title: Tunicamycin|0.1uM|DTXSID8036730|24h|S26_S24-tuncamycin-0.1-24-1

description:
Library name: S26_S24-tuncamycin-0.1-24-1
TempO-LINC

value: Tunicamycin


title: Etoposide|25.0uM|DTXSID5023035|24h|S26_S23-etopiside-25-24-1

status: Public on Jun 10 2025

type: SRA

city: Research Triangle Park

first: Imran

last: Shah

state: NC

address: Mail Code: D143-02

department: Office of Research and Development

country: USA

institute: US Environmental Protection Agency

description:
Library name: S26_S23-etopiside-25-24-1
TempO-LINC

library_source: transcriptomic single cell

data_processing:
To generate the TempO-LINC® single-cell expression data, barcoded reads were demultiplexed using an in-house developed software. Briefly, reads were scanned to find the sequences of the barcodes, allowing an offset of up to 3 nucleotides from their expected positions and 1 mismatch from their expected sequence to allow for gaps and variations due to minor sequencing errors. Reads featuring the same barcode combination were pooled together into barcode-associated clusters. A cell calling read threshold was set at 10,000 reads/cell based on inflection point analysis of a ranked barcode distribution plot (knee plot). Cell-associated reads were then aligned to the reference human whole transcriptome TempO-Seq probe sequences using bwa v. 0.7.17 (mem algorithm, parameters: -v 1 -c 2 -L 100). UMIs were used to collapse the reads originating from the same transcript and remove any PCR duplicates. The probes featuring a UMI count >0 for each single-cell alignment indicated an expressed/detected gene. Cell count tables were generated using the software featureCount v 2.0.1 (BioSpyder human transcriptome probes v2.1).
Assembly: BioSpyder human transcriptome probes v2.1 (GRCh38)
Supplementary files format and content: AnnData single-cell format using gzip compression. Created using scanpy v1.10.3

molecule: total RNA

organism: Homo sapiens

source_name: liver

growth_protocol: Terminally differentiated human hepatic cells (NoSpin HepaRG™) provided directly from the distributer (Lonza, Morrisville, NC) were seeded at 3X10^3 cells/cm2 in 24-well plates coated with rat tail collagen (Sigma-Aldrich, Saint Louis, MO) at a density of approximately 5 µg/cm2. After dispersion and seeding, cells were allowed to settle in the plate at room temperature for ~2 hrs in a biosafety cabinet before being transferred to an incubator set at 37°C, 5% CO2. Cells were incubated for 7 days in HepaRG Base Medium with Supplement (MH100; Lonza) plus Thawing and Plating additive (MHTAP; Lonza) before treatments, changing the media every 48-72 hrs. During cellular treatment, 0.1% DMSO was used as a vehicle control, corresponding to the final vehicle percentage for all solubilized chemicals. Treatments were carried out for 24 hrs before termination.

