title: PA08_5_R3_P3

description: Library name: s239

value: chemical exposure


title: 3-week, Resilient, mouse 1, replicate 2

status: Public on Jul 01 2026

type: SRA

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

country: USA

institute: Virginia Tech

description: Library name: 3wRES_1_rep2

library_source: transcriptomic

data_processing:
Illumina NovaSeq X plus with double-end 150-nt read was used to sequence each library, generating ~15 million reads for each sample.
Read trimming was performed using default settings by Trim Galore!
Raw RNA-seq reads were then mapped to mouse mm10 genome (GRCm38) using Hisat2.
FeatureCounts was used to count reads. Genes for which more than 6 libraries (out of 10-12 libraries per condition) had fewer than 20 counts were excluded from downstream analysis.
The differentially expressed genes (DEGs) were determined by pairwise comparison using DESeq2 (34) with FDR < 0.05. The gene expression was normalized by variance stabilizing transformation (VST) from the DESeq2 and, DEGs were separated into two groups using k-means clustering.then the heatmap showing the gene expression of DEGs were plotted by ComplexHeatmap (2.16.0). The Gene Ontology (GO) analysis was conducted based on DEGs using ShinyGO 0.77 with FDR <0.05. The expression pattern of all the genes in each comparison was shown in the volcano plot by using ggplot2 (3.5.2). Volcano plot illustrating gene expression differences between each pairwise comparison. Genes upregulated at 1-week group are highlighted in red, while genes upregulated in the 3-week group are highlighted in blue. Significantly differentially expressed genes (|log2(fold change)| > 1 and -log10 adjusted p-value > 1.3) are labeled.
Assembly: mm10
Supplementary files format and content: Raw reads count (.csv)

molecule: polyA RNA

organism: Mus musculus

source_name: Nucleus Accumbens

extract_protocol:
Bilateral NAc tissue (2.0 mm punch) samples were collected, frozen, and randomized before processing to prevent batch effects. Nuclei were isolated via dounce homogenization of NAc tissue in a cold extraction buffer, followed by filtration and iodixanol gradient centrifugation. NeuN+ nuclei were labeled with an Alexa Fluor 488-conjugated antibody (MAB377X, EMD Millipore Sigma) and sorted using FACS (BD Biosciences) (PMID: 35402909; PMID: 38508188; PMID: 34686347).
~8000 NeuN+ nuclei were used to produce one RNA-seq library and two technical replicates were generated on each NAc sample. RNA was extracted from sorted NeuN+ nuclei (RNeasy Mini Kit 74104, Qiagen), and cDNA were reverse transcribed using Smart-seq3 protocol (PMID: 32518404) with minor modifications. We used a tagmentation-based protocol to construct RNA-seq libraries(PMID: 40164799). The library fragment size was checked using high sensitivity DNA analysis kit (5067-4626, Agilent) on a TapeStation system (4150, Agilent), and any primer-dimers were removed using SPRIselect beads purification. Library was pooled based on the concentrations examined quantified by  using a KAPA library quantification kit (KK4824,Roche).

treatment_protocol: Male C57BL/6 (B6) mice were exposed daily to aggressive male CD-1 mice to induce CSDS first, then the mice were classified either stress-susceptible or resilient based on social interaction test. The nucleus accumbens (NAc) of susceptible and resilient mice, along with non-stressed control mice was collected at 1 week and 3 weeks after CSDS, resulting in six distinct experimental groups: 1wRES, 1wSUS, 1wNS, 3wRES, 3wSUS and 3wNS (n=5-6 per group).

tag: tissue

value: Nucleus Accumbens

tag: cell type

value: Neuron

tag: Sex

value: male

tag: treatment

value: 3-week, Resilient


title: 3-week, Resilient, mouse 1, replicate 1

description: Library name: 3wRES_1_rep1


title: RDY235 SLAM-seq, 25 min IAA, rep A

city: Oklahoma City

first: John

middle: B

last: Ridenour

state: OK

address: 825 NE 13th St.

department: Cell Cycle and Cancer Biology Research Program

institute: Oklahoma Medical Research Foundation

description: Library name: RDHTS270

data_processing:
Paired-end 150 bp reads were preprocessed using fastp (version 0.23.2) and bbduk (BBMap version 39.06). Forward reads were processed using SLAM-DUNK (version 0.4.3), where reads were aligned against the Saccharomyces cerevisiae genome using NextGenMap (version 0.5.5) and SNPs were called using VarScan 2 (version 2.4.5). Total read counts were defined as all reads remaining after filtering in SLAM-DUNK. A conversion per read threshold of ≥ 2 T>C conversions was used to define T>C read counts. Preprocessing and processing steps were implemented as a Snakemake workflow (https://github.com/DonczewLab/SLAM-Seq_Analysis).
Assembly: Saccharomyces cerevisiae strain S288C version R64-3-1 (RefSeq Assembly GCF_000146045.2)
Supplementary files format and content: Raw read count tables are provided in tab-separated values (.tsv) format. *_scer_twotcreadcount_tcount.tsv provides total read counts and T>C read counts with ≥ 2 T>C conversions.

molecule: total RNA

organism: Saccharomyces cerevisiae

growth_protocol: Saccharomyces cerevisiae cells were grown in YPD medium (10 g/l yeast extract, 20 g/l peptone, 20 g/l glucose, 20 mg/ml adenine sulfate) at 30°C with shaking at 220 rpm.

extract_protocol:
RNA purification and DNase I treatment were performed using a Quick-RNA Fungal/Bacterial Miniprep kit and DNase I set (Zymo Research) following the manufacturer’s recommendations with minor modifications. Reagents used during RNA purification were supplemented with DTT to maintain reducing conditions. RNA was treated with 10 mM iodoacetamide for 15 min at 50°C in the dark. Samples were protected from light when possible.
Libraries were constructed as previously described in detail (https://doi.org/10.1186/s44330-024-00008-1) and sequenced on an Illumina NovaSeq 6000 at the Oklahoma Medical Research Foundation Clinical Genomics Center.

treatment_protocol: Saccharomyces cerevisiae cells were grown to an OD600 of ~0.45. Cultures were treated with 1 mM 3-indoleacetic acid (IAA) freshly prepared in DMSO or DMSO alone, vigorously mixed, and incubated for 25 min. Immediately after IAA treatment, cultures were treated with 5 mM 4-thiouracil (4tU) freshly prepared in DMSO or DMSO alone, vigorously mixed, and incubated for 4 min. Immediately after 4tU treatment, each culture was decanted into cold 100% methanol on dry ice. The final OD600 of the cultures was ~0.7. Cells were pelleted at 3,000 g then resuspended in DNA/RNA shield (Zymo Research), flash frozen on dry ice, and stored at –80°C.

tag: cell line

value: yeast cell

tag: genotype

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD30:TRP1

value: 25 min IAA treatment, 4 min 4tU treatment


title: PA08_1_R3_P3

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description: Library name: s238

data_processing:
Reads were demultiplexed from the BCL files and processed into FASTQ files using  DRAGEN analysis v1.3.0 on the Illumina BaseSpace Sequence Hub (Illumina, Inc., San Diego, CA, USA). Processing and quality control of the FASTQ files, differential expression analysis, and exploratory statistical analyses were performed using the R-ODAF_Health_Canada pipeline (https://github.com/R-ODAF/R-ODAF_Health_Canada; accessed March 2025), which manages workflows using Snakemake v8.0 (Mölder et al. 2021) and relies on scripts in R (v.4.3.2). The preprocessing steps use fastp v0.23.2 for trimming (Chen et al. 2018), STAR v2.7.8a (Dobin et al. 2013) to perform alignment of raw reads to the reference sequence and the qCount function of the QuasR R package (v1.30.0; (Gaidatzis et al. 2015) to extract the feature counts from the aligned reads (BAM files) using features specified in a GTF file. A samples-by-probes count matrix was produced.
Assembly: Probe sequence set provided by biospyder based on Human Whole Transcriptome kit v2.1
Supplementary files format and content: Tab-delimited table containing read counts per TempO-Seq probe

organism: Homo sapiens

source_name: Mammary

growth_protocol: MCF-7 cells (ATCC, Manassas, Virginia) were cultured in 10 cm dishes (Corning Falcon No. 353003, Corning, New York) with Dulbecco’s modified Eagle’s medium (DMEM; Gibco, Thermo Fisher Scientific, Waltham, Massachusetts) containing 10% fetal bovine serum (FBS; Wisent Bioproducts, Saint-Jean Baptiste, QC, Canada), and 1% penicillin and streptomycin (P/S; Wisent), at 37°C in a humidified atmosphere (5% CO2).

extract_protocol:
Cells were washed with phosphate-buffered saline and lysed in situ using 2x TempO-Seq lysis buffer diluted with an equal amount of PBS for TempO-Seq library building.
Gene expression was measured using the TempO-Seq Human Whole Transcriptome v2.1 kit (BioSpyder Technologies Inc, Carlsbad, California) as per the manufacturer’s instructions

treatment_protocol: For the experiment, cells were washed with phosphate-buffered saline (PBS) and the media were replaced with phenol red-free DMEM supplemented with 5% charcoal-dextran stripped FBS (CD-FBS) to eliminate estrogens present in commercial media and serum (Atlas et al. 2003) for 24 h. Cells were then seeded into clear 96-well plates (Corning Falcon No. 353075) at a density of 2.0 x 104 cells per well in phenol red-free DMEM supplemented with 5% CD-FBS and 1% P/S. After 24 h, the medium was removed and replaced with phenol red-free DMEM containing 5% CD-FBS and 1% P/S and chemicals of interest. Cells were exposed for 48 h, in quadruplicates, to BPA, the 12 chemicals of interest at eight different concentrations (0.001, 0.01, 0.1, 0.5, 1, 5, 10, 50 µM), 17β-estradiol (E2; 0.1, 1 nM) as a positive control, and at least four plate-matched solvent controls (0.1% DMSO).

value: Mammary

value: Epithelial

value: WT

tag: chemical

value: plastic additive 08

tag: dose

tag: batch


title: 3-week, Susceptible, mouse 6, replicate 2

description: Library name: 3wSUS_6_rep2

value: 3-week, Susceptible


title: RDY235 SLAM-seq, 25 min DMSO, rep C

description: Library name: RDHTS269

value: 25 min DMSO treatment, 4 min 4tU treatment


title: HepG2.batch1.MET.rep3.B07

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

institute: McGill University

description: Library name: HepG2_Batch1_MET_3_B07

library_source: other

data_processing:
Reads were aligned using STAR alignment on QIAGEN's CLC workbench software (v25.0.1) and Kallisto alignment on ExpressAnalyst
Raw counts were logCPM normalized and filtered for low abundance (5) and variance (15) using ExpressAnalyst
Normalized counts were analyzed for differential expression using DESeq2
Assembly: CLC workbench used hg38.p14 Ensembl v113 GCA_000001405.29; ExpressAnalyst used hg38.p14 GCA_000001405
Supplementary files format and content: raw files and count files are provided as fastq.gz files and .txt files, respectively.

molecule: other

source_name: cell lysate

growth_protocol: from ms

extract_protocol:
cells were lysed in Qiagen's proprietary lysis buffer and used directly for library preparation
ultraplex 3' transcriptome library preparation following Qiagen's UPXome protocol

treatment_protocol: cells were exposed to various concentrations of 6ppd-quinone for 24 hours after seeding at 35,000 cells per well

