using the Agilent 2100 Bioanalyser and Agilent’s High Sensitivity DNA Kit (Agilent Technologies, USA). Finally, the library was prepared for sequencing by using the Nextera DNA Library Preparation Kit (Illumina, USA) with 100-150pg of amplified cDNA.

value: neural crest

value: sox10:H2B-Dendra2 (Tg)

value: control


description:
Library name: migratory 6
dataset Migratory trunk neural crest at 24 hours post-fertilisation, biological replica 6


title: BENIGN CTRL 03 PBMC/buffy coat single-cell RNA-seq

description:
Library name: SC16_13AS
Cryopreserved buffy coat/PBMC cells from a non-malignant gynecological control donor. Single-cell RNA-seq library prepared using 10x Genomics Chromium Next GEM Single Cell 3'. Processed matrix files are sample-prefixed for GEO upload uniqueness.

value: peripheral blood

value: PBMC/buffy coat cell fraction

value: no ex vivo treatment; blood collected prior to processing

value: non-malignant control

value: benign ovarian lesion / benign gynecological control

value: benign gynecological control

value: not applicable

value: not provided

tag: grade

tag: library platform

tag: processing site

tag: source fraction

value: PBMC/buffy coat fraction

value: BENIGN CTRL 03; SC_OC_087


title: ribose-seq of HEK293T RNase H2 KO (T3-17) genomic DNA with dsF fragmentation, replicate 1

description:
Library name: FS329
To construct ribose-seq libraries with human cell lines, genomic DNA samples were fragmented using NEBNext dsDNA Fragmentase or a combination of restriction enzymes to generate small DNA fragments. Various sets of restriction enzymes were applied to fragment human genomic DNA samples, as indicated in table S1. The used combinations were (i) RE1: [HpyCH4V] + [Hpy116II, Eco53KI, RsaI and StuI]; (ii) RE2: [AleI, AluI and PvuII] + [DraI, HaeIII and SspI]; (iii) RE3: [CviKl-1] + [Mly, MscI and MslI].After fragmentation with restriction enzymes or NEBNext dsDNA Fragmentase, DNA was purified (QIAquick Kit). For Fragmentase-treated samples, NEBNext End Repair Module created blunt ends. Fragments underwent dA-tailing using Klenow Fragment (35 exo-), followed by adapter ligation (T4 DNA ligase, 16C/overnight) and purification. Adapter-ligated DNA was treated with 0.3 M NaOH (55C/2h) to denature strands and cleave rNMP sites, then neutralized (HCl) and purified.ssDNA fragments were circularized using Arabidopsis tRNA ligase, linear DNA removed with T5 Exonuclease, and 2-phosphates eliminated via Tpt1 treatment. Two PCR rounds (6 + 11 cycles) with Q5 polymerase added Illumina indexes, followed by size selection (250700 bp) and normalization. Libraries were sequenced on Illumina NextSeq 500/HiSeq X Ten platforms

value: human embryonic kidney

value: RNase H2A KO (T3-17)


title: Male Hypoxia IgG 10 mg/kg Control Hx4

description: Library name: FG24014_04

value: Lung

value: IgG control antibody


title: ribose-seq of HEK293T RNase H2 KO (T3-8) genomic DNA with dsF fragmentation, replicate 1

description:
Library name: FS327
To construct ribose-seq libraries with human cell lines, genomic DNA samples were fragmented using NEBNext dsDNA Fragmentase or a combination of restriction enzymes to generate small DNA fragments. Various sets of restriction enzymes were applied to fragment human genomic DNA samples, as indicated in table S1. The used combinations were (i) RE1: [HpyCH4V] + [Hpy116II, Eco53KI, RsaI and StuI]; (ii) RE2: [AleI, AluI and PvuII] + [DraI, HaeIII and SspI]; (iii) RE3: [CviKl-1] + [Mly, MscI and MslI].After fragmentation with restriction enzymes or NEBNext dsDNA Fragmentase, DNA was purified (QIAquick Kit). For Fragmentase-treated samples, NEBNext End Repair Module created blunt ends. Fragments underwent dA-tailing using Klenow Fragment (35 exo-), followed by adapter ligation (T4 DNA ligase, 16C/overnight) and purification. Adapter-ligated DNA was treated with 0.3 M NaOH (55C/2h) to denature strands and cleave rNMP sites, then neutralized (HCl) and purified.ssDNA fragments were circularized using Arabidopsis tRNA ligase, linear DNA removed with T5 Exonuclease, and 2-phosphates eliminated via Tpt1 treatment. Two PCR rounds (6 + 11 cycles) with Q5 polymerase added Illumina indexes, followed by size selection (250700 bp) and normalization. Libraries were sequenced on Illumina NextSeq 500/HiSeq X Ten platforms

value: RNase H2A wild-type


title: Male Hypoxia IgG 10 mg/kg Control Hx3

description: Library name: FG24014_03

value: Male


title: Male Hypoxia IgG 10 mg/kg Control Hx6

description: Library name: FG24014_06


description:
Library name: migratory 7
dataset Migratory trunk neural crest at 24 hours post-fertilisation, biological replica 7