extract_protocol:
Following treatment, cells were dissociated into a single cell suspension, cell counts and viability were determined with a fluorometric Nexcelom Cellometer automated cell counter (Nexcelom Biosciences, Lawrence, MA) using Acridine Orange (AO)/Propidium Iodide (PI) stain (Perkin Elmer, Inc., Waltham, MA), following manufacturer’s instructions, and then the cells were fixed and processed for single-cell library construction. Cells were initially incubated for 11 min at 37°C in 0.25% Trypsin-EDTA (Thermo Fisher Scientific) with 40 mM DTT, 0.1 mg/ml actinomycin D, 1 mg/ml anisomycin, and 6 mM RNaseOUT recombinant ribonuclease inhibitor (Thermo Fisher Scientific, Waltham, MA) in 250 µl volume, followed by an additional 15 min 37°C incubation after adding 250 µl 0.5% Collagenase Type 1 (Worthington, Lakewood, NJ) in EBSS (Earle's Balanced Salt Solution) and DTT (Dithiothreitol) 40mM  DTT (Dithiothreitol) and 6mM RNaseOUT. Using a wide-bore pipette tip, cells were then dissociated by gentle pipetting for 10 min, 2 ml of 37°C HepaRG Base Medium was added to stop enzymatic activity, and cells were pelleted at 200 xg for 3 min at 4°C. After media removal, cells were resuspended in 1 ml cell suspension media (1X PBS, 0.5% Opti-Prep Density Gradient Medium (Sigma-Aldrich), 0.1% Bovine Serum Albumin Fraction V (Thermo Fisher Scientific, Waltham, MA), 6 mM RNaseOUT) pre-chilled to 4°C. The cells were pelleted twice more at 200 xg for 3 min at 4°C, washing each time with fresh Cell Suspension Media. After the final wash, cells were filtered through a 40 µm nylon cell strainer, transferred, and stored in a Lo-Bind tube. For the TempO-LINC® assay samples, dissociated cells were fixed in 1% paraformaldehyde solution in 1 X PBS at room temp for 25 min with slow rocking, then quenched in 1:1 volume of 10 mM Tris 0.1% Pluronic F-68 (Thermo Fisher Scientific). Cells were then pelleted at 500xg for 5 min at 4°C and washed in 0.1% Pluronic F-68, 0.1% BSA Bovine Serum Albumin Fraction V, 0.1 U/µl Superase*In (Thermo Fisher Scientific) and 0.1 U/µl Enzymatics (Qiagen, Germantown, MD) ribonuclease inhibitors, and 40 mM DTT. After a final spin, most of the supernatant was removed, and cells were frozen at -20°C overnight, then stored at -80°C until library prep.
TempO-LINC® single-cell sequencing libraries were prepared using the TempO-LINC v1.0 protocol (BioSpyder, Carlsbad, CA) by BioSpyder. Briefly, saponin permeabilized cells from each sample were first hybridized with BioSpyder TempO-Seq whole transcriptome WT v2.1 Detector Oligos (DOs) that had been 5’ phosphorylated. Following hybridization, excess DOs were washed away, and the remaining DOs hybridized to target mRNA were ligated at 37°C for 1 hr. Samples were then labeled by distributing them into 48 wells of a microplate. Each well contained fixed cells from one of the treatment samples and one of 48 unique molecular barcodes (“barcode 1”) Then the barcodes were ligated to the 5’ phosphorylated detector oligos - still hybridized to mRNA within the fixed cells. This first barcode not only comprised a portion of each cell-specific barcode but since each treatment sample was placed into a unique well for ligating on barcode 1, barcode 1 also identified the treatment condition. Cells were pooled following the first sample barcode ligation and then redistributed into wells of a plate containing 48 additional barcodes (“barcode 2”) were ligated onto barcode 1. Following pooling and a third round of barcode addition by ligation (“barcode 3”), after which unique molecular indexes (UMIs) were also added, cells were pooled once again and then distributed into 12 PCR tubes, and the fully barcoded DOs were amplified with indexed primers, a separate unique index being added to each PCR tube. Combining these barcodes and UMIs allows single-cell RNA sequencing to efficiently process large numbers of cells from multiple samples, allowing for comprehensive analysis of cellular heterogeneity and gene expression patterns (Eastburn et al. 2024). Amplified DNA was pooled, purified, and quantified before paired-end sequencing on an Illumina NovaSeq 6000 using a S4 flow cell.