value: liver

value: hepatocyte

value: cell line


title: HepG2.batch1.MET.rep3.A07

description: Library name: HepG2_Batch1_MET_3_A07


title: 3-week, Susceptible, mouse 6, replicate 1

description: Library name: 3wSUS_6_rep1


title: PA08_0-5_R3_P3

description: Library name: s237

value: chemical exposure


title: RDY235 SLAM-seq, 25 min DMSO, rep B

description: Library name: RDHTS268


title: HepG2.batch1.MET.rep2.H07

description: Library name: HepG2_Batch1_MET_2_H07


title: HepG2.batch1.MET.rep2.G07

description: Library name: HepG2_Batch1_MET_2_G07


title: RDY235 SLAM-seq, 25 min DMSO, rep A

description: Library name: RDHTS267


title: PA08_0-05_R3_P3

description: Library name: s235


title: 3-week, Susceptible, mouse 5, replicate 2

description: Library name: 3wSUS_5_rep2

value: Nucleus Accumbens


title: PA08_0-1_R3_P3

description: Library name: s236


title: RDY262 SLAM-seq, 25 min IAA, rep C

description: Library name: RDHTS500

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD63:TRP1


title: HepG2.batch1.MET.rep2.F07

description: Library name: HepG2_Batch1_MET_2_F07


title: PA08_0-01_R3_P3

description: Library name: s234


title: RDY262 SLAM-seq, 25 min IAA, rep B

description: Library name: RDHTS499


title: 3-week, Susceptible, mouse 4, replicate 2

description: Library name: 3wSUS_4_rep2

value: Neuron

value: male


title: HepG2.batch1.MET.rep2.E07

description: Library name: HepG2_Batch1_MET_2_E07


title: PA08_0-001_R3_P3

description: Library name: s233


title: 3-week, Susceptible, mouse 4, replicate 1

description: Library name: 3wSUS_4_rep1


title: RDY262 SLAM-seq, 25 min IAA, rep A

description: Library name: RDHTS498

value: yeast cell


title: HepG2.batch1.MET.rep2.D07

description: Library name: HepG2_Batch1_MET_2_D07


title: TBBPS_50_R3_P3

description: Library name: s232

value: tetrabromo bisphenol S


title: RDY262 SLAM-seq, 25 min DMSO, rep C

description: Library name: RDHTS497


title: 3-week, Susceptible, mouse 3, replicate 2

description: Library name: 3wSUS_3_rep2


title: HepG2.batch1.MET.rep2.C07

description: Library name: HepG2_Batch1_MET_2_C07


title: TBBPS_10_R3_P3

description: Library name: s231


title: 3-week, Susceptible, mouse 3, replicate 1

description: Library name: 3wSUS_3_rep1


title: RDY262 SLAM-seq, 25 min DMSO, rep B

description: Library name: RDHTS496


title: TBBPS_5_R3_P3

description: Library name: s230


title: HepG2.batch1.MET.rep2.B07

description: Library name: HepG2_Batch1_MET_2_B07


title: RDY262 SLAM-seq, 25 min DMSO, rep A

description: Library name: RDHTS495


title: 3-week, Susceptible, mouse 2, replicate 2

description: Library name: 3wSUS_2_rep2


title: HepG2.batch1.MET.rep2.A07

description: Library name: HepG2_Batch1_MET_2_A07


title: TBBPS_1_R3_P3

description: Library name: s229


title: RDY252 SLAM-seq, 25 min IAA, rep C

description: Library name: RDHTS338

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD47:TRP1

value: 25 min IAA treatment, 4 min 4tU treatment


title: TBBPS_0-5_R3_P3

description: Library name: s228

value: Mammary

value: Epithelial


title: HepG2.batch1.MET.rep1.H07

description: Library name: HepG2_Batch1_MET_1_H07


title: 3-week, Susceptible, mouse 1, replicate 2

description: Library name: 3wSUS_1_rep2


title: 3-week, Susceptible, mouse 2, replicate 1

description: Library name: 3wSUS_2_rep1


title: RDY252 SLAM-seq, 25 min IAA, rep B

description: Library name: RDHTS337


title: HepG2.batch1.MET.rep1.G07

description: Library name: HepG2_Batch1_MET_1_G07


title: TBBPS_0-1_R3_P3

description: Library name: s227

value: WT


title: RDY252 SLAM-seq, 25 min IAA, rep A

description: Library name: RDHTS336


title: HepG2.batch1.MET.rep1.F07

description: Library name: HepG2_Batch1_MET_1_F07


title: TBBPS_0-01_R3_P3

description: Library name: s226


title: 3-week, Susceptible, mouse 1, replicate 1

description: Library name: 3wSUS_1_rep1

value: 3-week, Susceptible


title: 1-week, Resilient, mouse 6, replicate 2

description: Library name: 1wRES_6_rep2

value: 1-week, Resilient


title: RDY252 SLAM-seq, 25 min DMSO, rep C

description: Library name: RDHTS335

value: 25 min DMSO treatment, 4 min 4tU treatment


title: HepG2.batch1.MET.rep1.E07

description: Library name: HepG2_Batch1_MET_1_E07

value: liver

value: hepatocyte


title: 1-week, Resilient, mouse 6, replicate 1

description: Library name: 1wRES_6_rep1


title: TBBPS_0-001_R3_P3

description: Library name: s225

value: chemical exposure


title: RDY252 SLAM-seq, 25 min DMSO, rep B

description: Library name: RDHTS334


title: DABPA_10_R3_P3

description: Library name: s224

value: diallyl bisphenol A


title: 1-week, Resilient, mouse 5, replicate 2

description: Library name: 1wRES_5_rep2

value: Nucleus Accumbens


title: HepG2.batch1.MET.rep1.D07

description: Library name: HepG2_Batch1_MET_1_D07

value: cell line


title: HepG2.batch1.MET.rep1.C07

description: Library name: HepG2_Batch1_MET_1_C07


title: DABPA_5_R3_P3

description: Library name: s223


title: 1-week, Resilient, mouse 5, replicate 1

description: Library name: 1wRES_5_rep1

value: Neuron

value: male


title: HepG2.batch1.MET.rep1.B07

description: Library name: HepG2_Batch1_MET_1_B07


title: RDY252 SLAM-seq, 25 min DMSO, rep A

description: Library name: RDHTS333

value: yeast cell


title: DABPA_1_R3_P3

description: Library name: s222


title: 1-week, Resilient, mouse 4, replicate 2

description: Library name: 1wRES_4_rep2


title: RDY247 SLAM-seq, 25 min IAA, rep C

description: Library name: RDHTS452

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD42:TRP1


title: HepG2.batch1.MET.rep1.A07

description: Library name: HepG2_Batch1_MET_1_A07


title: DABPA_0-5_R3_P3

description: Library name: s221


title: 1-week, Resilient, mouse 4, replicate 1

description: Library name: 1wRES_4_rep1


title: RDY247 SLAM-seq, 25 min IAA, rep A

description: Library name: RDHTS450

value: 25 min IAA treatment, 4 min 4tU treatment


title: DABPA_0-1_R3_P3

description: Library name: s220

value: Mammary


title: HepG2.batch1.IMZ.rep3.H04

description: Library name: HepG2_Batch1_IMZ_3_H04


title: RDY247 SLAM-seq, 25 min DMSO, rep C

description: Library name: RDHTS449


title: HepG2.batch1.IMZ.rep3.G04

description: Library name: HepG2_Batch1_IMZ_3_G04


title: DABPA_0-05_R3_P3

description: Library name: s219

value: Epithelial


title: 1-week, Resilient, mouse 3, replicate 1

description: Library name: 1wRES_3_rep1


title: RDY247 SLAM-seq, 25 min DMSO, rep B

description: Library name: RDHTS448


title: HepG2.batch1.IMZ.rep3.F04

description: Library name: HepG2_Batch1_IMZ_3_F04


title: DABPA_0-01_R3_P3

description: Library name: s218

value: WT


title: 1-week, Resilient, mouse 3, replicate 2

description: Library name: 1wRES_3_rep2


title: RDY247 SLAM-seq, 25 min DMSO, rep A

description: Library name: RDHTS447


title: 1-week, Resilient, mouse 2, replicate 2

description: Library name: 1wRES_2_rep2


title: RDY247 SLAM-seq, 25 min IAA, rep B

description: Library name: RDHTS451


title: HepG2.batch1.IMZ.rep3.E04

description: Library name: HepG2_Batch1_IMZ_3_E04


title: 1-week, Resilient, mouse 2, replicate 1

description: Library name: 1wRES_2_rep1


title: DABPA_0-001_R3_P3

description: Library name: s217


title: HepG2.batch1.IMZ.rep3.D04

description: Library name: HepG2_Batch1_IMZ_3_D04


title: RDY246 SLAM-seq, 25 min IAA, rep C

description: Library name: RDHTS446

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD41:TRP1


title: BPK_50_R3_P3

description: Library name: s216

value: bisphenol K


title: 1-week, Resilient, mouse 1, replicate 2

description: Library name: 1wRES_1_rep2

value: 1-week, Resilient


title: RDY246 SLAM-seq, 25 min IAA, rep B

description: Library name: RDHTS445


title: BPK_10_R3_P3

description: Library name: s215


title: 1-week, Resilient, mouse 1, replicate 1

description: Library name: 1wRES_1_rep1


title: HepG2.batch1.IMZ.rep3.C04

description: Library name: HepG2_Batch1_IMZ_3_C04

value: liver


title: HepG2.batch1.IMZ.rep3.B04

description: Library name: HepG2_Batch1_IMZ_3_B04

value: hepatocyte


title: 1-week, Susceptible, mouse 5, replicate 2

description: Library name: 1wSUS_5_rep2

value: 1-week, Susceptible


title: RDY246 SLAM-seq, 25 min DMSO, rep C

description: Library name: RDHTS443

value: 25 min DMSO treatment, 4 min 4tU treatment


title: BPK_5_R3_P3

description: Library name: s214

value: chemical exposure


title: BPK_1_R3_P3

description: Library name: s213


title: 1-week, Susceptible, mouse 5, replicate 1

description: Library name: 1wSUS_5_rep1

value: Nucleus Accumbens


title: RDY246 SLAM-seq, 25 min DMSO, rep B

description: Library name: RDHTS442


title: HepG2.batch1.IMZ.rep3.A04

description: Library name: HepG2_Batch1_IMZ_3_A04

value: cell line


title: HepG2.batch1.IMZ.rep2.H04

description: Library name: HepG2_Batch1_IMZ_2_H04


title: 1-week, Susceptible, mouse 4, replicate 2

description: Library name: 1wSUS_4_rep2

value: Neuron

value: male


title: RDY246 SLAM-seq, 25 min DMSO, rep A

description: Library name: RDHTS441

value: yeast cell


title: HepG2.batch1.IMZ.rep2.G04

description: Library name: HepG2_Batch1_IMZ_2_G04


title: BPK_0-1_R3_P3

description: Library name: s211


title: 1-week, Susceptible, mouse 4, replicate 1

description: Library name: 1wSUS_4_rep1


title: BPK_0-5_R3_P3

description: Library name: s212


title: BPK_0-01_R3_P3

description: Library name: s210


title: HepG2.batch1.IMZ.rep2.F04

description: Library name: HepG2_Batch1_IMZ_2_F04


title: RDY245 SLAM-seq, 25 min IAA, rep C

description: Library name: RDHTS428

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD40:TRP1

value: 25 min IAA treatment, 4 min 4tU treatment


title: BPK_0-001_R3_P3

description: Library name: s209

value: Mammary

value: Epithelial


title: HepG2.batch1.IMZ.rep2.E04

description: Library name: HepG2_Batch1_IMZ_2_E04


title: 1-week, Susceptible, mouse 3, replicate 1

description: Library name: 1wSUS_3_rep1


title: RDY245 SLAM-seq, 25 min IAA, rep B

description: Library name: RDHTS427


title: RDY245 SLAM-seq, 25 min IAA, rep A

description: Library name: RDHTS426


title: HepG2.batch1.IMZ.rep2.D04

description: Library name: HepG2_Batch1_IMZ_2_D04


title: 1-week, Susceptible, mouse 2, replicate 2

description: Library name: 1wSUS_2_rep2


title: 1-week, Susceptible, mouse 3, replicate 2

description: Library name: 1wSUS_3_rep2


title: BPM_10_R3_P3

description: Library name: s208

value: WT

value: bisphenol M


title: HepG2.batch1.IMZ.rep2.C04

description: Library name: HepG2_Batch1_IMZ_2_C04


title: RDY245 SLAM-seq, 25 min DMSO, rep C

description: Library name: RDHTS425


title: 1-week, Susceptible, mouse 2, replicate 1

description: Library name: 1wSUS_2_rep1


title: BPM_5_R3_P3

description: Library name: s207


title: RDY245 SLAM-seq, 25 min DMSO, rep B

description: Library name: RDHTS424


title: HepG2.batch1.IMZ.rep2.B04

description: Library name: HepG2_Batch1_IMZ_2_B04


title: 1-week, Susceptible, mouse 1, replicate 2

description: Library name: 1wSUS_1_rep2


title: BPM_1_R3_P3

description: Library name: s206


title: RDY245 SLAM-seq, 25 min DMSO, rep A

description: Library name: RDHTS423


title: BPM_0-5_R3_P3

description: Library name: s205


title: HepG2.batch1.IMZ.rep2.A04

description: Library name: HepG2_Batch1_IMZ_2_A04


title: RDY244 SLAM-seq, 25 min IAA, rep C

description: Library name: RDHTS470

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD39:TRP1


title: HepG2.batch1.IMZ.rep1.H05

description: Library name: HepG2_Batch1_IMZ_1_H05

value: liver


title: 1-week, Susceptible, mouse 1, replicate 1

description: Library name: 1wSUS_1_rep1


title: BPM_0-1_R3_P3

description: Library name: s204


title: Mouse Brain R8

city: CHICACO

first: Feng

last: Yue

state: ILLINOIS

address: 303 E. Superior Simpson Querrey

institute: Northwestern University Feinberg School of Medicine

description:
Library name: Mouse Brain R8
ligated genomic DNA

library_source: genomic

data_processing:
The raw fastq reads adapters were first detected and trimmed with Trim-Garole (0.6.10) (https://github.com/FelixKrueger/TrimGalore). The cleaned fastq files were processed using bbduk function from BBtools (BBMap 39.01) (https://sourceforge.net/projects/bbmap/), retaining only reads that contained linker sequences (linker1 and linker2). The filtered reads were then converted to Cell Ranger ATAC format (10x Genomics). Specifically, the original paired-end fastq files included Read1 and Read2, with Read2 containing both the genomic DNA sequences and barcode sequences. The original Read2 were split into genomic DNA sequences as the new Read1 and barcode (barcode A and barcode B) sequences as new Read2, and the original Read1 sequences were retained as the new Read3. For spatial ATAC-seq analysis, the resulting fastq files were aligned to the mouse (mm10) or human (GRCh38) reference genome using Cell Ranger ATAC v2.0 (https://support.10×genomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac) (10x Genomics). The resulting fragment.tsv file was used for downstream analysis. For spatial Hi-C analysis, the newly generated Read1 and Read3 were aligned to the corresponding reference genome using the runHiC pipeline (https://github.com/XiaoTaoWang/HiC_pipeline). The resulting pairs files were further split into 2,500 separate pairs files based on the barcode information in the new Read2. These pairs files were used for downstream analysis.
Assembly: mm10
Supplementary files format and content: fragments.tsv.gz: a BED-like tabular file, where each line represents a unique fragment captured by the assay.
Supplementary files format and content: fragments.tsv.gz.tbi: the index file for the fragments.tsv.gz file.
Supplementary files format and content: hic.fragments.sorted.tsv.gz: a BED-like tabular file, where each line represents a unique fragment that was one end of the hic pairs.
Supplementary files format and content: hic.fragments.sorted.tsv.gz.tbi: the index file for the hic.fragments.sorted.tsv.gz file.
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: metadata.json: metadata in json format
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue

molecule: genomic DNA

source_name: mouse brain anterior hippocampus/thalamus section

extract_protocol:
brains of C57BL/6 mice are sectioned in coronal (cross) oreintation. Brains are snapped frozen in OCT without any fixative, sectioned in coronal orientation at a thickness of 7-10 microns. Sections are mounted on microarray grade slides and crosslinked with 2% (final concentration) formaldehyde to preserve native chromatin structure.
After nuclei permeabilization with 0.55% SDS solution, enzyme digestion and proximity ligation of chromatin DNA fragments was performed on the tissue slide. Next, Tn5 transposition is performed directly on tissue sections using in-house assembled Tn5 transposome complex to fragment proximity-ligated chromatin DNA. Horizonal barcodes A (A1–A50) and vertical barcodes B (B1–B50) are sequentially delivered across tissue surface, using microchannels and ligated to the universal ligation linker. This creates a two-dimensional grid of spatially barcoded tissue pixels (n = 2,500). After reverse crosslinking and purification, the biotin-ligated chromatin fragments are enriched for sequencing library preparation. Finally, based on the barcode information, we can build the chromatin interaction maps for each pixel from the original tissue slides.


title: RDY244 SLAM-seq, 25 min IAA, rep B

description: Library name: RDHTS469


title: HepG2.batch1.IMZ.rep1.G05

description: Library name: HepG2_Batch1_IMZ_1_G05

value: hepatocyte


title: BPM_0-05_R3_P3

description: Library name: s203


title: RDY244 SLAM-seq, 25 min IAA, rep A

description: Library name: RDHTS468


title: Mouse Brain R6

description:
Library name: Mouse Brain R6
ligated genomic DNA

source_name: mouse brain anterior hypothalamus coronal section


title: HepG2.batch1.IMZ.rep1.F05

description: Library name: HepG2_Batch1_IMZ_1_F05


title: BPM_0-01_R3_P3

description: Library name: s202


title: RDY244 SLAM-seq, 25 min DMSO, rep C

description: Library name: RDHTS467


title: WT-MCD-3

city: Guangzhou

first: Yongjian

last: zhou

address: No.1, Pan Fu Road, Yuexiu District

country: China

institute: Guangzhou First People’s Hospital

description:
Library name: sample6
WT_MCD-3_count

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp  (version 0.18.0).
Short reads alignment tool Bowtie2  (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2 2.1.0 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference_x0002_based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: GRCm39
Supplementary files format and content: excel files include raw counts and TPM values for each Sample

source_name: liver

extract_protocol:
total RNA was extracted by Trizol(Life technologies)
The extracted mRNA is enriched using mRNA Capture Beads. After purification with beads, the mRNA is fragmented using high temperatures. The fragmented mRNA is then used as a template to synthesize the first strand of cDNA in a reverse transcription enzyme mixture system. While synthesizing the second strand of cDNA, end repair and A-tailing are completed. Next, adapters are ligated, and Hieff NGS® DNA Selection Beads are used for purification to select target fragments.

value: MCD


title: HepG2.batch1.IMZ.rep1.E05

description: Library name: HepG2_Batch1_IMZ_1_E05


title: WT-MCD-2

description:
Library name: sample5
WT_MCD-2_count


title: BPM_0-001_R3_P3

description: Library name: s201


title: HepG2.batch1.IMZ.rep1.D05

description: Library name: HepG2_Batch1_IMZ_1_D05


title: RDY244 SLAM-seq, 25 min DMSO, rep B

description: Library name: RDHTS466

value: 25 min DMSO treatment, 4 min 4tU treatment


title: BPE_50_R3_P3

description: Library name: s200

value: chemical exposure

value: bisphenol E


title: WT-MCD-1

description:
Library name: sample4
WT_MCD-1_count


title: RDY244 SLAM-seq, 25 min DMSO, rep A

description: Library name: RDHTS465


title: BPE_10_R3_P3

description: Library name: s199


title: WT-MCS-3

description:
Library name: sample3
WT_MCS-3_count

value: MCS


title: HepG2.batch1.IMZ.rep1.C05

description: Library name: HepG2_Batch1_IMZ_1_C05

value: cell line


title: RDY243 SLAM-seq, 25 min IAA, rep C

description: Library name: RDHTS332

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD38:TRP1


title: HepG2.batch1.IMZ.rep1.B05

description: Library name: HepG2_Batch1_IMZ_1_B05


title: BPE_5_R3_P3

description: Library name: s198


title: RDY243 SLAM-seq, 25 min IAA, rep B

description: Library name: RDHTS331

value: yeast cell


title: WT-MCS-2

description:
Library name: sample2
WT_MCS-2_count


title: BPE_1_R3_P3

description: Library name: s197


title: HepG2.batch1.IMZ.rep1.A05

description: Library name: HepG2_Batch1_IMZ_1_A05


title: WT-MCS-1

description:
Library name: sample1
WT_MCS-1_count


title: RDY243 SLAM-seq, 25 min IAA, rep A

description: Library name: RDHTS330


title: HepG2.batch1.IMI.rep3.H05

description: Library name: HepG2_Batch1_IMI_3_H05


title: BPE_0-5_R3_P3

description: Library name: s196


title: BPE_0-1_R3_P3

description: Library name: s195


title: HepG2.batch1.IMI.rep3.G05

description: Library name: HepG2_Batch1_IMI_3_G05


title: Pool 2, Epithelium, Diestrus

city: Houston

first: Peixin

last: Jiang

state: TX

address: 1515 Holcombe Blvd

institute: UT MD Anderson Cancer Center

description: Library name: Sample 4

library_source: transcriptomic single cell

data_processing:
Raw data from the sequencer was processed 10x Genomics Cell Ranger 8.0.0. pipeline to generate gene-cell matrices.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: Endometrium

extract_protocol:
The uterine horns were dissected and divided into approximately four segments, which were then placed in a 1% trypsin solution. Following digestion for 45 minutes at 37°C, the uterine epithelium was carefully separated using a mouth pipette and fine tweezers. The isolated epithelium was further digested with 5 mg/ml collagenase and mechanically disrupted into a single-cell suspension using a syringe plunger. After staining with DAPI, live cells were sorted using a cell sorter prior to library construction.
Library was construed by following the manufactor's manual (10x Genomics Chromium Single Cell 3' Gene Expression v4 protocol). Briefly, cells, master mix, gel beads, and partitioning oil onto the Chromium Chip and run on the Chromium Controller to generate Gel Bead Emulsions (GEMs). GEMs was incubated on PCR thermocycler for reverse transcription. The cDNA was enzymatically fragmented, end repaired, ligated with sequencing adapater, and amplified with sample-specific index primers. Library was purtified using SPRIselect beads, quantified with Qubit, and assesssed for size distribution using TapeStation before sequencing.

value: Endometrium

value: Epithelium


title: Pool 1, Epithelium, Estrus

description: Library name: Sample 1


title: RDY243 SLAM-seq, 25 min DMSO, rep C

description: Library name: RDHTS329


title: BPE_0-01_R3_P3

description: Library name: s194

value: Mammary


title: HepG2.batch1.IMI.rep3.F05

description: Library name: HepG2_Batch1_IMI_3_F05


title: RDY243 SLAM-seq, 25 min DMSO, rep B

description: Library name: RDHTS328


title: Pool 2, ALDH-Low, Replicate 2

description:
Library name: Sample 10
LO_7

data_processing:
Raw sequencing reads were preprocessed using fastp for low-quality reads filtering and adapter-trimming.
Reads were aligned to reference genome using STAR Aligner.
The gene count table was generated using featureCounts.
The raw counts were filtered, normalized, and analyzed using DESeq2.
Assembly: GRCm39
Supplementary files format and content: Tab-sperated value files.

extract_protocol:
We used Direct-zol RNA Miniprep Kit (Zymo Research) to extract RNA.
Library was prepared using Illumina TruSeq RNA Library Prep Kit and sequenced with Illumina Novaseq.


title: RDY243 SLAM-seq, 25 min DMSO, rep A

description: Library name: RDHTS327


title: BPE_0-001_R3_P3

description: Library name: s193

value: Epithelial


title: HepG2.batch1.IMI.rep3.E05

description: Library name: HepG2_Batch1_IMI_3_E05


title: Pool 2, ALDH-Low, Replicate 1

description:
Library name: Sample 9
LO_6

value: WT


title: RDY242 SLAM-seq, 25 min IAA, rep C

description: Library name: RDHTS284

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD37:TRP1

value: 25 min IAA treatment, 4 min 4tU treatment


title: PC_UH_R2_P2

description: Library name: s192

value: technical control

value: universal human RNA


title: Pool 1, ALDH-Low, Replicate 3

description:
Library name: Sample 8
LO_5


title: HepG2.batch1.IMI.rep3.D05

description: Library name: HepG2_Batch1_IMI_3_D05

value: liver

value: hepatocyte


title: RDY242 SLAM-seq, 25 min IAA, rep B

description: Library name: RDHTS283


title: Pool 1, ALDH-Low, Replicate 2

description:
Library name: Sample 7
LO_4


title: HepG2.batch1.IMI.rep3.C05

description: Library name: HepG2_Batch1_IMI_3_C05


title: RDY242 SLAM-seq, 25 min IAA, rep A

description: Library name: RDHTS282


title: HepG2.batch1.IMI.rep3.B05

description: Library name: HepG2_Batch1_IMI_3_B05


title: DMSO_0-1_R20_P2

description: Library name: s190

value: vehicle control

value: dimethyl sulfoxide


title: PC_B_R2_P2

description: Library name: s191

value: brain RNA


title: Pool 1, ALDH-Low, Replicate 1

description:
Library name: Sample 6
LO_3


title: RDY242 SLAM-seq, 25 min DMSO, rep C

description: Library name: RDHTS281

value: 25 min DMSO treatment, 4 min 4tU treatment


title: HepG2.batch1.IMI.rep3.A05

description: Library name: HepG2_Batch1_IMI_3_A05

value: cell line


title: DMSO_0-1_R19_P2

description: Library name: s189


title: RDY242 SLAM-seq, 25 min DMSO, rep B

description: Library name: RDHTS280

value: yeast cell


title: Pool 2, ALDH-High, Replicate 2

description:
Library name: Sample 5
HI_7

value: Endometrium


title: HepG2.batch1.IMI.rep2.H06

description: Library name: HepG2_Batch1_IMI_2_H06


title: DMSO_0-1_R18_P2

description: Library name: s188


title: Pool 2, ALDH-High, Replicate 1

description:
Library name: Sample 4
HI_6

value: Epithelium


title: HepG2.batch1.IMI.rep2.G06

description: Library name: HepG2_Batch1_IMI_2_G06


title: DMSO_0-1_R17_P2

description: Library name: s187

value: Mammary


title: Pool 1, ALDH-High, Replicate 3

description:
Library name: Sample 3
HI_5


title: RDY291 ChEC-seq, 25 min IAA, rep C

description: Library name: RDHTS744

data_processing:
Paired-end 150 bp reads were preprocessed using bbduk (BBMap version 39.06) and aligned using Bowtie 2 (version 2.5.0). BAM files were created, sorted, and indexed using Samtools (version 1.18). Genome coverage was calculated and normalized by counts per million (CPM) using deepTools2 (version 3.5.4). Average genome coverage across replicates was calculated using BEDTools (version 2.30.0) and bedGraphToBigWig. Preprocessing and processing steps were implemented as a Snakemake workflow (https://github.com/DonczewLab/ChEC-Seq_Analysis).
Assembly: Saccharomyces cerevisiae strain S288C version R64-3-1 (RefSeq Assembly GCF_000146045.2)
Supplementary files format and content: Processed data (counts per million [CPM] normalized genome coverage) are provided in bigwig (.bw) format.
Library strategy: ChEC-seq

extract_protocol:
DNA was purified using a ChIP DNA Clean and Concentrator kit (Zymo Research). Cleaved DNA was selected based on size using Sera-Mag Speedbeads (Cytiva) prepared as described (dx.doi.org/10.17504/protocols.io.x54v9p7b1g3e/v2).
Libraries were constructed using a Next Ultra II DNA Library Prep kit (New England Biolabs) as described (https://doi.org/10.1371/journal.pgen.1010945) and sequenced on an Illumina NovaSeq 6000 at the Oklahoma Medical Research Foundation Clinical Genomics Center.

treatment_protocol: Saccharomyces cerevisiae cells were grown to an OD600 of ~0.5. Cultures were treated with 1 mM 3-indoleacetic acid (IAA) freshly prepared in DMSO or DMSO alone, vigorously mixed, and incubated for 25 min. The final OD600 of the cultures was ~0.7. Cells were pelleted at 3,000 g then resuspended in Buffer A, permeabilized, and treated with calcium chloride to induce DNA cleavage.