value: neural crest

value: sox10:H2B-Dendra2 (Tg)

value: control

tag: batch


title: Male Hypoxia IgG 10 mg/kg Control Hx5

description: Library name: FG24014_05


title: ribose-seq of hESC-H9 genomic DNA with RE2 fragmentation

description:
Library name: FS331
To construct ribose-seq libraries with human cell lines, genomic DNA samples were fragmented using NEBNext dsDNA Fragmentase or a combination of restriction enzymes to generate small DNA fragments. Various sets of restriction enzymes were applied to fragment human genomic DNA samples, as indicated in table S1. The used combinations were (i) RE1: [HpyCH4V] + [Hpy116II, Eco53KI, RsaI and StuI]; (ii) RE2: [AleI, AluI and PvuII] + [DraI, HaeIII and SspI]; (iii) RE3: [CviKl-1] + [Mly, MscI and MslI].After fragmentation with restriction enzymes or NEBNext dsDNA Fragmentase, DNA was purified (QIAquick Kit). For Fragmentase-treated samples, NEBNext End Repair Module created blunt ends. Fragments underwent dA-tailing using Klenow Fragment (35 exo-), followed by adapter ligation (T4 DNA ligase, 16C/overnight) and purification. Adapter-ligated DNA was treated with 0.3 M NaOH (55C/2h) to denature strands and cleave rNMP sites, then neutralized (HCl) and purified.ssDNA fragments were circularized using Arabidopsis tRNA ligase, linear DNA removed with T5 Exonuclease, and 2-phosphates eliminated via Tpt1 treatment. Two PCR rounds (6 + 11 cycles) with Q5 polymerase added Illumina indexes, followed by size selection (250700 bp) and normalization. Libraries were sequenced on Illumina NextSeq 500/HiSeq X Ten platforms

source_name: embryo

value: embryo


description:
Library name: migratory 4
dataset Migratory trunk neural crest at 24 hours post-fertilisation, biological replica 4


title: BENIGN CTRL 02 PBMC/buffy coat single-cell RNA-seq

description:
Library name: SC15_12AS
Cryopreserved buffy coat/PBMC cells from a non-malignant gynecological control donor. Single-cell RNA-seq library prepared using 10x Genomics Chromium Next GEM Single Cell 3'. Processed matrix files are sample-prefixed for GEO upload uniqueness.

value: peripheral blood

value: PBMC/buffy coat cell fraction

value: no ex vivo treatment; blood collected prior to processing

tag: disease state

value: non-malignant control

tag: diagnosis

tag: age

value: Institute of Bioorganic Chemistry PAS, Poznan

value: BENIGN CTRL 02; SC_OC_093


description:
Library name: migratory 5
dataset Migratory trunk neural crest at 24 hours post-fertilisation, biological replica 5

tag: cell type


title: HGSOC 02 PBMC/buffy coat single-cell RNA-seq

description:
Library name: SC15_11AS
Cryopreserved buffy coat/PBMC cells from a patient with high-grade serous ovarian carcinoma. Single-cell RNA-seq library prepared using 10x Genomics Chromium Next GEM Single Cell 3'. Processed matrix files are sample-prefixed for GEO upload uniqueness.

tag: tissue

value: cancer

value: high-grade serous ovarian carcinoma

tag: sample group

value: high-grade serous ovarian cancer

value: ovarian cancer

value: IIIC

value: PBMC/buffy coat fraction

tag: original sample id

value: HGSOC 02; SC_OC_086


title: ribose-seq of HEK293T genomic DNA with dsF fragmentation, replicate 1

description:
Library name: FS326
To construct ribose-seq libraries with human cell lines, genomic DNA samples were fragmented using NEBNext dsDNA Fragmentase or a combination of restriction enzymes to generate small DNA fragments. Various sets of restriction enzymes were applied to fragment human genomic DNA samples, as indicated in table S1. The used combinations were (i) RE1: [HpyCH4V] + [Hpy116II, Eco53KI, RsaI and StuI]; (ii) RE2: [AleI, AluI and PvuII] + [DraI, HaeIII and SspI]; (iii) RE3: [CviKl-1] + [Mly, MscI and MslI].After fragmentation with restriction enzymes or NEBNext dsDNA Fragmentase, DNA was purified (QIAquick Kit). For Fragmentase-treated samples, NEBNext End Repair Module created blunt ends. Fragments underwent dA-tailing using Klenow Fragment (35 exo-), followed by adapter ligation (T4 DNA ligase, 16C/overnight) and purification. Adapter-ligated DNA was treated with 0.3 M NaOH (55C/2h) to denature strands and cleave rNMP sites, then neutralized (HCl) and purified.ssDNA fragments were circularized using Arabidopsis tRNA ligase, linear DNA removed with T5 Exonuclease, and 2-phosphates eliminated via Tpt1 treatment. Two PCR rounds (6 + 11 cycles) with Q5 polymerase added Illumina indexes, followed by size selection (250700 bp) and normalization. Libraries were sequenced on Illumina NextSeq 500/HiSeq X Ten platforms

value: human embryonic kidney

tag: cell line

value: RNase H2A wild-type


title: BENIGN CTRL 01 PBMC/buffy coat single-cell RNA-seq

description:
Library name: SC11_9AS
Cryopreserved buffy coat/PBMC cells from a non-malignant gynecological control donor. Single-cell RNA-seq library prepared using 10x Genomics Chromium Next GEM Single Cell 3'. Processed matrix files are sample-prefixed for GEO upload uniqueness.