treatment_protocol: A set of 8 chemicals (including DMSO control) was tested to investigate distinct mechanisms of cellular stress responses. Chemical concentrations were selected to ensure that they did not induce significant cell dealth in HepaRG cells by keeping them below the AC50 for cytotoxicity.   Brefeldin A, recognized for its role in inducing the unfolded protein response (UPR) by disrupting ER-to-Golgi protein transport, was used at concentrations ranging from 0.001, 0.01, and  0.100 µM. Etoposide, a well-known DNA damage response (DDR) activator and a topoisomerase II inhibitor, was included at doses of 0.25, 2.5, and 25 µM to assess DDR activation and cytotoxicity. For investigating oxidative stress response (OSR), tert-butylhydroquinone was chosen for its ability to activate the NRF2 pathway, a key player in cellular defense against oxidative stress, and was tested at concentrations of 3, 30, and 300 µM. Rotenone, known to induce mitochondrial stress by inhibiting the mitochondrial electron transport chain, was tested at concentrations of 0.2, 0.4, and 0.8 µM. Cycloheximide, a protein synthesis inhibitor impacting many cellular processes, was tested at concentrations of 0.200, 2.000, and 20.000 µM. Tunicamycin, another UPR inducer known for inhibiting N-linked glycosylation, was tested at concentrations of 0.001, 0.010, and 0.100 µM. Lastly, troglitazone, a PPARγ agonist influencing lipid metabolism and mitochondrial function and can modulate PPARα pathway activity, was tested at concentrations of 0.001, 0.010, and 0.100 µM. 0.1% dimethyl sulfoxide (DMSO) was used as the vehicle control for all treatments. These test chemicals, spanning a range of concentrations, were selected to provide a comprehensive view of transcriptional concentration responses across different cellular stress pathways without reaching a concentration level of each producing significant cell loss.