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD17:TRP1

value: 25 min IAA treatment


title: RDY278 SLAM-seq, 25 min IAA, rep C

description: Library name: RDHTS548

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD72:TRP1


title: RDY242 SLAM-seq, 25 min DMSO, rep A

description: Library name: RDHTS279

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD37:TRP1


title: AO425_0-01_R1_P5

description: Library name: s386

value: Epithelial

value: WT

value: chemical exposure

value: antioxidant 425


title: HepG2.batch2.DIQ.rep2.A01

description: Library name: HepG2_Batch2_DIQ_2_A01

value: liver

value: hepatocyte


title: mNSC, control R2

city: Planegg

first: Anna

last: Danese

address: Grosshaderner strasse 9

country: Germany

institute: Ludwig Maximilians University

description:
Library name: EKDL250034816
reads_psite_list_th_all.csv

data_processing:
sequencing primers and adpaters were removed with Cutadapt v5.2
UMIs were processed with UMI-tools v1.1.6
reads were aligned with STAR v2.7.10b
psites were obtained using RiboWaltz
Assembly: GRCm39 M35 primary assembly
Supplementary files format and content: contains number of psites for all genes and all samples
Library strategy: Ribo-Seq

source_name: Neural Stem Cells

extract_protocol:
Total RNA and Ribosomoe pulldown was done by Immagina biotechnology
library preparation was done by Immagina biotechnology using LACEseq library preparation

value: Neural Stem Cells

value: GF, control


title: HepG2.batch1.IMI.rep2.F06

description: Library name: HepG2_Batch1_IMI_2_F06

value: cell line


title: RDY291 ChEC-seq, 25 min IAA, rep B

description: Library name: RDHTS742

value: yeast cell


title: DMSO_0-1_R16_P2

description: Library name: s186

value: vehicle control

value: dimethyl sulfoxide


title: Pool 1, ALDH-High, Replicate 2

description:
Library name: Sample 2
HI_4

value: Endometrium

value: Epithelium


title: RDY278 SLAM-seq, 25 min IAA, rep B

description: Library name: RDHTS547

value: 25 min IAA treatment, 4 min 4tU treatment


title: 3-week, Susceptible, mouse 5, replicate 1

description: Library name: 3wSUS_5_rep1

value: Nucleus Accumbens

value: Neuron

value: male

value: 3-week, Susceptible


title: HepG2.batch1.IMI.rep2.E06

description: Library name: HepG2_Batch1_IMI_2_E06


title: Pool 1, ALDH-High, Replicate 1

description:
Library name: Sample 1
HI_3

value: WT


title: DMSO_0-1_R15_P2

description: Library name: s185

value: Mammary

value: Epithelial


title: RDY278 SLAM-seq, 25 min IAA, rep A

description: Library name: RDHTS546

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD72:TRP1


title: HepG2.batch1.IMI.rep2.D06

description: Library name: HepG2_Batch1_IMI_2_D06

value: liver

value: hepatocyte


title: CD4+ cells from IRI-6h mice

city: Sendai

first: Kosuke

last: Sato

state: Miyagi

address: 2-1 Seiryo-machi, Aoba-ku

country: Japan

institute: Tohoku University

description: Library name: PR4106_04_a

data_processing:
Sample demultiplexing, barcode processing, single cell 3' and 5' gene counting and aggregation were made using the Cell Ranger software v7.1.0.
Assembly: mm10
Supplementary files format and content: 10X Genomics Chromium gene BC Cellular Barcodes (Tab-separated values files)
Supplementary files format and content: 10X Genomics Chromium gene BC Cellular Features (Tab-separated values files)
Supplementary files format and content: 10X Genomics Chromium gene BC Cellular Matrix (matrix files)

source_name: Small intestine

extract_protocol:
Small intestinal lamina propria cells were collected utilizing a Lamina Propria Dissociation Kit (Miltenyi Biotec) following the manufacturer’s protocol, followed by density gradient separation using Percoll (Cytiva). Single-cell suspensions were obtained from gradient layers between 30 % and 70 % Percoll. Live CD4+ cells were enriched using Dead Cell Removal Kit and CD11b or CD4 Microbeads (all from Miltenyi Biotec), and fixed for 19 hours at 4 °C with Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10x Genomics).
For each fixed sample, the detection probe of the Chromium Fixed RNA Kit was hybridized to RNA in the cells, and a ligation reaction performed to bind adjacent hybridized probes. After mixing each sample, barcode primer beads and the cells were encapsulated, annealing the probes and the primers, and an extension reaction performed to add a cell identification adapter sequence to the detection probe using ChromiumX. To construct the library, samples were amplified and purified by polymerase chain reaction using index primers.

value: Small intestine


title: NC_R4_P2

description: Library name: s184

value: technical control

value: lysis buffer


title: RDY278 SLAM-seq, 25 min DMSO, rep C

description: Library name: RDHTS545

value: yeast cell

value: 25 min DMSO treatment, 4 min 4tU treatment


title: CD4+ cells from IRI-0h mice

description: Library name: PR4106_03_a


title: DMSO_0-1_R14_P2

description: Library name: s182

value: vehicle control

value: dimethyl sulfoxide


title: HepG2.batch1.IMI.rep2.C06

description: Library name: HepG2_Batch1_IMI_2_C06

value: cell line


title: RDY278 SLAM-seq, 25 min DMSO, rep A

description: Library name: RDHTS543


title: HepG2.batch1.IMI.rep2.B06

description: Library name: HepG2_Batch1_IMI_2_B06


title: NC_R3_P2

description: Library name: s183


title: RDY278 SLAM-seq, 25 min DMSO, rep B

description: Library name: RDHTS544


title: HepG2.batch1.IMI.rep2.A06

description: Library name: HepG2_Batch1_IMI_2_A06


title: Old7

city: Zurich-Schlieren

first: Ataman

last: Sendoel

address: Wagistrasse 12

country: Switzerland

institute: University of Zurich

description:
Total RNA footprint
P662

data_processing:
*library strategy: sc-Ribo-seq
We utilized fastp for trimming adapters and moving 10nt UMI sequence to the fastq header with final read length between 26-34 using the options: --umi --umi_loc=read1 --umi_len=10 -a TGGAATTCTCGG --trim_poly_g --trim_poly_x -l 26 --length_limit 34. Next the rRNA and tRNA sequences were removed with the bowtie2 with options -D 20 -R 3 -N 1 -L 15. The remaining  rRNA and tRNA sequencing were removed by ribodetector with the options -t 12 --chunk_size 6000 -l 29. A custom python script was used to generate a fastq file containing 10nt cell barcode and 10nt UMI sequence. The resulting fastq files were aligned to the mouse genome using STAR with options: --soloType CB_UMI_Simple  --soloFeatures Gene Velocyto  --soloUMIlen 10 --soloUMIstart 11 --soloCBlen 10 --soloCBstart 1 --outSAMattributes UR CR AS NH HI nM MD CB --outFilterMultimapNmax 20 --quantMode TranscriptomeSAM --alignEndsType EndToEnd  --outFilterMismatchNmax 1 --soloUMIdedup 1MM_Directional_UMItools --soloCBmatchWLtype 1MM. We created a custom STAR reference genome with sjdb overhang of 33 to match the max(read length)-1. The STAR alignment to the mouse genome was performed in end to end mode with maximum one mismatch allowed for accurate mapping of ribosome footprints. The resulting bam file was cleared up for empty cell barcodes with sambamba followed by UMi deduplication by umi_tools with options --extract-umi-method tag --umi-tag=UR --cell-tag=CB --per-cell. The deduplicated bam files were split into 384 cells by a custom python script based on the pysam library. Then the reads mapping to the CDS regions of the genome in forward strand were counted by featureCounts with options: -M -O --fraction -s 1 -t CDS -g gene_name
Assembly: Gencode version M25 (GRCm38.p6)
Supplementary files format and content: *counts.csv.gz files contain CDS UMI footprint counts per cell for read length 26-34.

source_name: epidermis

growth_protocol: All mice were housed at the Laboratory Animal Services Center (LASC) of the University of Zurich in individually-ventilated cages in a humidity- and light-controlled environment (22 °C, 45–50%, 12 h light/dark cycle), and had access to food and water ad libitum.

extract_protocol:
Cycloheximide (CHX) was injected into the tail vein of female young (2 month) and old (22-26 month) mice two minutes before euthanasia. The back skin was surgically removed and submerged in 1x PBS supplemented with CHX (10 mg/ml) for 5 minutes. The fat was scraped from the back skin and washed once in cold PBS-CHX and then placed in 15 ml 0.25% trypsin for 37 minutes at 37 °C on an orbital shaker, dermis-side facing down. Next, the epidermis was separated from dermis by scraping with a scalpel and torn into smaller pieces. Trypsin was neutralized by adding 1x PBS buffer containing 2% chelexed FBS (FBS-) and CHX, followed by vigorous pipetting to create a single-cell suspension. The cell suspension was filtered sequentially through a 70 μm and a 40 μm strainer, centrifuged for 10 minutes at 400 g and then resuspended in FACS buffer (1x PBS, 2% FBS-, 0.1 mg/ml CHX, 0.05 ng/ml DAPI). Live single cells were sorted on a BD Aria II with a 70 µm nozzle and a flow rate of <300 events per second into 384-well hard-shell plates, pre-filled with 5 μl of light mineral and 50 nl of lysis buffer. Single-cell sequencing libraries were performed as described in Methods.
After ribosome footprint digestion, libraries were generated using the Mosquito® liquid handler (SPT Labtech). As previously described14, a one-pot small-RNA library preparation protocol included the end repair, two RNA ligations, cDNA synthesis, and an indexing PCR. End repair: First, 50 nl of end-repair mix (4.1× T4 RNA Ligase Buffer (New England Biolabs), 16.4 mM MgCl2, 4.1 mM uridine triphosphate (New England Biolabs), 1.37 U/μl T4 Polynucleotide Kinase (New England Biolabs) and 0.77 U/μl SUPERase·In™ RNase Inhibitor was added to each well, and plates were incubated at 37 °C for 1 hour, then held at 4 °C. 3ʹ Ligation: Next, 264 nl of 3ʹ ligation brew (1× T4 RNA Ligase Buffer (New England Biolabs), 1 μM pre-adenylated 3ʹ adapter (OMV630_miRNA4_3App, Integrated DNA Technologies), 35.5% PEG-8000 (New England Biolabs), 0.1% Tween-20 (Sigma-Aldrich), 0.98 U/μl SUPERase In RNase Inhibitor (Invitrogen), and 21.3 U/μl T4 RNA Ligase 2 Truncated KQ (New England Biolabs)) was added to each well and plates were incubated at 4 °C for 18 hours. The cDNA synthesis primer was then pre-annealed to the 3ʹ ligation products by adding 50 nl of the reverse transcription primer mix (5.2 μM reverse transcription primer (OMV572_miRNA4_RT, Integrated DNA Technologies), 13.5 μM adenosine triphosphate (ATP, New England Biolabs), and 1% Tween-20) to each well. The plates were heated to 65 °C for 1 minute, then incubated sequentially at 37 °C for 2 minutes, 25 °C for 2 minutes and finally held at 4 °C.  5ʹ Ligation: 5ʹ adapters were then ligated by adding 156 nl of 5ʹ ligation brew (1× T4 RNA Ligase Buffer, 30.75% PEG-8000, 0.1% Tween-20, 0.5 μM 5ʹ adapter (OMV632_miRNA5_5A_10U, Integrated DNA Technologies), 1.25 U/μl T4 RNA Ligase (Thermo Scientific) and incubated at 37 °C for 2 h and then held at 4 °C. cDNA synthesis: Complementary DNA synthesis was performed by adding 770 nl of reverse transcription reaction with 2.66x of the standard concentration of the RT Buffer (5x RT Buffer, Thermo Fisher Scientific, EP0752), 1.25 mM dNTPs (Promega), 0.1875% Tween-20, 1.875 U/μl SUPERase In RNase Inhibitor, and 9.375 U/μl Maxima H Minus Reverse Transcriptase (Thermo Fisher Scientific) to each well. The plate was incubated at 50 °C for 1 hour, followed by 85 °C for 5 minutes, then held at 4 °C. Indexing PCR: For library indexing, 150 nl of 20 μM unique forward index primers (miRv6-PCR_F-cbc; Integrated DNA Technologies) and 3.2 μl of PCR mix (1.5× Q5 Hot Start High-Fidelity 2× Master Mix (New England Biolabs), 0.15% Tween-20, and 0.94 μM reverse index primer (RPI-; Integrated DNA Technologies)) were added to each well. Plates were then incubated at 98 °C for 30 seconds followed by 10 cycles of 98 °C for 15 seconds, 65 °C for 30 sesonds, 72 °C for 30 seconds, and then a final incubation at 72 °C for 5 minutes. Plates were then held at 4 °C before freezing at −20 °C until pooling.