value: benign ovarian lesion / benign gynecological control

value: benign gynecological control

tag: cancer type

value: not applicable

tag: subtype

value: not provided

tag: Stage

value: BENIGN CTRL 01; SC_OC_092


title: HGSOC 01 PBMC/buffy coat single-cell RNA-seq

description:
Library name: SC11_10AS
Cryopreserved buffy coat/PBMC cells from a patient with high-grade serous ovarian carcinoma. Single-cell RNA-seq library prepared using 10x Genomics Chromium Next GEM Single Cell 3'. Processed matrix files are sample-prefixed for GEO upload uniqueness.

value: peripheral blood

value: PBMC/buffy coat cell fraction

tag: treatment

value: no ex vivo treatment; blood collected prior to processing

value: HGSOC 01; SC_OC_096


title: Male Hypoxia IgG 10 mg/kg Control Hx2

description: Library name: FG24014_02

value: Lung

tag: Sex

value: Male

tag: genotype

value: IgG control antibody


title: ribose-seq of HEK293T RNase H2 KO (T3-17) genomic DNA with RE3 fragmentation

description:
Library name: FS310
To construct ribose-seq libraries with human cell lines, genomic DNA samples were fragmented using NEBNext dsDNA Fragmentase or a combination of restriction enzymes to generate small DNA fragments. Various sets of restriction enzymes were applied to fragment human genomic DNA samples, as indicated in table S1. The used combinations were (i) RE1: [HpyCH4V] + [Hpy116II, Eco53KI, RsaI and StuI]; (ii) RE2: [AleI, AluI and PvuII] + [DraI, HaeIII and SspI]; (iii) RE3: [CviKl-1] + [Mly, MscI and MslI].After fragmentation with restriction enzymes or NEBNext dsDNA Fragmentase, DNA was purified (QIAquick Kit). For Fragmentase-treated samples, NEBNext End Repair Module created blunt ends. Fragments underwent dA-tailing using Klenow Fragment (35 exo-), followed by adapter ligation (T4 DNA ligase, 16C/overnight) and purification. Adapter-ligated DNA was treated with 0.3 M NaOH (55C/2h) to denature strands and cleave rNMP sites, then neutralized (HCl) and purified.ssDNA fragments were circularized using Arabidopsis tRNA ligase, linear DNA removed with T5 Exonuclease, and 2-phosphates eliminated via Tpt1 treatment. Two PCR rounds (6 + 11 cycles) with Q5 polymerase added Illumina indexes, followed by size selection (250700 bp) and normalization. Libraries were sequenced on Illumina NextSeq 500/HiSeq X Ten platforms

value: RNase H2A KO (T3-17)


description:
Library name: migratory 3
dataset Migratory trunk neural crest at 24 hours post-fertilisation, biological replica 3

value: neural crest

value: sox10:H2B-Dendra2 (Tg)

value: control


title: HEK293T, Control, rep 2

city: Los Angeles

first: Isabella

last: Lin

address: 615 Charles E Young Dr S

institute: University of California Los Angeles

description:
Library name: MS-2-HEK293T-WT2
HEK293T_star_featureCounts_GeneTable_final.csv

data_processing:
Samples were demultiplexed after sequencing, and fastq sequencing files were processed using established pipelines in the Arboleda lab. Raw read quality, adaptor content, and duplication rates were assessed with FastQC v0.11.8.
Raw reads were then aligned against the Gencode human genome version hg38 (GR38) version 31 using STAR 2.7.0e (3) with default parameters.
Gene counts from raw reads were generated using featureCounts 1.6.5 (4) from the Subread package. Only reads that uniquely mapped to exons of a gene were counted per gene.
Differential expression analysis was completed using DESeq2 v1.24.0 (5).
Assembly: GRCh38
Supplementary files format and content: csv file with gene counts generated using featureCounts

source_name: Human embryonic kidney

growth_protocol: Human embryonic kidney (HEK293T) and colorectal adenocarcinoma (Caco-2) were maintained in DMEM with 10% FBS and 1% penicillin-streptomycin

extract_protocol:
Total RNA extraction via RNeasy Plus Mini Kit (Qiagen, 74136)
All samples were then prepared with QIAseq FastSelect −rRNA HMR (Qiagen, 334386) and TruSeq Stranded Total RNA Library Prep Gold (Illumina, 20020599)

treatment_protocol: Using Lipofectamine™ 3000, cells were transfected with 2.5ug of plasmid or mock. Transfected cells were incubated for 48 hours transfection.