tag: tissue

value: liver

tag: cell line

value: HepaRG

tag: cell type

value: differentiated HepaRG hepatocyte-like cells

tag: treatment

value: Etoposide|25.0uM|DTXSID5023035 for 24h in HepaRG cells

tag: timeh

tag: chem name

value: Etoposide

tag: conc

tag: dtxsid

tag: batch


title: Cycloheximide|20.0uM|DTXSID6024882|24h|S26_S22-cycloheximide-20-24-1

description:
Library name: S26_S22-cycloheximide-20-24-1
TempO-LINC

value: Cycloheximide|20.0uM|DTXSID6024882 for 24h in HepaRG cells

value: Cycloheximide


title: tert-Butylhydroquinone|300.0uM|DTXSID6020220|24h|S26_S20-tBHQ-300-24-1

description:
Library name: S26_S20-tBHQ-300-24-1
TempO-LINC

value: tert-Butylhydroquinone|300.0uM|DTXSID6020220 for 24h in HepaRG cells

value: tert-Butylhydroquinone


title: Cycloheximide|2.0uM|DTXSID6024882|24h|S26_S16-cycloheximide-2-24-1

description:
Library name: S26_S16-cycloheximide-2-24-1
TempO-LINC

value: Cycloheximide|2.0uM|DTXSID6024882 for 24h in HepaRG cells


title: Troglitazone|0.1uM|DTXSID8023719|24h|S26_S19-troglitazone-0.1-24-1

description:
Library name: S26_S19-troglitazone-0.1-24-1
TempO-LINC

value: Troglitazone|0.1uM|DTXSID8023719 for 24h in HepaRG cells

value: Troglitazone


title: Brefeldin A|0.01uM|DTXSID00880041|24h|S27_S15-brefeldin-a-0.01-24-1

description:
Library name: S27_S15-brefeldin-a-0.01-24-1
TempO-LINC

value: Brefeldin A|0.01uM|DTXSID00880041 for 24h in HepaRG cells

value: Brefeldin A


title: tert-Butylhydroquinone|30.0uM|DTXSID6020220|24h|S26_S14-tBHQ-30-24-1

description:
Library name: S26_S14-tBHQ-30-24-1
TempO-LINC

value: tert-Butylhydroquinone|30.0uM|DTXSID6020220 for 24h in HepaRG cells


title: Brefeldin A|0.1uM|DTXSID00880041|24h|S26_S21-brefeldin-a-0.1-24-1

description:
Library name: S26_S21-brefeldin-a-0.1-24-1
TempO-LINC

value: Brefeldin A|0.1uM|DTXSID00880041 for 24h in HepaRG cells


title: Brefeldin A|0.01uM|DTXSID00880041|24h|S26_S15-brefeldin-a-0.01-24-1

description:
Library name: S26_S15-brefeldin-a-0.01-24-1
TempO-LINC


title: Tunicamycin|0.01uM|DTXSID8036730|24h|S26_S18-tuncamycin-0.01-24-1

description:
Library name: S26_S18-tuncamycin-0.01-24-1
TempO-LINC

value: Tunicamycin|0.01uM|DTXSID8036730 for 24h in HepaRG cells

value: Tunicamycin


title: tert-Butylhydroquinone|300.0uM|DTXSID6020220|24h|S25_S20-tBHQ-300-24-1

description:
Library name: S25_S20-tBHQ-300-24-1
TempO-LINC

value: liver

value: HepaRG


title: Brefeldin A|0.1uM|DTXSID00880041|24h|S25_S21-brefeldin-a-0.1-24-1

description:
Library name: S25_S21-brefeldin-a-0.1-24-1
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells


title: Troglitazone|0.01uM|DTXSID8023719|24h|S26_S13-troglitazone-0.01-24-1

description:
Library name: S26_S13-troglitazone-0.01-24-1
TempO-LINC

value: Troglitazone|0.01uM|DTXSID8023719 for 24h in HepaRG cells


title: Tunicamycin|0.01uM|DTXSID8036730|24h|S25_S18-tuncamycin-0.01-24-1

description:
Library name: S25_S18-tuncamycin-0.01-24-1
TempO-LINC


title: Cycloheximide|20.0uM|DTXSID6024882|24h|S25_S22-cycloheximide-20-24-1

description:
Library name: S25_S22-cycloheximide-20-24-1
TempO-LINC

value: Cycloheximide|20.0uM|DTXSID6024882 for 24h in HepaRG cells


title: Tunicamycin|0.1uM|DTXSID8036730|24h|S25_S24-tuncamycin-0.1-24-1

description:
Library name: S25_S24-tuncamycin-0.1-24-1
TempO-LINC

value: Tunicamycin|0.1uM|DTXSID8036730 for 24h in HepaRG cells


title: Etoposide|2.5uM|DTXSID5023035|24h|S26_S17-etopiside-2.5-24-1

description:
Library name: S26_S17-etopiside-2.5-24-1
TempO-LINC

value: Etoposide|2.5uM|DTXSID5023035 for 24h in HepaRG cells

value: Etoposide


title: Etoposide|25.0uM|DTXSID5023035|24h|S25_S23-etopiside-25-24-1

description:
Library name: S25_S23-etopiside-25-24-1
TempO-LINC

value: Etoposide|25.0uM|DTXSID5023035 for 24h in HepaRG cells


title: Brefeldin A|0.01uM|DTXSID00880041|24h|S25_S15-brefeldin-a-0.01-24-1

description:
Library name: S25_S15-brefeldin-a-0.01-24-1
TempO-LINC


title: tert-Butylhydroquinone|30.0uM|DTXSID6020220|24h|S25_S14-tBHQ-30-24-1

description:
Library name: S25_S14-tBHQ-30-24-1
TempO-LINC

value: tert-Butylhydroquinone


title: Etoposide|2.5uM|DTXSID5023035|24h|S25_S17-etopiside-2.5-24-1

description:
Library name: S25_S17-etopiside-2.5-24-1
TempO-LINC


title: Etoposide|25.0uM|DTXSID5023035|24h|S24_S23-etopiside-25-24-1

description:
Library name: S24_S23-etopiside-25-24-1
TempO-LINC


title: Troglitazone|0.01uM|DTXSID8023719|24h|S25_S13-troglitazone-0.01-24-1

description:
Library name: S25_S13-troglitazone-0.01-24-1
TempO-LINC

value: Troglitazone


title: Cycloheximide|2.0uM|DTXSID6024882|24h|S25_S16-cycloheximide-2-24-1

description:
Library name: S25_S16-cycloheximide-2-24-1
TempO-LINC

value: Cycloheximide|2.0uM|DTXSID6024882 for 24h in HepaRG cells

value: Cycloheximide


title: Cycloheximide|20.0uM|DTXSID6024882|24h|S24_S22-cycloheximide-20-24-1

description:
Library name: S24_S22-cycloheximide-20-24-1
TempO-LINC


title: Tunicamycin|0.1uM|DTXSID8036730|24h|S24_S24-tuncamycin-0.1-24-1

description:
Library name: S24_S24-tuncamycin-0.1-24-1
TempO-LINC


title: tert-Butylhydroquinone|300.0uM|DTXSID6020220|24h|S24_S20-tBHQ-300-24-1

description:
Library name: S24_S20-tBHQ-300-24-1
TempO-LINC

value: tert-Butylhydroquinone|300.0uM|DTXSID6020220 for 24h in HepaRG cells


title: Brefeldin A|0.1uM|DTXSID00880041|24h|S24_S21-brefeldin-a-0.1-24-1

description:
Library name: S24_S21-brefeldin-a-0.1-24-1
TempO-LINC

value: Brefeldin A|0.1uM|DTXSID00880041 for 24h in HepaRG cells

value: Brefeldin A


title: Troglitazone|0.1uM|DTXSID8023719|24h|S24_S19-troglitazone-0.1-24-1

description:
Library name: S24_S19-troglitazone-0.1-24-1
TempO-LINC

value: Troglitazone|0.1uM|DTXSID8023719 for 24h in HepaRG cells


title: Tunicamycin|0.01uM|DTXSID8036730|24h|S24_S18-tuncamycin-0.01-24-1

description:
Library name: S24_S18-tuncamycin-0.01-24-1
TempO-LINC

value: liver

value: Tunicamycin|0.01uM|DTXSID8036730 for 24h in HepaRG cells

value: Tunicamycin


title: Etoposide|2.5uM|DTXSID5023035|24h|S24_S17-etopiside-2.5-24-1

description:
Library name: S24_S17-etopiside-2.5-24-1
TempO-LINC

value: HepaRG

value: differentiated HepaRG hepatocyte-like cells


title: Cycloheximide|2.0uM|DTXSID6024882|24h|S24_S16-cycloheximide-2-24-1

description:
Library name: S24_S16-cycloheximide-2-24-1
TempO-LINC


title: Troglitazone|0.01uM|DTXSID8023719|24h|S24_S13-troglitazone-0.01-24-1