value: epidermis

value: primary skin cells

value: epidermal cells

tag: age

value: old (22-26 months old)

value: female

value: back skin treated with cycloheximide (Methods)


title: DMSO_0-1_R13_P2

description: Library name: s181

value: Mammary

value: Epithelial

value: WT


title: Old11

description:
Total RNA footprint
P662


title: RDY277 SLAM-seq, 25 min IAA, rep C

description: Library name: RDHTS542

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD71:TRP1

value: 25 min IAA treatment, 4 min 4tU treatment


title: HepG2.batch1.IMI.rep1.H06

description: Library name: HepG2_Batch1_IMI_1_H06

value: liver

value: hepatocyte


title: DMSO_0-1_R12_P2

description: Library name: s180


title: Actin-RFP2-p10

city: Shanghai

first: Qing

last: Li

state: Shanghai

address: Xuhui Yueyang road 320, ShangHai, China

institute: Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences

data_processing:
Raw RNA-seq reads were cleaned using fastp (v0.20.0) program, aligned to mm10 using STAR (v2.7.3a)
Only unique mapped reads were kept and counted by featureCounts (v2.0.0)
FPKM and TPM were calculated by stringtie (v2.0)
Genome coverage was counted by bamCoverage (v3.3.1). Differential gene expression was carried out using DESeq2 (v1.30.0), and clusterProfiler (v3.18.1) was used for GO and KEGG analysis in R
Assembly: mm10
Supplementary files format and content: For deep-seq, tale-delimited text file includes number of different reads for each sample. For RNA-seq, tab-delimited text file includes RPKM values for each sample. For WGBS, bed file includes the average methylation sites per 200bp in the genome. For scRNA-seq of E7.5 embryos, cellfocus file includes the representation matrix of different cells.
Library strategy: deep-seq

source_name: cells

extract_protocol:
For deep-seq, The genomic DNA of various tissues (brain, heart, liver, testis, and tail) from wild-type mice and Gjb235delG/35delG mice derived from diploid compensation, was isolated using the TIANamp Genomic DNA Kit (TIANGEN). This was followed by PCR amplification for Sanger sequencing. Target sites were amplified from the extracted genomic DNA using Phanta® Max Super-Fidelity DNA Polymerase (Vazyme)For RNA-seq, single cells were picked using a Piezo-drill micromanipulator and transferred into a 200 µl tube containing 1.2 µl of lysis buffer. The lysate underwent cDNA amplification with the Single Cell Full Length mRNA Amplification Kit (Vazyme, Cat#N712)
For deep-seq,  the PCR products were then ligated with different barcodes and pooled together. Libraries were generated from adapter-modified PCR products. For RNA-seq, the RNA-seq library was prepared using the TruePrep DNA Library Prep Kit V2 (Vazyme, Cat#TD503) for Illumina sequencing
Libraries of deep-seq and RNA-seq subjected to deep sequencing on Illumina NovaSeq6000 platform following the manufacturer’s instructions (Illumina) to produce 150bp paired-end reads by Genergy Biotechnology Co. Ltd. (Shanghai, China).

value: cells

tag: strain

tag: genetic modification

value: Actin-RFP transgene

tag: time


title: HepG2.batch1.IMI.rep1.G06

description: Library name: HepG2_Batch1_IMI_1_G06


title: RDY277 SLAM-seq, 25 min IAA, rep B

description: Library name: RDHTS541

value: yeast cell


title: RDY277 SLAM-seq, 25 min IAA, rep A

description: Library name: RDHTS540


title: Gjb2-35G-p7

value: Gjb2 35delG


title: HepG2.batch1.IMI.rep1.F06

description: Library name: HepG2_Batch1_IMI_1_F06

value: cell line


title: MEF-p2

value: wild-type


title: HepG2.batch1.IMI.rep1.E06

description: Library name: HepG2_Batch1_IMI_1_E06


title: E2_0-1_R2_P2

description: Library name: s177

value: chemical exposure


title: HepG2.batch1.IMI.rep1.D06

description: Library name: HepG2_Batch1_IMI_1_D06


title: RDY277 SLAM-seq, 25 min DMSO, rep B

description: Library name: RDHTS538

value: 25 min DMSO treatment, 4 min 4tU treatment


title: DMSO_0-1_R11_P2

description: Library name: s179

value: vehicle control

value: dimethyl sulfoxide


title: BPA_50_R2_P2

description: Library name: s176

value: Mammary

value: bisphenol A


title: DMSO_0-1_R38_P4

description: Library name: s380

value: Epithelial


title: DMSO_0-1_R39_P4

description: Library name: s381


title: DMSO_0-1_R40_P4

description: Library name: s382

value: WT


title: mNSC, gRNA R1

description:
Library name: EKDL250034813
reads_psite_list_th_all.csv

value: Neural Stem Cells

value: GF, gRNA


title: MutuDC cells, Fanchinoline treatment, 12 hours

first: Kun

last: Wang

address: 232 Waihuandong Road, Panyu district

institute: Guangzhou University of Chinese Medicine

data_processing:
Raw sequencing reads were first processed to remove adapters and low-quality bases using trim-galore software. The cleaned reads were subsequently aligned to the mouse reference genome (GRCm38) using HISAT2, a fast and sensitive alignment program designed for high-throughput RNA-Seq data.
Assembly: The genome assembly used for mapping and analysis was the GRCm38 mouse reference genome, obtained from the NCBI database. This assembly provides a comprehensive representation of the mouse genome, facilitating accurate mapping and annotation of RNA-Seq reads.
Supplementary files format and content: The processed data files are provided in CSV format and include raw counts of gene expression across different time points.

source_name: MutuDC

extract_protocol:
Total RNA was isolated from MutuDC cells using the TRIzol Reagent (Invitrogen) following the manufacturer's protocol. Briefly, cells were lysed directly in the culture dish using TRIzol reagent, and the lysates were transferred to tubes. Chloroform was added, and the mixture was centrifuged to separate phases. The aqueous phase was transferred to a new tube, and RNA was precipitated with isopropanol, washed with ethanol, and solubilized in RNase-free water. The quality and quantity of RNA were assessed using the Agilent 2100 Bioanalyzer.
Libraries for RNA sequencing were prepared using the Illumina TruSeq RNA Sample Preparation Kit v2. The protocol involved purifying poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA was fragmented using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second-strand cDNA synthesis using DNA Polymerase I and RNase H. After end repair, A-tailing, and adapter ligation, the products were purified and enriched with PCR to create the final cDNA library.
The library strategy used was RNA-Seq, which involves direct sequencing of cDNA derived from RNA. This approach is particularly effective for identifying transcript isoforms, studying gene expression levels, and discovering new transcripts. RNA-Seq provides a comprehensive view of the transcriptome and allows for the precise measurement of transcript levels and their isoforms across different biological conditions.

value: MutuDC

value: dendritic cells

value: Fanchinoline treatment


title: HepG2.batch1.IMI.rep1.C06

description: Library name: HepG2_Batch1_IMI_1_C06

value: liver

value: hepatocyte


title: RDY277 SLAM-seq, 25 min DMSO, rep A

description: Library name: RDHTS537

value: yeast cell

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD71:TRP1


title: BPA_10_R2_P2

description: Library name: s175

value: chemical exposure


title: MutuDC cells, Fanchinoline treatment, 6 hours


title: HepG2.batch1.IMI.rep1.B06

description: Library name: HepG2_Batch1_IMI_1_B06

value: cell line


title: RDY276 SLAM-seq, 25 min IAA, rep C

description: Library name: RDHTS536

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD70:TRP1

value: 25 min IAA treatment, 4 min 4tU treatment


title: BPA_5_R2_P2

description: Library name: s174

value: Mammary


title: RDY276 SLAM-seq, 25 min IAA, rep B

description: Library name: RDHTS535


title: HepG2.batch1.IMI.rep1.A06

description: Library name: HepG2_Batch1_IMI_1_A06


title: RDY276 SLAM-seq, 25 min IAA, rep A

description: Library name: RDHTS534


title: Primary mouse hepatocytes, FDMn replicate #3

city: New York

first: Jennifer

last: Gamarra

state: New York

address: 1150 St Nicholas Ave, Russ Berrie Building, Floor 6-613

institute: Columbia University

description: Library name: RJ030

data_processing:
We use bases2fastq version 1.1.0.593880262  for converting BCL to fastq format, coupled with adaptor trimming. We perform a pseudoalignment to a kallisto index created from transcriptomes (Ensembl v96, Mouse:GRCm38.p6) using kallisto (0.44.0). We test for differentially expressed genes under various conditions using DESeq2, R packages designed to test differential expression between two experimental groups from RNA-seq counts data.
Assembly: GRCm38.p6
Supplementary files format and content: Tab-delimited text files containing number of raw counts for each gene.

source_name: primary hepatocytes

extract_protocol:
RNA was extracted from primary hepatocyte samples using RNeasy Mini Kit (Qiagen #73404). RNA concentration and quality was determined by Qubit Bioanalyzer. Standard RNA-seq pipeline at Columbia Genome Center: poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1µg per sample, RIN>8).
STRPOLYA libraries were constructed using Illumina TruSeq RNA Preparation Kit according to the manufacturer’s instructions.

treatment_protocol: Primary hepatocytes were extracted from a WT C57/Bl6J mouse using a two-step collagenase protocol. Primary hepatocytes were plated in Corning M199 +10%FBS + 1%PenStrep for at least 2 hours, that evening cells were switched to serum-free medium (M199 + 1% PenStrep) for 16 hours overnight with or without 6 𝜇M MnCl2. Hepatocytes were pre-treated with 1 or 100 nM of insulin (Gibco #12585014) for 1 hour prior to 10 𝜇M forskolin/1 𝜇M dexamethasone treatment in serum-free medium for 5 hours before cell lysis.

value: primary hepatocytes

value: Forskolin (10uM)/Dexamethasone(1uM) + 6 uM Mn


title: RDY276 SLAM-seq, 25 min DMSO, rep C

description: Library name: RDHTS533

value: 25 min DMSO treatment, 4 min 4tU treatment


title: HepG2.batch1.GLY.rep3.G03

description: Library name: HepG2_Batch1_GLY_3_G03


title: RDY276 SLAM-seq, 25 min DMSO, rep B

description: Library name: RDHTS532


title: HepG2.batch1.GLY.rep3.F03

description: Library name: HepG2_Batch1_GLY_3_F03


title: BPA_0-001_R2_P2

description: Library name: s170

value: Epithelial

value: WT

value: bisphenol A


title: Primary mouse hepatocytes, FDMn replicate #1

description: Library name: RJ028


title: BPA_0-01_R2_P2

description: Library name: s169


title: RDY234 SLAM-seq, 25 min IAA, rep F

description: Library name: RDHTS392

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD28:TRP1


title: HepG2.batch1.GLY.rep3.E03

description: Library name: HepG2_Batch1_GLY_3_E03


title: TBPB_50_R2_P2

description: Library name: s168

value: tetrabromophenol blue


title: Primary mouse hepatocytes, FDI replicate #2

description: Library name: RJ026

value: Forskolin (10uM)/Dexamethasone(1uM) + 100 nM Insulin


title: HepG2.batch1.GLY.rep3.C03

description: Library name: HepG2_Batch1_GLY_3_C03

value: liver

value: hepatocyte


title: Primary mouse hepatocytes, FDI replicate #1

description: Library name: RJ025


title: TBPB_10_R2_P2

description: Library name: s167


title: RDY234 SLAM-seq, 25 min IAA, rep D

description: Library name: RDHTS390

value: yeast cell


title: HepG2.batch1.GLY.rep3.B03

description: Library name: HepG2_Batch1_GLY_3_B03


title: TBPB_5_R2_P2

description: Library name: s166

value: chemical exposure


title: Primary mouse hepatocytes, FD replicate #3

description: Library name: RJ024

value: Forskolin (10uM)/Dexamethasone(1uM)