value: Human embryonic kidney

value: WT

value: Untransfected


title: Male Hypoxia IgG 10 mg/kg Control Hx1

description: Library name: FG24014_01


description:
Library name: migratory 2
dataset Migratory trunk neural crest at 24 hours post-fertilisation, biological replica 2


title: ribose-seq of HEK293T RNase H2 KO (T3-8) genomic DNA with RE3 fragmentation

description:
Library name: FS309
To construct ribose-seq libraries with human cell lines, genomic DNA samples were fragmented using NEBNext dsDNA Fragmentase or a combination of restriction enzymes to generate small DNA fragments. Various sets of restriction enzymes were applied to fragment human genomic DNA samples, as indicated in table S1. The used combinations were (i) RE1: [HpyCH4V] + [Hpy116II, Eco53KI, RsaI and StuI]; (ii) RE2: [AleI, AluI and PvuII] + [DraI, HaeIII and SspI]; (iii) RE3: [CviKl-1] + [Mly, MscI and MslI].After fragmentation with restriction enzymes or NEBNext dsDNA Fragmentase, DNA was purified (QIAquick Kit). For Fragmentase-treated samples, NEBNext End Repair Module created blunt ends. Fragments underwent dA-tailing using Klenow Fragment (35 exo-), followed by adapter ligation (T4 DNA ligase, 16C/overnight) and purification. Adapter-ligated DNA was treated with 0.3 M NaOH (55C/2h) to denature strands and cleave rNMP sites, then neutralized (HCl) and purified.ssDNA fragments were circularized using Arabidopsis tRNA ligase, linear DNA removed with T5 Exonuclease, and 2-phosphates eliminated via Tpt1 treatment. Two PCR rounds (6 + 11 cycles) with Q5 polymerase added Illumina indexes, followed by size selection (250700 bp) and normalization. Libraries were sequenced on Illumina NextSeq 500/HiSeq X Ten platforms

value: human embryonic kidney

value: RNase H2A KO (T3-8)


title: HEK293T, Control, rep 1

description:
Library name: MS-1-HEK293T-WT1
HEK293T_star_featureCounts_GeneTable_final.csv


title: SAMP1/YitFc ileum, male biol rep 2, snRNAseq

city: Cleveland

first: Katreya

last: Lovrenert

address: 10900 Euclid Avenue

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

description: Library name: SAMP4

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using Cell Ranger v7.2.0
Technical artifacts were removed using CellBender v0.2.2
Samples were merged in a Seurat object in R, SCT normalized, batch corrected with Harmony, and filtered to remove both doublets (using DoubletFinder) and nuclei with high levels of RNA degradation
Assembly: mm10
Supplementary files format and content: Filtered datasets in h5 format (CellBender output)
Supplementary files format and content: annotated Seurat object (in .rds format) containing all cells post-normalization, batch correction, and removal of doublets and degraded nuclei

source_name: Ileum

extract_protocol:
We used CitraPrep to isolate nucle from high degradative tissues. Frozen tissue was placed into a petri dish on ice and cut into 0.2cm cubed pieces or smaller using clean scissors and forceps in 1mL of CitraHB (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH pH 7.8, 10mM citric acid, 0.5U/uL RNasin, 0.5U/uL SUPERase RNase inhibitor, 1mM DTT, 0.15mM spermine tetrahydrochloride, 0.5mM spermidine trihydrochloride, and cOmplete, EDTA-free protease inhibitor). Chopped tissue (totaling less than 1.5cm cubed) was transferred to the glass dounce homogenizer on ice and 4mL of CitraHB was added. Tissue was incubated on ice for 7 minutes. Tissue was homogenized 20x with loose pestle before adding 320uL of NP-40 and homogenizing 40x with tight pestle. If tissue does not homogenize, an electric homogenizer with short bursts may be used. Nuclei were observed under the microscope for quality control before proceeding. Tissue lysate was filtered through a 40um strainer into a 50mL conical tube. Next, 5mL of 50% iodixanol solution (5 volumes OptiPrep and 1 volume of Diluent composed of 150mM KCl, 30mM MgCl2, 120mM Tricine-KOH pH 7.8 mixed, plus 10mM citric acid, 0.5U/uL RNasin, 0.5U/uL SUPERase RNase inhibitor, 1mM DTT, 0.15mM spermine, and 0.5mM spermidine) was added to the filtered tissue lysate to make a 25% iodixanol solution and vortexed to mix. The tissue lysate was slowly underlaid with 30% iodixanol solution (30% OptiPrep in CitraHB with 0.5U/uL RNasin, 0.5U/uL SUPERase RNase inhibitor, 1mM DTT, 0.15mM spermine, and 0.5mM spermidine), then slowly underlaid with 40% iodixanol solution (40% OptiPrep in CitraHB with 0.5U/uL RNasin, 0.5U/uL SUPERase RNase inhibitor, 1mM DTT, 0.15mM spermine, and 0.5mM spermidine). Without disturbing the layers, the 50mL tube was weighed and balanced before centrifugation at 10,000g for 18 minutes at 4oC with no brake. Nuclei were collected from the interface layer with a 1000mL pipette and placed into a new tube with 10mL nuclei wash buffer (1x PBS, 1% BSA, 0.5U/uL RNasin, and 0.5U/uL SUPERase RNase inhibitor) and vortexed before filtering through a 20um filter. Nuclei were pelleted by centrifugation at 500g for 5 minutes at 4oC. Supernatant was removed and tissue was washed a second time. The pellet was resuspended in 250uL of nuclei wash buffer and nuclei were counted using a hemocytometer.
Library was performed according to the manufacter’s instructions (single cell 3’ GEM v3.1 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Ileum