description:
Library name: S24_S13-troglitazone-0.01-24-1
TempO-LINC

value: Troglitazone|0.01uM|DTXSID8023719 for 24h in HepaRG cells


title: tert-Butylhydroquinone|30.0uM|DTXSID6020220|24h|S24_S14-tBHQ-30-24-1

description:
Library name: S24_S14-tBHQ-30-24-1
TempO-LINC

value: tert-Butylhydroquinone|30.0uM|DTXSID6020220 for 24h in HepaRG cells


title: Troglitazone|0.1uM|DTXSID8023719|24h|S25_S19-troglitazone-0.1-24-1

description:
Library name: S25_S19-troglitazone-0.1-24-1
TempO-LINC


title: Tunicamycin|0.1uM|DTXSID8036730|24h|S23_S24-tuncamycin-0.1-24-1

description:
Library name: S23_S24-tuncamycin-0.1-24-1
TempO-LINC

value: Tunicamycin|0.1uM|DTXSID8036730 for 24h in HepaRG cells


title: Brefeldin A|0.01uM|DTXSID00880041|24h|S24_S15-brefeldin-a-0.01-24-1

description:
Library name: S24_S15-brefeldin-a-0.01-24-1
TempO-LINC

value: Brefeldin A|0.01uM|DTXSID00880041 for 24h in HepaRG cells


title: Etoposide|25.0uM|DTXSID5023035|24h|S23_S23-etopiside-25-24-1

description:
Library name: S23_S23-etopiside-25-24-1
TempO-LINC

value: Etoposide|25.0uM|DTXSID5023035 for 24h in HepaRG cells

value: Etoposide


title: Brefeldin A|0.1uM|DTXSID00880041|24h|S23_S21-brefeldin-a-0.1-24-1

description:
Library name: S23_S21-brefeldin-a-0.1-24-1
TempO-LINC


title: tert-Butylhydroquinone|300.0uM|DTXSID6020220|24h|S23_S20-tBHQ-300-24-1

description:
Library name: S23_S20-tBHQ-300-24-1
TempO-LINC

value: tert-Butylhydroquinone


title: Tunicamycin|0.01uM|DTXSID8036730|24h|S23_S18-tuncamycin-0.01-24-1

description:
Library name: S23_S18-tuncamycin-0.01-24-1
TempO-LINC


title: Etoposide|2.5uM|DTXSID5023035|24h|S23_S17-etopiside-2.5-24-1

description:
Library name: S23_S17-etopiside-2.5-24-1
TempO-LINC

value: Etoposide|2.5uM|DTXSID5023035 for 24h in HepaRG cells


title: Troglitazone|0.1uM|DTXSID8023719|24h|S23_S19-troglitazone-0.1-24-1

description:
Library name: S23_S19-troglitazone-0.1-24-1
TempO-LINC

value: Troglitazone


title: Brefeldin A|0.01uM|DTXSID00880041|24h|S23_S15-brefeldin-a-0.01-24-1

description:
Library name: S23_S15-brefeldin-a-0.01-24-1
TempO-LINC


title: Cycloheximide|2.0uM|DTXSID6024882|24h|S23_S16-cycloheximide-2-24-1

description:
Library name: S23_S16-cycloheximide-2-24-1
TempO-LINC

value: Cycloheximide|2.0uM|DTXSID6024882 for 24h in HepaRG cells

value: Cycloheximide


title: Troglitazone|0.01uM|DTXSID8023719|24h|S23_S13-troglitazone-0.01-24-1

description:
Library name: S23_S13-troglitazone-0.01-24-1
TempO-LINC


title: Cycloheximide|20.0uM|DTXSID6024882|24h|S23_S22-cycloheximide-20-24-1

description:
Library name: S23_S22-cycloheximide-20-24-1
TempO-LINC

value: Cycloheximide|20.0uM|DTXSID6024882 for 24h in HepaRG cells


title: Cycloheximide|20.0uM|DTXSID6024882|24h|S22_S22-cycloheximide-20-24-1

description:
Library name: S22_S22-cycloheximide-20-24-1
TempO-LINC

value: liver


title: Etoposide|25.0uM|DTXSID5023035|24h|S22_S23-etopiside-25-24-1

description:
Library name: S22_S23-etopiside-25-24-1
TempO-LINC


title: Tunicamycin|0.1uM|DTXSID8036730|24h|S22_S24-tuncamycin-0.1-24-1

description:
Library name: S22_S24-tuncamycin-0.1-24-1
TempO-LINC


title: Brefeldin A|0.1uM|DTXSID00880041|24h|S22_S21-brefeldin-a-0.1-24-1

description:
Library name: S22_S21-brefeldin-a-0.1-24-1
TempO-LINC

value: Brefeldin A|0.1uM|DTXSID00880041 for 24h in HepaRG cells

value: Brefeldin A


title: Tunicamycin|0.01uM|DTXSID8036730|24h|S22_S18-tuncamycin-0.01-24-1

description:
Library name: S22_S18-tuncamycin-0.01-24-1
TempO-LINC

value: HepaRG

value: Tunicamycin|0.01uM|DTXSID8036730 for 24h in HepaRG cells

value: Tunicamycin


title: Troglitazone|0.1uM|DTXSID8023719|24h|S22_S19-troglitazone-0.1-24-1

description:
Library name: S22_S19-troglitazone-0.1-24-1
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells

value: Troglitazone|0.1uM|DTXSID8023719 for 24h in HepaRG cells


title: Etoposide|2.5uM|DTXSID5023035|24h|S22_S17-etopiside-2.5-24-1

description:
Library name: S22_S17-etopiside-2.5-24-1
TempO-LINC


title: hc98

city: La Jolla

first: Seoyeon

last: Lee

state: California

address: 9500 Gilman Dr.

institute: University of California, San Diego

description:
Library name: hc98
snm3C v1

library_source: genomic

data_processing:
The snm3C-seq FASTQ reads were demultiplexed and mapped using YAP (Yet Another Pipeline) software (cemba-data v1.6.9). First, FASTQ files were demultiplexed for each cell barcode. Next, two-pass mapping was performed with bismark  (v0.20), using bowtie2 (v2.3). BAM file processing and QC was performed using samtools  (v1.9) and picard (v3.0.0). Chromatin contacts were called and methylome profiles were generated using Allcools (v1.0.23). All reads were mapped to the hg38 reference genome assembly.
Assembly: hg38 GRCh38
Supplementary files format and content: 3C.contact.tsv.gz, mC.allc.tsv.gz; YAP outputs
Supplementary files format and content: human_aging_snm3C_metadata.csv; a metadata for snm3C data

molecule: genomic DNA

source_name: hippocampus

extract_protocol:
Fresh frozen hippocampus tissues were pulverized in liquid nitrogen using a mortar and pestle on dry ice. Around 20mg of pulverized brain tissue was added to a ice-cold dounce homogenizer containing 1mL of chilled NIM-DP-L buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl pH 7.5, 1mM DTT, 1X Protease Inhibitor (Pierce), 1U/μL Recombinant RNase inhibitor (Promega, PAN2515), and 0.1% Triton X-100). Tissue was dounce homogenized with a loose pestle (5-10 strokes) to shear large pieces, followed by a tight pestle (15-25 strokes) until the solution was uniform. Homogenate was filtered through a 30μm CellTrics filter (Sysmex, 04-0042-2316) into a LoBind tube (Eppendorf, 22431021) and pelleted (1000 rcf, 10 min at 4˚C) (Eppendorf, 5920 R). Pellets were resuspended in 2% formaldehyde in DPBS for 5 minutes at room temperature on a rotator. Glycine was added to obtain 0.2M glycine and tubes were incubated for 5 min on a rotator at room temperature. Lysate was centrifuged at 1,000 x g for 10 min at 4°C (in bucket rotor). Supernatant was removed and the pellet was resuspended in 1mL of cold DPBS. Lysate was centrifuged at 2,500 x g for 5 min at 4°C (in bucket rotor). Supernatant was removed and the pellets were used for in situ 3C following the steps in the Arima-3C Single Cell Beta Kit (Arima Genomics), with some modifications. Briefly, 44uL of Conditioning Solution was added, and lysate was transferred to a 0.2 mL PCR tube, and mixed gently by pipetting. Tubes were incubated at 62°C for 30 min in a thermal cycler, with the lid temperature set to 85°C. 20µL of Stop Solution 2 was added, and mixed gently by pipetting. Tubes were incubated at 37°C for 15 min in a thermal cycler with a lid temperature set to 85°C. 28µL of the restriction enzyme digestion mix (9.8uL water, 9.2uL Buffer H, 4.5uL Enzyme H1, 4.5uL Enzyme H2) was added and gently pipette mixed. Tubes were incubated in a thermal cycler for 37°C for 60 min, 65°C for 20 min, then 25°C for 10 min. 82uL of ligation mix was added (70uL Buffer C, 12uL Enzyme C) and gently mixed by pipetting, then incubated at 25°C for 15 min. Lysate was transferred to a tube containing 850μL 1% BSA in DPBS on ice and filtered through a 30um Celltrics strainer to a new tube on ice. Lysate was centrifuged at 1,000 x g for 10 min at 4°C (in bucket rotor). Supernatant was removed and pellets were resuspended each sample in 800uL of 1% BSA in DPBS. Nuclei were stained with DRAQ7 at 1:200 and mixed gently with a pipette and incubated on ice for 5 min. One tube of Proteinase K (Zymo cat. no. D3001-2-D) was dissolved in 1mL of Proteinase K Resuspension Buffer (Zymo cat. no. D3001-2-B) then added to a mix of 15mL M-Digestion Buffer 2x (Zymo cat. no. D5021-9) and 14mL water to make pK Digestion Buffer. 2uL of pK Digestion Buffer were added to each well of an Eppendorf twin.tec® PCR Plate 384 LoBind®, skirted, 45 µL, PCR clean (Eppendorf cat. No. 0030129547). Single DRAQ7 positive nuclei were sorted into individual wells of the 384-well plate using a Sony SH800 cell sorter. Plates were sealed then incubated in a thermal cycler at 50°C for 20 min with a heated lid at 85°C for nuclei digestion.
The snm3C-seq samples followed the library preparation protocol detailed previously (H. Liu, J. Zhou et al., DNA methylation atlas of the mouse brain at single-cell resolution. Nature 598, 120–128 (2021)). This protocol has been automated using the Beckman Coulter Biomek i7 liquid handlers for reactions in 384 and 96-well plates. The snm3C-seq libraries were shallow sequenced on the Illumina NextSeq 2000 to 2-10M reads to check quality. Successful libraries were deeply sequenced on the NovaSeq 6000 instrument, using one lane of 25B flow cell per 4 384-well plates and using 150 bp paired-end mode.