title: RDY234 SLAM-seq, 25 min IAA, rep C

description: Library name: RDHTS410


title: DMSO_0-1_R37_P4

description: Library name: s379

value: vehicle control

value: dimethyl sulfoxide


title: RDY234 SLAM-seq, 25 min IAA, rep B

description: Library name: RDHTS409

value: 25 min IAA treatment, 4 min 4tU treatment


title: HepG2.batch1.GLY.rep2.H03

description: Library name: HepG2_Batch1_GLY_2_H03

value: cell line


title: TBPB_0-5_R2_P2

description: Library name: s164

value: Mammary


title: Primary mouse hepatocytes, FD replicate #1

description: Library name: RJ022

value: primary hepatocytes


title: RDY234 SLAM-seq, 25 min IAA, rep A

description: Library name: RDHTS408


title: HepG2.batch1.GLY.rep2.G03

description: Library name: HepG2_Batch1_GLY_2_G03


title: RDY234 SLAM-seq, 25 min DMSO, rep F

description: Library name: RDHTS389

value: 25 min DMSO treatment, 4 min 4tU treatment


title: TBPB_0-01_R2_P2

description: Library name: s162

value: Epithelial

value: WT


title: Primary mouse hepatocytes, Mock replicate #2

description: Library name: RJ020

value: Mock


title: HepG2.batch1.GLY.rep2.E03

description: Library name: HepG2_Batch1_GLY_2_E03


title: HepG2.batch2.DIQ.rep1.A01

description: Library name: HepG2_Batch2_DIQ_1_A01


title: HepG2.batch2.DIP.rep3.H07

description: Library name: HepG2_Batch2_DIP_3_H07


title: RDY290 ChEC-seq, 25 min DMSO, rep B

description: Library name: RDHTS931

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD16:TRP1

value: 25 min DMSO treatment


title: TBPB_0-001_R2_P2

description: Library name: s161

value: tetrabromophenol blue


title: Primary mouse hepatocytes, Mock replicate #1

description: Library name: RJ019

value: hepatocyte


title: RDY234 SLAM-seq, 25 min DMSO, rep D

description: Library name: RDHTS387

value: yeast cell

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD28:TRP1


title: PRed_50_R2_P2

description: Library name: s160

value: chemical exposure

value: phenol red


title: HepG2.batch1.GLY.rep2.C03

description: Library name: HepG2_Batch1_GLY_2_C03

value: liver


title: SSA-0451mutant Rep4

city: Richmond

first: Ping

last: Xu

address: 521 North 11th street

department: School of Dentistry

institute: Virginia Commonwealth University

data_processing:
Reads obtained from RNA-seq were aligned against theS. sanguinisSK36 genome using EDGE-pro.
Gene sequence reads for S. sanguinisSK36 were compared to the SSA_0451 mutant sample using DESeq2 in R (version 4.0.5) to determine log2 fold changes and adjusted p-values.
Assembly: Streptococcus sanguinis reference genome
Supplementary files format and content: tab-delimited text file includes gene_ID, start_coordinates,end_coordinates, average_coverage, Reads and RPKM  values for each sample

organism: Streptococcus sanguinis

growth_protocol: The wild type and mutant were cultured in brain-heart infusion media (BHI) at 37°C under microaerobic conditions. Kanamycin (500 µg/mL) was added to the SSA_0451 mutant to select the antibiotic resistance cassette.

extract_protocol:
SSA_0451 mutant and S. sanguinisSK36 wildtype were cultured in BHI medium overnight,  diluted into fresh BHI medium, and grown for another 4 hours under microaerobic conditions at 37 °C. Samples were collected and treated with RNA protect bacteria reagent (Qiagen, Valencia, CA) for 5 min to stabilize RNA and stored at −80 °C.
Cells were lysed by mechanical disruption using FastPrep lysing matrix B (Qbiogene, Irvine, CA). Total RNA was treated with DNase I (Qiagen) and prepared using RNA easy mini kits (Qiagen) according to the manufacturer’s instructions.  Total RNA quantity and integrity were determined using a Bioanalyzer (Agilent). All samples passed quality control assessment with RNA Integrity Numbers (RIN) above 8. rRNA depletion was carried out from 100ng of total RNA with NEBNext bacterial rRNA depletion kit (NEB#e7850). NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs) was used for the following RNA-seq library preparation according to the manufacturer’s protocol.

value: SSA-0451deletion mutant


title: SSA-0451mutant Rep3

treatment_protocol: SSA_0451 mutant and S. sanguinisSK36 wildtype were cultured in BHI medium overnight,  diluted into fresh BHI medium, and grown for another 4 hours under microaerobic conditions at 37 °C.


title: RDY234 SLAM-seq, 25 min DMSO, rep B

description: Library name: RDHTS406


title: HepG2.batch1.GLY.rep2.B03

description: Library name: HepG2_Batch1_GLY_2_B03

value: cell line


title: PRed_5_R2_P2

description: Library name: s158

value: Mammary


title: SSA-0451mutant Rep2


title: BPA_50_R4_P4

description: Library name: s368

value: bisphenol A


title: RDY234 SLAM-seq, 25 min DMSO, rep A

description: Library name: RDHTS405

value: 25 min DMSO treatment, 4 min 4tU treatment


title: HepG2.batch1.GLY.rep3.A03

description: Library name: HepG2_Batch1_GLY_3_A03


title: PRed_1_R2_P2

description: Library name: s157

value: Epithelial


title: HepG2.batch1.GLY.rep2.A03

description: Library name: HepG2_Batch1_GLY_2_A03


title: Primary mouse hepatocytes, FD replicate #2

description: Library name: RJ023

value: primary hepatocytes

value: WT

value: Forskolin (10uM)/Dexamethasone(1uM)


title: TBPB_0-1_R2_P2

description: Library name: s163


title: RDY73 SLAM-seq, 25 min IAA, rep C

description: Library name: RDHTS320

value: 25 min IAA treatment, 4 min 4tU treatment


title: HepG2.batch1.GLY.rep2.F03

description: Library name: HepG2_Batch1_GLY_2_F03


title: PRed_0-5_R2_P2

description: Library name: s156


title: HepG2.batch1.GLY.rep1.H03

description: Library name: HepG2_Batch1_GLY_1_H03


title: Wild-type SK36 Rep4

value: wild type


title: HepG2.batch1.GLY.rep1.G03

description: Library name: HepG2_Batch1_GLY_1_G03

value: hepatocyte


title: RDY234 SLAM-seq, 25 min DMSO, rep E

description: Library name: RDHTS388

value: yeast cell


title: PRed_0-1_R2_P2

description: Library name: s155


title: Wild-type SK36 Rep3


title: RDY73 SLAM-seq, 25 min IAA, rep A

description: Library name: RDHTS318


title: HepG2.batch1.GLY.rep1.F03

description: Library name: HepG2_Batch1_GLY_1_F03


title: Wild-type SK36 Rep2


title: RDY73 SLAM-seq, 25 min DMSO, rep C

description: Library name: RDHTS317


title: HepG2.batch1.GLY.rep2.D03

description: Library name: HepG2_Batch1_GLY_2_D03


title: HepG2.batch1.GLY.rep1.E03

description: Library name: HepG2_Batch1_GLY_1_E03


title: PRed_0-001_R2_P2

description: Library name: s153


title: Wild-type SK36 Rep1


title: HepG2.batch1.GLY.rep1.D03

description: Library name: HepG2_Batch1_GLY_1_D03


title: mtDNA sequencing of WAL2A cells

city: Philadelphia

first: Ting

last: Peng

state: PA

address: CTRB 6200

department: Pathology and Laboratory Medicine

institute: Children's hospital of Philadelphia

description:
Library name: WAL2A
PacBio

data_processing:
scRNA-seq was analyzed by using scMOCHA; PacBio long-read DNA-seq data analysis: Reads were aligned with pbmm2 to the GRCh38 reference genome, in which the mitochondrial contig (chrM) was duplicated head-to-tail (33,138 bp) to accommodate mitochondrial genome circularity; mitochondrial positions were folded to canonical 16,569 bp rCRS coordinates. Reads with mapping quality (MAPQ)≥40 and PacBio predicted read quality (rq)≥0.998 were retained. Reads in the following categories were excluded: putative NUMT-derived reads identified from supplementary alignments (≥500 bp, MAPQ≥20), reads outside the expected long-range PCR amplicon boundaries (±100 bp from primer positions), and reads<10 kb. Variant AF was calculated as the number of reads carrying the variant allele divided by the total number of reads spanning that position. Homopolymer-associated indels were excluded based on the systematic error pattern characterized in a 2.5 kb mtDNA plasmid control, with position-level assessment against the control applied within the region it covered. Variants with AF≥5% were reported.
Assembly: GRCh38, rCRS
Supplementary files format and content: RDS, sc_azimuth.rds

extract_protocol:
All cell lines were maintained at 37°C in a humidified incubator with 5% CO2. The human osteosarcoma thymidine kinase-deficient cell line 143B(TK−) (ATCC CRL-8303) and human embryonic kidney HEK293 cells were maintained in Dulbecco’s Modified Eagle Medium GlutaMAX (DMEM; Thermo Fisher Scientific, 10569044) containing high glucose (4.5 g/L) and sodium pyruvate (110 mg/L), supplemented with 1% non-essential amino acids (NEAA) and 10% fetal bovine serum (FBS). The human lung adenocarcinoma cell line A549 and the WAl2A WAL2A lymphoblastoid49 cell line were cultured in RPMI 1640 medium with ATCC modifications (Thermo Fisher Scientific, A1049101), supplemented with 1% NEAA and 10% FBS. Corresponding mitochondrial DNA-depleted (ρ⁰ or Rho0) derivatives were maintained in the same medium supplemented with 50 μg/mL uridine (Sigma-Aldrich, U3750-100G). Adherent cell lines were passaged at 70-95% confluence by washing with PBS (Thermo Fisher Scientific, 14190250) and dissociating with 0.25% trypsin-EDTA (Thermo Fisher Scientific, 25200114). Cells used for comparative experiments were harvested at the same passage number.
Single-cell RNA-seq Library Preparation
For the WT and Rho0 samples, an equal mixture of four cell lines (143B, WAL2A, HEK293, A549) was processed using the Chromium Single Cell 3′ Reagent Kit v3.1 (10x Genomics). Cell barcoding, reverse transcription, cDNA amplification, and 3′ gene expression library preparation were performed according to the manufacturer's protocol.
PacBio Library Preparation
Genomic DNA was extracted from cell pellets and quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Q33231). Full-length mitochondrial genomes were amplified by long-range PCR using using PrimeSTAR GXL DNA Premix (Takara, R051B) with custom primers and reaction conditions as previously described50. PCR products were purified with SMRTbell Cleanup Beads (PacBio, 102-158-300), and assessed for fragment size distribution using the Femto Pulse system (Agilent, FP-1002-0275). PacBio libraries were prepared using the SMRTbell Prep Kit 3.0 (PacBio, 102-182-700) according to their standard protocol. Following adapter ligation and nuclease treatment, libraries were size-selected using AMPure PB beads (PacBio, 100-265-900). Libraries were annealed to sequencing primers using the Sequel II Binding Kit 3.2 (PacBio, 102-333-300), bound to Sequel II Polymerase 2.2, loaded onto SMRT Cell 8M (PacBio, 102-281-700).

value: lymphoblastoid cell line


title: RDY73 SLAM-seq, 25 min DMSO, rep A

description: Library name: RDHTS315


title: THPE_10_R2_P2

description: Library name: s151

value: chemical exposure


title: WT_8th_Rep3

city: Harpenden

first: Stephen

last: Pearce

state: Hertfordshire

address: West Common

department: Sustainable Soils and Crops

country: United Kingdom

institute: Rothamsted Research

description: Library name: Sample_24

data_processing:
Sequencing reads were trimmed for quality and adapter sequences using Trimmomatic 0.39 (Bolger, Lohse and Usadel 2014) (SLIDINGWINDOW:4:20; MINLEN:50). The trimmed reads were paired and quantified using Kallisto against the IWGSC RefSeq v1.2 annotated gene models (Consortium, Appels et al. 2018, Zhu, Wang et al. 2021). Transcript per million (TPM) values were calculated for each gene based on raw counts.
Assembly: Reads were mapped to the Oryza sativa (Xian/Indica-1B1 var. IR64) OsIR64RS1
Supplementary files format and content: .csv file containing raw count values for all annotated rice gene models in each RNA-seq library.

organism: Oryza sativa

source_name: Young panicle at pollen maturation stage

growth_protocol: Rice plants were grown in Rothamsted standard potting mix in 10 cm2 pots. The conditions in the growth chambers were during seedling stage 25oC/20oC day and night cycle, irradiance of 400 µmol m-2 s-1; during tillering stage reproductive stage 28oC/23oC day and night cycle,  irradiance 500 µmol m-2 s-1; during reproductive stage maturity 32oC/ 25oC day and night cycle, irradiance 600 µmol m-2 s-1. Relative humidity 80% and 12-hour days were used throughout.