tag: strain

value: 20 weeks


title: HEK293T, Control Transfection STOP, rep 3

description:
Library name: HEK293T_StopsCTRL_Rep3
HEK293T_star_featureCounts_GeneTable_final.csv

value: Transfection (control)


description:
Library name: migratory 1
dataset Migratory trunk neural crest at 24 hours post-fertilisation, biological replica 1


title: ribose-seq of HEK293T RNase H2 KO (T3-17) genomic DNA with RE2 fragmentation

description:
Library name: FS307
To construct ribose-seq libraries with human cell lines, genomic DNA samples were fragmented using NEBNext dsDNA Fragmentase or a combination of restriction enzymes to generate small DNA fragments. Various sets of restriction enzymes were applied to fragment human genomic DNA samples, as indicated in table S1. The used combinations were (i) RE1: [HpyCH4V] + [Hpy116II, Eco53KI, RsaI and StuI]; (ii) RE2: [AleI, AluI and PvuII] + [DraI, HaeIII and SspI]; (iii) RE3: [CviKl-1] + [Mly, MscI and MslI].After fragmentation with restriction enzymes or NEBNext dsDNA Fragmentase, DNA was purified (QIAquick Kit). For Fragmentase-treated samples, NEBNext End Repair Module created blunt ends. Fragments underwent dA-tailing using Klenow Fragment (35 exo-), followed by adapter ligation (T4 DNA ligase, 16C/overnight) and purification. Adapter-ligated DNA was treated with 0.3 M NaOH (55C/2h) to denature strands and cleave rNMP sites, then neutralized (HCl) and purified.ssDNA fragments were circularized using Arabidopsis tRNA ligase, linear DNA removed with T5 Exonuclease, and 2-phosphates eliminated via Tpt1 treatment. Two PCR rounds (6 + 11 cycles) with Q5 polymerase added Illumina indexes, followed by size selection (250700 bp) and normalization. Libraries were sequenced on Illumina NextSeq 500/HiSeq X Ten platforms


title: SAMP1/YitFc ileum, male biol rep 1, snRNAseq

description: Library name: SAMP3


description:
Library name: premigratory 4
dataset premigratory trunk neural crest at 16 hours post-fertilisation, biological replica 4


title: HEK293T, Control Transfection STOP, rep 2

description:
Library name: HEK293T_StopsCTRL_Rep2
HEK293T_star_featureCounts_GeneTable_final.csv


title: ribose-seq of HEK293T RNase H2 KO (T3-8) genomic DNA with RE2 fragmentation

description:
Library name: FS306
To construct ribose-seq libraries with human cell lines, genomic DNA samples were fragmented using NEBNext dsDNA Fragmentase or a combination of restriction enzymes to generate small DNA fragments. Various sets of restriction enzymes were applied to fragment human genomic DNA samples, as indicated in table S1. The used combinations were (i) RE1: [HpyCH4V] + [Hpy116II, Eco53KI, RsaI and StuI]; (ii) RE2: [AleI, AluI and PvuII] + [DraI, HaeIII and SspI]; (iii) RE3: [CviKl-1] + [Mly, MscI and MslI].After fragmentation with restriction enzymes or NEBNext dsDNA Fragmentase, DNA was purified (QIAquick Kit). For Fragmentase-treated samples, NEBNext End Repair Module created blunt ends. Fragments underwent dA-tailing using Klenow Fragment (35 exo-), followed by adapter ligation (T4 DNA ligase, 16C/overnight) and purification. Adapter-ligated DNA was treated with 0.3 M NaOH (55C/2h) to denature strands and cleave rNMP sites, then neutralized (HCl) and purified.ssDNA fragments were circularized using Arabidopsis tRNA ligase, linear DNA removed with T5 Exonuclease, and 2-phosphates eliminated via Tpt1 treatment. Two PCR rounds (6 + 11 cycles) with Q5 polymerase added Illumina indexes, followed by size selection (250700 bp) and normalization. Libraries were sequenced on Illumina NextSeq 500/HiSeq X Ten platforms


title: SAMP1/YitFc ileum, female biol rep 2, snRNAseq

description: Library name: SAMP2


description:
Library name: premigratory 3
dataset premigratory trunk neural crest at 16 hours post-fertilisation, biological replica 3


title: ribose-seq of HEK293T genomic DNA with RE3 fragmentation

description:
Library name: FS305
To construct ribose-seq libraries with human cell lines, genomic DNA samples were fragmented using NEBNext dsDNA Fragmentase or a combination of restriction enzymes to generate small DNA fragments. Various sets of restriction enzymes were applied to fragment human genomic DNA samples, as indicated in table S1. The used combinations were (i) RE1: [HpyCH4V] + [Hpy116II, Eco53KI, RsaI and StuI]; (ii) RE2: [AleI, AluI and PvuII] + [DraI, HaeIII and SspI]; (iii) RE3: [CviKl-1] + [Mly, MscI and MslI].After fragmentation with restriction enzymes or NEBNext dsDNA Fragmentase, DNA was purified (QIAquick Kit). For Fragmentase-treated samples, NEBNext End Repair Module created blunt ends. Fragments underwent dA-tailing using Klenow Fragment (35 exo-), followed by adapter ligation (T4 DNA ligase, 16C/overnight) and purification. Adapter-ligated DNA was treated with 0.3 M NaOH (55C/2h) to denature strands and cleave rNMP sites, then neutralized (HCl) and purified.ssDNA fragments were circularized using Arabidopsis tRNA ligase, linear DNA removed with T5 Exonuclease, and 2-phosphates eliminated via Tpt1 treatment. Two PCR rounds (6 + 11 cycles) with Q5 polymerase added Illumina indexes, followed by size selection (250700 bp) and normalization. Libraries were sequenced on Illumina NextSeq 500/HiSeq X Ten platforms

value: RNase H2A wild-type


title: HEK293T, Control Transfection STOP, rep 1

description:
Library name: HEK293T_StopsCTRL_Rep1
HEK293T_star_featureCounts_GeneTable_final.csv


description:
Library name: premigratory 2
dataset premigratory trunk neural crest at 16 hours post-fertilisation, biological replica 2


title: SAMP1/YitFc ileum, female biol rep 1, snRNAseq

description: Library name: SAMP1


title: ribose-seq of hESC-H9 genomic DNA with RE3 fragmentation

description:
Library name: FS303
To construct ribose-seq libraries with human cell lines, genomic DNA samples were fragmented using NEBNext dsDNA Fragmentase or a combination of restriction enzymes to generate small DNA fragments. Various sets of restriction enzymes were applied to fragment human genomic DNA samples, as indicated in table S1. The used combinations were (i) RE1: [HpyCH4V] + [Hpy116II, Eco53KI, RsaI and StuI]; (ii) RE2: [AleI, AluI and PvuII] + [DraI, HaeIII and SspI]; (iii) RE3: [CviKl-1] + [Mly, MscI and MslI].After fragmentation with restriction enzymes or NEBNext dsDNA Fragmentase, DNA was purified (QIAquick Kit). For Fragmentase-treated samples, NEBNext End Repair Module created blunt ends. Fragments underwent dA-tailing using Klenow Fragment (35 exo-), followed by adapter ligation (T4 DNA ligase, 16C/overnight) and purification. Adapter-ligated DNA was treated with 0.3 M NaOH (55C/2h) to denature strands and cleave rNMP sites, then neutralized (HCl) and purified.ssDNA fragments were circularized using Arabidopsis tRNA ligase, linear DNA removed with T5 Exonuclease, and 2-phosphates eliminated via Tpt1 treatment. Two PCR rounds (6 + 11 cycles) with Q5 polymerase added Illumina indexes, followed by size selection (250700 bp) and normalization. Libraries were sequenced on Illumina NextSeq 500/HiSeq X Ten platforms

value: embryo


title: AKR ileum, male biol rep 2, snRNAseq

description: Library name: AKR3

value: AKR/J


description:
Library name: premigratory 1
dataset premigratory trunk neural crest at 16 hours post-fertilisation, biological replica 1


title: HEK293T, ASXL1 Transfection 1-479, rep 3

description:
Library name: HEK293T_479_Rep3
HEK293T_star_featureCounts_GeneTable_final.csv

value: Transfection


title: ribose-seq of HEK293T RNase H2 KO (T3-17) genomic DNA with RE1 fragmentation

description:
Library name: FS301
To construct ribose-seq libraries with human cell lines, genomic DNA samples were fragmented using NEBNext dsDNA Fragmentase or a combination of restriction enzymes to generate small DNA fragments. Various sets of restriction enzymes were applied to fragment human genomic DNA samples, as indicated in table S1. The used combinations were (i) RE1: [HpyCH4V] + [Hpy116II, Eco53KI, RsaI and StuI]; (ii) RE2: [AleI, AluI and PvuII] + [DraI, HaeIII and SspI]; (iii) RE3: [CviKl-1] + [Mly, MscI and MslI].After fragmentation with restriction enzymes or NEBNext dsDNA Fragmentase, DNA was purified (QIAquick Kit). For Fragmentase-treated samples, NEBNext End Repair Module created blunt ends. Fragments underwent dA-tailing using Klenow Fragment (35 exo-), followed by adapter ligation (T4 DNA ligase, 16C/overnight) and purification. Adapter-ligated DNA was treated with 0.3 M NaOH (55C/2h) to denature strands and cleave rNMP sites, then neutralized (HCl) and purified.ssDNA fragments were circularized using Arabidopsis tRNA ligase, linear DNA removed with T5 Exonuclease, and 2-phosphates eliminated via Tpt1 treatment. Two PCR rounds (6 + 11 cycles) with Q5 polymerase added Illumina indexes, followed by size selection (250700 bp) and normalization. Libraries were sequenced on Illumina NextSeq 500/HiSeq X Ten platforms