extract_protocol:
Total RNA was extracted from young panicle tissues using the Trizol method follwed by a DNase treatment according to the manufacturer’s instructions (Qiagen) Biolabs, Ipswich, Massachusetts, USA). The quality of the RNA was assessed using the Agilent RNA 6000 Nano Chip and Agilent 2100 Bioanalyzer (Agilent, Santa Clara, USA).
Paired-end Illumina libraries were constructred by Novogene Bioinformatics Technology Co. Ltd. (Cambridge UK).

value: Wild type


title: HepG2.batch1.GLY.rep1.B03

description: Library name: HepG2_Batch1_GLY_1_B03

value: liver


title: THPE_5_R2_P2

description: Library name: s150


title: mtDNA sequencing of A549 cells

description:
Library name: A549
PacBio

value: lung adenocarcinoma cell line


title: HepG2.batch1.GLY.rep1.A03

description: Library name: HepG2_Batch1_GLY_1_A03

value: cell line


title: THPE_1_R2_P2

description: Library name: s149

value: Mammary


title: WT_8th_Rep1

description: Library name: Sample_22

value: Young panicle at pollen maturation stage


title: HepG2.batch1.DIZ.rep3.H11

description: Library name: HepG2_Batch1_DIZ_3_H11


title: THPE_0-5_R2_P2

description: Library name: s148


title: M1 from animal_55

city: Tempe

first: Noah

last: Snyder-Mackler

state: Arizona

address: 214 Life Sciences C

department: School of Life Sciences

institute: Arizona State University

description:
Library name: NSM1645-b2
3 lvl sciRNAseq

data_processing:
Converts base calls to fastq files with bcl2fastq/ v.2.20 (RRID:SCR_015058) (Illumina), merge read 1 which contains the barcode to read 2 files.
Removes polyA tails using Trim Galore/v.0.6.7 (RRID:SCR_011847)
Aligns trimmed reads to a reference genome with STAR/v.2.7.6 (RRID:SCR_004463)
Extracts mapped reads and removes duplicates.
Generates UMI counts for exonic and intronic regions of each gene, tabulated according to the unique three-level barcode design in sci-RNA-seq3.
Assembly: rhesus macaque reference genome (Mmul_10)
Supplementary files format and content: all_regions_cell_annotate.csv
Supplementary files format and content: all_regions_count.npz
Supplementary files format and content: all_regions_gene_annotate.csv

molecule: nuclear RNA

organism: Macaca mulatta

source_name: primary motor cortex

growth_protocol: free-ranging population

extract_protocol:
Briefly, tissue was manually pulverized on dry ice, transferred to pre-chilled tubes, and stored at −80°C. For lysis, pulverized tissue was suspended in hypotonic lysis buffer A (0.3 M sucrose, 0.1% Triton X-100, 3 mM MgCl₂, 0.025% IGEPAL CA-630, 1% DEPC in PBS) for 10 min, filtered (40-μm), pelleted, and resuspended in SPBSTM buffer (0.3 M sucrose, 1X PBS, 0.1% TritonX-100, 3 mM MgCl₂, and 1% DEPC). Nuclei were fixed for 10 min in 1.5 mM dithiobis(succinimidyl propionate) (DSP), diluted from a 123 mM stock in DMSO into methanol. After washing in 0.3 M SPBSTM, nuclei were layered onto a 10:1 volume of 1.4 M SPBSTM, centrifuged (3,000 x g, 20 min, 4°C), and resuspended. Nuclei were filtered (20-μm), counted, aliquoted, and cryopreserved in 90% 0.3 M SPBSTM with 10% anhydrous DMSO at -80°C. One library per region was generated using the optimized sci-RNA-seq3 protocol with the following modifications: nuclei were counted using the ImageExpress Pico System (Molecular Devices), and 15,000-20,000 nuclei were loaded per reverse transcription well. Tagmentation used N7 adaptor-loaded Tn5 transposase (Diagenode, C01070010-20), with 6-9 μL of Tn5 per 550 μL of 2X TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl₂, 20% dimethylformamide), distributed at 5uL per well.
sci-RNA-seq3

treatment_protocol: Following veterinary euthanasia, a necropsy was immediately performed during which the brain was perfused by transcardial perfusion with sterile saline. The brain was then removed from the cranium and sagittally sectioned into left and right hemispheres. The left hemisphere was fixed in 10% formalin and not used for this study. The right hemisphere was further sectioned prior to cryopreservation. First, the cerebellum was separated from the cerebrum. The cerebrum was then placed on a custom mold and sectioned coronally into 11 ~0.5 cm-thick slices. All 12 slices (including the cerebellar hemisphere) were individually stored in Whirl-pak bags and flash frozen in a dry-ice/ethanol bath immediately before storage in ultralow (-80°C) freezers. Regions of interest were dissected in sterile, RNase-free conditions on dry ice to minimize RNA degradation. Six 1-mm tissue biopsies were then collected by biopsy punch.

value: primary motor cortex


title: HepG2.batch1.DIZ.rep3.G11

description: Library name: HepG2_Batch1_DIZ_3_G11


title: THPE_0-1_R2_P2

description: Library name: s147

data_processing:
Reads were demultiplexed from the BCL files and processed into FASTQ files using  DRAGEN analysis v1.3.0 on the Illumina BaseSpace Sequence Hub (Illumina, Inc., San Diego, CA, USA). Processing and quality control of the FASTQ files, differential expression analysis, and exploratory statistical analyses were performed using the R-ODAF_Health_Canada pipeline (https://github.com/R-ODAF/R-ODAF_Health_Canada; accessed March 2025), which manages workflows using Snakemake v8.0 (Mölder et al. 2021) and relies on scripts in R (v.4.3.2). The preprocessing steps use fastp v0.23.2 for trimming (Chen et al. 2018), STAR v2.7.8a (Dobin et al. 2013) to perform alignment of raw reads to the reference sequence and the qCount function of the QuasR R package (v1.30.0; (Gaidatzis et al. 2015) to extract the feature counts from the aligned reads (BAM files) using features specified in a GTF file. A samples-by-probes count matrix was produced.
Assembly: Probe sequence set provided by biospyder based on Human Whole Transcriptome kit v2.1
Supplementary files format and content: Tab-delimited table containing read counts per TempO-Seq probe

extract_protocol:
Cells were washed with phosphate-buffered saline and lysed in situ using 2x TempO-Seq lysis buffer diluted with an equal amount of PBS for TempO-Seq library building.
Gene expression was measured using the TempO-Seq Human Whole Transcriptome v2.1 kit (BioSpyder Technologies Inc, Carlsbad, California) as per the manufacturer’s instructions

value: Epithelial


title: SSA-0451mutant Rep1

value: SSA-0451deletion mutant


title: M1 from animal_54

description:
Library name: NSM1644-b2
3 lvl sciRNAseq


title: WT_7th_Rep2

description: Library name: Sample_20

source_name: Young panicle at pollen conent filling stage


title: PRed_0-01_R2_P2

description: Library name: s154

value: WT

value: phenol red


title: HepG2.batch1.DIZ.rep3.F11

description: Library name: HepG2_Batch1_DIZ_3_F11

data_processing:
Reads were aligned using STAR alignment on QIAGEN's CLC workbench software (v25.0.1) and Kallisto alignment on ExpressAnalyst
Raw counts were logCPM normalized and filtered for low abundance (5) and variance (15) using ExpressAnalyst
Normalized counts were analyzed for differential expression using DESeq2
Assembly: CLC workbench used hg38.p14 Ensembl v113 GCA_000001405.29; ExpressAnalyst used hg38.p14 GCA_000001405
Supplementary files format and content: raw files and count files are provided as fastq.gz files and .txt files, respectively.

extract_protocol:
cells were lysed in Qiagen's proprietary lysis buffer and used directly for library preparation
ultraplex 3' transcriptome library preparation following Qiagen's UPXome protocol


title: THPE_0-01_R2_P2

description: Library name: s146


title: RDY73 SLAM-seq, 25 min IAA, rep B

description: Library name: RDHTS319

data_processing:
Paired-end 150 bp reads were preprocessed using fastp (version 0.23.2) and bbduk (BBMap version 39.06). Forward reads were processed using SLAM-DUNK (version 0.4.3), where reads were aligned against the Saccharomyces cerevisiae genome using NextGenMap (version 0.5.5) and SNPs were called using VarScan 2 (version 2.4.5). Total read counts were defined as all reads remaining after filtering in SLAM-DUNK. A conversion per read threshold of ≥ 2 T>C conversions was used to define T>C read counts. Preprocessing and processing steps were implemented as a Snakemake workflow (https://github.com/DonczewLab/SLAM-Seq_Analysis).
Assembly: Saccharomyces cerevisiae strain S288C version R64-3-1 (RefSeq Assembly GCF_000146045.2)
Supplementary files format and content: Raw read count tables are provided in tab-separated values (.tsv) format. *_scer_twotcreadcount_tcount.tsv provides total read counts and T>C read counts with ≥ 2 T>C conversions.

extract_protocol:
RNA purification and DNase I treatment were performed using a Quick-RNA Fungal/Bacterial Miniprep kit and DNase I set (Zymo Research) following the manufacturer’s recommendations with minor modifications. Reagents used during RNA purification were supplemented with DTT to maintain reducing conditions. RNA was treated with 10 mM iodoacetamide for 15 min at 50°C in the dark. Samples were protected from light when possible.
Libraries were constructed as previously described in detail (https://doi.org/10.1186/s44330-024-00008-1) and sequenced on an Illumina NovaSeq 6000 at the Oklahoma Medical Research Foundation Clinical Genomics Center.