title: AKR ileum, male biol rep 1, snRNAseq

description: Library name: AKR2


title: HEK293T, ASXL1 Transfection 1-479, rep 2

description:
Library name: HEK293T_479_Rep2
HEK293T_star_featureCounts_GeneTable_final.csv


title: blank, negativeControl, batch2

city: Godinne

first: Nicolas

last: Debortoli

address: avenue Docteur G. Thérasse, 1

country: Belgium

institute: CHU UCL Namur

description:
Library name: CtrlNeg-2
column in raw_counts_run2.txt: CtrlNeg-2

data_processing:
Trimming and quality filtering with fastp
Mapping on reference genome with STAR using STARlong mode
Mapping quality evaluation with QUALIMAP
Count table generated with featureCounts
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file containing the output of featureCounts.
Supplementary files format and content: Columns are: GeneID, Chr, Start, End, Strand, Length and one column per sample containing raw counts.

organism: blank sample

source_name: control

growth_protocol: At the age of two months, mice were exposed to spinal cord surgery. Preoperative analgesia was administered via subcutaneous injections of buprenorphine (0.05 mg/kg; Vetergesic) and carprofen (5 mg/kg; Rycarfa). Anesthesia was induced by intraperitoneal administration of ketamine (120 mg/kg; Nimatek) and xylazine (8 mg/kg; Sedaxylan). Mice of contusion group underwent C5 laminectomy followed by 30kDynes contusion while sham were only exposed to laminectomy. Postoperative analgesia included a second injection of buprenorphine at 6 and 24 hours post-surgery, as well as additional carprofen administrations at 24 and 48 hours. Mice were finally sacrificed two days post surgery by anesthetic overdose followed by cold saline intracardiac injection.

extract_protocol:
Spinal cord samples were homogenized in 500 µL of TRIzol reagent (Invitrogen, 15596018) using a grinder device and incubated at room temperature for 5 min. Homogenates were centrifuged at 15,800 × g for 10 min at 4 °C, and the supernatant was transferred to a new tube. Chloroform (200 µL) was added, and samples were vortexed and incubated for 3 min at room temperature. Following centrifugation at 15,800 × g for 15 min at 4 °C, 300 µL of the aqueous phase was collected and mixed with an equal volume of 70% ethanol. The mixture was then applied to an RNA extraction column (High Pure RNA Tissue Kit, Roche Diagnostics, 12033674001), and RNA was purified according to the manufacturer’s instructions.
Direct cDNA Library Prep Kit (SQK-NBD114.96; ONT)

treatment_protocol: Spinal cord tissues were immediately frozen in liquid nitrogen and stored at −80°C until further processing.


title: ribose-seq of HEK293T RNase H2 KO (T3-8) genomic DNA with RE1 fragmentation

description:
Library name: FS300
To construct ribose-seq libraries with human cell lines, genomic DNA samples were fragmented using NEBNext dsDNA Fragmentase or a combination of restriction enzymes to generate small DNA fragments. Various sets of restriction enzymes were applied to fragment human genomic DNA samples, as indicated in table S1. The used combinations were (i) RE1: [HpyCH4V] + [Hpy116II, Eco53KI, RsaI and StuI]; (ii) RE2: [AleI, AluI and PvuII] + [DraI, HaeIII and SspI]; (iii) RE3: [CviKl-1] + [Mly, MscI and MslI].After fragmentation with restriction enzymes or NEBNext dsDNA Fragmentase, DNA was purified (QIAquick Kit). For Fragmentase-treated samples, NEBNext End Repair Module created blunt ends. Fragments underwent dA-tailing using Klenow Fragment (35 exo-), followed by adapter ligation (T4 DNA ligase, 16C/overnight) and purification. Adapter-ligated DNA was treated with 0.3 M NaOH (55C/2h) to denature strands and cleave rNMP sites, then neutralized (HCl) and purified.ssDNA fragments were circularized using Arabidopsis tRNA ligase, linear DNA removed with T5 Exonuclease, and 2-phosphates eliminated via Tpt1 treatment. Two PCR rounds (6 + 11 cycles) with Q5 polymerase added Illumina indexes, followed by size selection (250700 bp) and normalization. Libraries were sequenced on Illumina NextSeq 500/HiSeq X Ten platforms


title: HEK293T, ASXL1 Transfection 1-479, rep 1

description:
Library name: HEK293T_479_Rep1
HEK293T_star_featureCounts_GeneTable_final.csv


title: AKR ileum,female biol rep 1, snRNAseq

description: Library name: AKR1


title: blank, negativeControl, batch1

description:
Library name: CtrlNeg-1
column in raw_counts_run1.txt: CtrlNeg-1


title: ribose-seq of HEK293T genomic DNA with RE1 fragmentation

description:
Library name: FS203
To construct ribose-seq libraries with human cell lines, genomic DNA samples were fragmented using NEBNext dsDNA Fragmentase or a combination of restriction enzymes to generate small DNA fragments. Various sets of restriction enzymes were applied to fragment human genomic DNA samples, as indicated in table S1. The used combinations were (i) RE1: [HpyCH4V] + [Hpy116II, Eco53KI, RsaI and StuI]; (ii) RE2: [AleI, AluI and PvuII] + [DraI, HaeIII and SspI]; (iii) RE3: [CviKl-1] + [Mly, MscI and MslI].After fragmentation with restriction enzymes or NEBNext dsDNA Fragmentase, DNA was purified (QIAquick Kit). For Fragmentase-treated samples, NEBNext End Repair Module created blunt ends. Fragments underwent dA-tailing using Klenow Fragment (35 exo-), followed by adapter ligation (T4 DNA ligase, 16C/overnight) and purification. Adapter-ligated DNA was treated with 0.3 M NaOH (55C/2h) to denature strands and cleave rNMP sites, then neutralized (HCl) and purified.ssDNA fragments were circularized using Arabidopsis tRNA ligase, linear DNA removed with T5 Exonuclease, and 2-phosphates eliminated via Tpt1 treatment. Two PCR rounds (6 + 11 cycles) with Q5 polymerase added Illumina indexes, followed by size selection (250700 bp) and normalization. Libraries were sequenced on Illumina NextSeq 500/HiSeq X Ten platforms


title: HEK293T, ASXL1 Transfection 1-1541, rep 3

description:
Library name: HEK293T_1541_Rep3
HEK293T_star_featureCounts_GeneTable_final.csv


title: P301S mouse,shControl,48h,biological replicate7

description:
Library name: PM203-1
column in raw_counts_run2.txt: PM203-1

source_name: mild spinal cord

value: mild spinal cord

value: sham C5 laminectomy


title: testis, BPA lineage, PFOS 0.02 mg/L, biol rep3

city: Columbia

first: Ramji

last: Bhandari

state: MO

address: 1200 University Ave

department: Division of Biological Sciences

institute: University of Missouri

description: Library name: TBR3C

data_processing:
The reads were first preprocessed with fastp (v0.23.2), an ultra-fast all-in-one FASTQ preprocessor, which does quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data
The fastp-processed reads were then mapped on medaka genome (Oryzias_latipes.ASM223467v1) using STAR (2.7.7a)
Finally, DESeq2 (v1.34.0) was used to generate normalized count data for all samples.
Assembly: Oryzias_latipes.ASM223467v1
Supplementary files format and content: testis_normExpr_DESeq2.tsv: Normalized expression values obtained from DESeq2 for all samples in tab-delimited text-file

organism: Oryzias latipes

source_name: testis

extract_protocol:
Total RNA was extracted from the testes of the control and BPA lineage using the Quick RNA/DNA Miniprep Plus Kit (#D-7003, Zymo Research, CA, USA), following the manufacturer's instructions.
Transcriptome libraries were prepared by Novogene Corporation (CA, USA) using the NEBNext Ultra II RNA Kit, following the manufacturer's protocol.

value: testis

tag: lineage

value: BPA

value: PFOS 0.02 mg/L


title: Whole genome DNA-seq of CD4T-1 with RE3 fragmentation

description:
Library name: DNA-CD4T-RE3
CD4T cells genomic DNA extracted was digested using RE3 combination in this study and sequenced using Illumina HiSeq X Ten Platform
DNA_rez_500K_counts.tsv

source_name: blood

value: blood


title: HEK293T, ASXL1 Transfection 1-1541, rep 2

description:
Library name: HEK293T_1541_Rep2
HEK293T_star_featureCounts_GeneTable_final.csv

value: Human embryonic kidney

value: WT

tag: batch


title: testis, BPA lineage, PFOS 0.02 mg/L, biol rep2

description: Library name: TBR2C


title: Whole genome DNA-seq of CD4T-1 with RE2 fragmentation

description:
Library name: DNA-CD4T-RE2
CD4T cells genomic DNA extracted was digested using RE2 combination in this study and sequenced using Illumina HiSeq X Ten Platform
DNA_rez_500K_counts.tsv


title: P301S mouse,shControl,48h,biological replicate6

description:
Library name: PM198-1
column in raw_counts_run2.txt: PM198-1


title: testis, BPA lineage, PFOS 0.02 mg/L, biol rep1

description: Library name: TBR1C


title: HEK293T, ASXL1 Transfection 1-1541, rep 1

description:
Library name: HEK293T_1541_Rep1
HEK293T_star_featureCounts_GeneTable_final.csv


title: P301S mouse,shControl,48h,biological replicate5

description:
Library name: PM204-1
column in raw_counts_run1.txt: PM204-1