value: 25 min IAA treatment, 4 min 4tU treatment


title: RDY73 SLAM-seq, 25 min DMSO, rep B

description: Library name: RDHTS316

value: 25 min DMSO treatment, 4 min 4tU treatment


title: THPE_50_R2_P2

description: Library name: s152


title: M1 from animal_53

description:
Library name: NSM1643-b2
3 lvl sciRNAseq


title: WT_7th_Rep1

description: Library name: Sample_19

value: Young panicle at pollen conent filling stage


title: HepG2.batch1.DIZ.rep3.E11

description: Library name: HepG2_Batch1_DIZ_3_E11

value: hepatocyte


title: THPE_0-001_R2_P2

description: Library name: s145


title: HepG2.batch1.GLY.rep1.C03

description: Library name: HepG2_Batch1_GLY_1_C03


title: M1 from animal_52

description:
Library name: NSM1642-b2
3 lvl sciRNAseq


title: mtDNA sequencing of HEK293 cells

description:
Library name: HEK293
PacBio

value: embryonic kidney cell line


title: HepG2.batch1.DIZ.rep3.D11

description: Library name: HepG2_Batch1_DIZ_3_D11


title: WT_6th_Rep3

description: Library name: Sample_18

source_name: Young panicle at pollen mother cell meiosis stage


title: PA08_10_R2_P2

description: Library name: s144

value: chemical exposure

value: plastic additive 08


title: M1 from animal_51

description:
Library name: NSM1641-b2
3 lvl sciRNAseq


title: WT_6th_Rep2

description: Library name: Sample_17

value: Young panicle at pollen mother cell meiosis stage

value: Wild type


title: PA08_5_R2_P2

description: Library name: s143


title: HepG2.batch1.DIZ.rep3.C11

description: Library name: HepG2_Batch1_DIZ_3_C11

value: liver

value: cell line


title: WT_8th_Rep2

description: Library name: Sample_23

value: Young panicle at pollen maturation stage


title: M1 from animal_50

description:
Library name: NSM1640-b2
3 lvl sciRNAseq

value: primary motor cortex


title: WT_6th_Rep1

description: Library name: Sample_16


title: HepG2.batch1.DIZ.rep3.B11

description: Library name: HepG2_Batch1_DIZ_3_B11


title: PA08_1_R2_P2

description: Library name: s142

value: Mammary

value: Epithelial


title: M1 from animal_49

description:
Library name: NSM1639-b2
3 lvl sciRNAseq


title: HepG2.batch1.DIZ.rep3.A11

description: Library name: HepG2_Batch1_DIZ_3_A11


title: WT_5th_Rep3

description: Library name: Sample_15

source_name: Young panicle at pollen mother cell formation stage


title: PA08_0-5_R2_P2

description: Library name: s141

source_name: Mammary

value: WT


title: WT_5th_Rep2

description: Library name: Sample_14

value: Young panicle at pollen mother cell formation stage


title: M1 from animal_48

description:
Library name: NSM1638-b2
3 lvl sciRNAseq


title: PA08_0-1_R2_P2

description: Library name: s140


title: mtDNA sequencing of 143B cells

description:
Library name: 143B
PacBio

value: osteosarcoma cell line


title: HepG2.batch1.DIZ.rep2.H11

description: Library name: HepG2_Batch1_DIZ_2_H11

source_name: cell lysate


title: WT_5th_Rep1

description: Library name: Sample_13


title: M1 from animal_47

description:
Library name: NSM1637-b2
3 lvl sciRNAseq


title: HepG2.batch1.DIZ.rep2.G11

description: Library name: HepG2_Batch1_DIZ_2_G11


title: PA08_0-05_R2_P2

description: Library name: s139


title: M1 from animal_46

description:
Library name: NSM1636-b2
3 lvl sciRNAseq


title: HepG2.batch1.DIZ.rep2.F11

description: Library name: HepG2_Batch1_DIZ_2_F11


title: MT_8th_Rep3

description: Library name: Sample_12

value: tps2/tps3/tps6 triple mutant


title: PA08_0-01_R2_P2

description: Library name: s138


title: MT_8th_Rep2

description: Library name: Sample_11


title: M1 from animal_45

description:
Library name: NSM1635-b2
3 lvl sciRNAseq


title: HepG2.batch1.DIZ.rep2.E11

description: Library name: HepG2_Batch1_DIZ_2_E11


title: PA08_0-001_R2_P2

description: Library name: s137


title: M1 from animal_44

description:
Library name: NSM1634-b2
3 lvl sciRNAseq


title: HepG2.batch1.DIZ.rep2.D11

description: Library name: HepG2_Batch1_DIZ_2_D11


title: MT_8th_Rep1

description: Library name: Sample_10


title: TBBPS_50_R2_P2

description: Library name: s136

value: tetrabromo bisphenol S


title: M1 from animal_43

description:
Library name: NSM1633-b2
3 lvl sciRNAseq


title: HepG2.batch1.DIZ.rep2.C11

description: Library name: HepG2_Batch1_DIZ_2_C11

value: hepatocyte


title: WT_7th_Rep3

description: Library name: Sample_21

value: Young panicle at pollen conent filling stage


title: MT_7th_Rep3

description: Library name: Sample_9


title: M1 from animal_42

description:
Library name: NSM1632-b2
3 lvl sciRNAseq


title: TBBPS_10_R2_P2

description: Library name: s135

value: chemical exposure


title: MT_7th_Rep2

description: Library name: Sample_8


title: TBBPS_5_R2_P2

description: Library name: s134


title: M1 from animal_41

description:
Library name: NSM1631-b2
3 lvl sciRNAseq


title: HepG2.batch1.DIZ.rep2.A11

description: Library name: HepG2_Batch1_DIZ_2_A11


title: MT_7th_Rep1

description: Library name: Sample_7


title: HepG2.batch1.DIZ.rep2.B11

description: Library name: HepG2_Batch1_DIZ_2_B11


title: M1 from animal_40

description:
Library name: NSM1630-b2
3 lvl sciRNAseq


title: TBBPS_1_R2_P2

description: Library name: s133


title: MT_6th_Rep3

description: Library name: Sample_6


title: HepG2.batch1.DIZ.rep1.H11

description: Library name: HepG2_Batch1_DIZ_1_H11


title: M1 from animal_39

description:
Library name: NSM1629-b2
3 lvl sciRNAseq


title: TBBPS_0-5_R2_P2

description: Library name: s132


title: MT_6th_Rep2

description: Library name: Sample_5


title: HepG2.batch1.DIZ.rep1.G11

description: Library name: HepG2_Batch1_DIZ_1_G11


title: MT_6th_Rep1

description: Library name: Sample_4


title: M1 from animal_37

description:
Library name: NSM1628-b2
3 lvl sciRNAseq


title: TBBPS_0-1_R2_P2

description: Library name: s131


title: HepG2.batch1.DIZ.rep1.F11

description: Library name: HepG2_Batch1_DIZ_1_F11


title: TBBPS_0-01_R2_P2

description: Library name: s130


title: M1 from animal_36

description:
Library name: NSM1627-b2
3 lvl sciRNAseq


title: MT_5th_Rep3

description: Library name: Sample_3


title: HepG2.batch1.DIZ.rep1.E11

description: Library name: HepG2_Batch1_DIZ_1_E11


title: M1 from animal_35

description:
Library name: NSM1626-b2
3 lvl sciRNAseq


title: TBBPS_0-001_R2_P2

description: Library name: s129


title: MT_5th_Rep2

description: Library name: Sample_2


title: HepG2.batch1.DIZ.rep1.D11

description: Library name: HepG2_Batch1_DIZ_1_D11


title: DABPA_10_R2_P2

description: Library name: s128

value: diallyl bisphenol A


title: MutuDC cells, Fanchinoline treatment, 24 hours

value: MutuDC

value: dendritic cells

value: Fanchinoline treatment


title: M1 from animal_34

description:
Library name: NSM1625-b2
3 lvl sciRNAseq


title: RDY277 SLAM-seq, 25 min DMSO, rep C

description: Library name: RDHTS539

value: yeast cell

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD71:TRP1

value: 25 min DMSO treatment, 4 min 4tU treatment


title: E2_1_R2_P2

description: Library name: s178

value: Mammary


title: HepG2.batch1.DIZ.rep1.C11

description: Library name: HepG2_Batch1_DIZ_1_C11

value: liver

value: cell line


title: MT_5th_Rep1

description: Library name: Sample_1

value: Young panicle at pollen mother cell formation stage


title: DABPA_5_R2_P2

description: Library name: s127

value: Epithelial

value: WT


title: M1 from animal_33

description:
Library name: NSM1624-b2
3 lvl sciRNAseq

value: primary motor cortex


title: HepG2.batch1.DIZ.rep1.B11

description: Library name: HepG2_Batch1_DIZ_1_B11

value: hepatocyte


title: DABPA_1_R2_P2

description: Library name: s126


title: M1 from animal_32

description:
Library name: NSM1623-b2
3 lvl sciRNAseq


title: HepG2.batch1.DIZ.rep1.A11

description: Library name: HepG2_Batch1_DIZ_1_A11


title: DABPA_0-5_R2_P2

description: Library name: s125


title: GroupA_3

city: Krakow

first: Tomasz

last: Szmatoła

state: Małopolskie

address: Mickiewicza 21

department: OMEI

country: Poland

institute: University of Agriculture in Krakow

description: Library name: 22_S22

data_processing:
The bioinformatic workflow began with Illumina bcl2fastq (v2.20) demultiplexing. Read trimming and quality filtering of paired-end data were carried out with fastp (v0.23.2), and adapter sequences were additionally removed using Skewer (v0.2.2). Trimming included automatic adapter detection, removal of low-quality bases, sliding-window filtering (Q ≥ 20), and discarding reads shorter than 36 bp or containing >10 ambiguous nucleotides. PolyG and polyX tails were also clipped to minimize artefacts. Read quality was evaluated with FastQC (v0.11.5) and summarized across samples using MultiQC (v1.14).  Filtered reads were aligned to the Equus caballus reference genome EquCab3.0 (NCBI assembly GCF_002863925.1) using STAR (v2.7.10a) in two-pass mode to enable detection of novel splice junctions. The alignment settings allowed up to 20 multimapped reads and mismatches not exceeding 4% of the read length. Gene-level counts were obtained with HTSeq-count (v0.13.5) from name-sorted BAM files using the Equus caballus gene annotation (GTF file matching EquCab3.0). Reads with mapping quality below 10, as well as secondary or supplementary alignments, were excluded. Mapping quality metrics and coverage statistics were generated with RNA-SeQC (v2.4.2). Differential gene expression analysis was performed in R (v4.2.2) using DESeq2 (v1.38.0). Genes were considered differentially expressed when they exhibited an adjusted p-value < 0.05 (Benjamini–Hochberg correction) and an absolute fold change ≥ 1.2.
Assembly: EquCab3.0 (NCBI assembly GCF_002863925.1)
Supplementary files format and content: counts.tsv

organism: Equus caballus

source_name: skeletal muscle derived cells

growth_protocol: Equine skeletal muscle cells were isolated from post-mortem tissue, which was selected as the most ethically appropriate source for this study. Muscle samples were obtained immediately after the death of a 10-month-old preterm foal that did not survive despite veterinary care, and only after explicit informed consent was provided by the owner.  Prior to extract preparation, skeletal muscle fragments were handled under aseptic conditions, kept at 4 °C during transport, and processed within 4 hours to ensure preservation of cellular integrity for subsequent culture and analysis.

extract_protocol:
Total RNA was isolated using the PureLink RNA Mini Kit with on-column DNase treatment (Ambion, Life Technologies). For each group, three technical replicates were prepared. RNA quantity and purity were measured with a NanoDrop 2000 spectrophotometer (Thermo Scientific, Waltham, MA, USA), and RNA integrity was verified using a TapeStation 2200 system (RNA ScreenTapes, Agilent Technologies, Santa Clara, CA, USA). RNA concentrations ranged from 32 ng/μL to 412 ng/μL, and all samples exhibited RIN values greater than 7.5.
The samples with RIN (RNA integrity number) sufficient RIN ranging from 9.6 – 10.0 (Schroeder et al. 2006), were sent to Library preparation and sequencing by a commercial company (CeGat gGmbH) on NovaSeq 6000 (Ilumina), and finally 100 bp (±50 bp) paired-end reads were generated.

treatment_protocol: Approximately 2 × 10⁵ cells were seeded into T25 flasks pre-coated with 2% gelatin and allowed to attach overnight under standard culture conditions (37 °C, 5% CO₂, atmospheric O₂). The following day, cultures were assigned to experimental groups differing in oxygen tension and exposure duration. Hypoxic cultures were transferred to a HypoxyLab incubator (Oxford Optronix) set to either 3% or 1% O₂, using custom gas mixtures based on N₂ with 5% CO₂ and controlled O₂ levels, delivered at a constant flow rate. Normoxic cultures remained in standard humidified incubators at 37 °C with 5% CO₂ (≈21% O₂). All cultures were maintained in parallel under otherwise identical conditions.

value: skeletal muscle derived cells


title: GroupA_2

description: Library name: 21_S21


title: HepG2.batch1.control.rep3.D06

description: Library name: HepG2_Batch1_control_3_D06


title: M1 from animal_31

description:
Library name: NSM1622-b2
3 lvl sciRNAseq


title: Primary mouse hepatocytes, FDMn replicate #2

description: Library name: RJ029

value: primary hepatocytes

value: Forskolin (10uM)/Dexamethasone(1uM) + 6 uM Mn


title: M1 from animal_30

description:
Library name: NSM1621-b2
3 lvl sciRNAseq


title: DABPA_0-1_R2_P2

description: Library name: s124

value: chemical exposure

value: diallyl bisphenol A


title: GroupA_1

description: Library name: 20_S20


title: DABPA_0-05_R2_P2

description: Library name: s123


title: GroupB_3

description: Library name: 19_S19


title: HepG2.batch1.control.rep3.C06

description: Library name: HepG2_Batch1_control_3_C06


title: HepG2.batch1.GLY.rep3.D03

description: Library name: HepG2_Batch1_GLY_3_D03


title: M1 from animal_29

description:
Library name: NSM1620-b2
3 lvl sciRNAseq


title: HepG2.batch1.control.rep3.B06

description: Library name: HepG2_Batch1_control_3_B06


title: DABPA_0-01_R2_P2

description: Library name: s122


title: M1 from animal_28

description:
Library name: NSM1619-b2
3 lvl sciRNAseq


title: RDY276 SLAM-seq, 25 min DMSO, rep A

first: John

last: Ridenour

address: 825 NE 13th St.

institute: Oklahoma Medical Research Foundation

description: Library name: RDHTS531

value: pGPD1-OsTIR1:HIS3 BDF2-3xV5-mAID::KanMX BDF1-3xV5-mAID::URA3 pMD70:TRP1


title: GroupB_2

description: Library name: 18_S18


title: DABPA_0-001_R2_P2

first: Matthew

last: Meier

address: 251 Sir Frederick Banting Driveway

institute: Government of Canada

description: Library name: s121


title: M1 from animal_27

description:
Library name: NSM1618-b2
3 lvl sciRNAseq


title: GroupB_1

description: Library name: 15_S15


title: HepG2.batch1.control.rep2.D05

first: Niladri

last: Basu

address: 21,1111 Lakeshore Blvd, Apt #2

institute: McGill University

description: Library name: HepG2_Batch1_control_2_D05


title: BPK_50_R2_P2

description: Library name: s120

value: bisphenol K


title: HepG2.batch1.control.rep3.A06

description: Library name: HepG2_Batch1_control_3_A06


title: M1 from animal_26

description:
Library name: NSM1617-b2
3 lvl sciRNAseq


title: GroupE_5

description: Library name: 13_S13


title: BPK_10_R2_P2

description: Library name: s119


title: M1 from animal_25

description:
Library name: NSM1616-b2
3 lvl sciRNAseq


title: HepG2.batch1.control.rep2.C05

description: Library name: HepG2_Batch1_control_2_C05


title: GroupE_4

description: Library name: 12_S12


title: HepG2.batch1.control.rep2.B05

description: Library name: HepG2_Batch1_control_2_B05


title: GroupE_3

description: Library name: 11_S11


title: HepG2.batch1.control.rep2.A05

description: Library name: HepG2_Batch1_control_2_A05


title: BPK_1_R2_P2

description: Library name: s117


title: M1 from animal_23

description:
Library name: NSM1614-b2
3 lvl sciRNAseq


title: BPK_5_R2_P2

description: Library name: s118


title: M1 from animal_24

description:
Library name: NSM1615-b2
3 lvl sciRNAseq