tag: donor id

tag: age

tag: Sex

value: female

value: hippocampus


title: tert-Butylhydroquinone|300.0uM|DTXSID6020220|24h|S22_S20-tBHQ-300-24-1

description:
Library name: S22_S20-tBHQ-300-24-1
TempO-LINC

value: tert-Butylhydroquinone|300.0uM|DTXSID6020220 for 24h in HepaRG cells


title: hc937

description:
Library name: hc937
snm3C v2


title: Cycloheximide|2.0uM|DTXSID6024882|24h|S22_S16-cycloheximide-2-24-1

description:
Library name: S22_S16-cycloheximide-2-24-1
TempO-LINC


title: hc9

description:
Library name: hc9
snm3C v1


title: hc81

description:
Library name: hc81
snm3C v1


title: Tunicamycin|0.1uM|DTXSID8036730|24h|S21_S24-tuncamycin-0.1-24-1

description:
Library name: S21_S24-tuncamycin-0.1-24-1
TempO-LINC

value: Tunicamycin|0.1uM|DTXSID8036730 for 24h in HepaRG cells


title: Etoposide|25.0uM|DTXSID5023035|24h|S21_S23-etopiside-25-24-1

description:
Library name: S21_S23-etopiside-25-24-1
TempO-LINC

value: Etoposide|25.0uM|DTXSID5023035 for 24h in HepaRG cells

value: Etoposide


title: Cycloheximide|20.0uM|DTXSID6024882|24h|S21_S22-cycloheximide-20-24-1

description:
Library name: S21_S22-cycloheximide-20-24-1
TempO-LINC


title: hc76

description:
Library name: hc76
snm3C v2


title: Brefeldin A|0.1uM|DTXSID00880041|24h|S21_S21-brefeldin-a-0.1-24-1

description:
Library name: S21_S21-brefeldin-a-0.1-24-1
TempO-LINC


title: hc78

description:
Library name: hc78
snm3C v1

value: male


title: hc8

description:
Library name: hc8
snm3C v1


title: hc73787

description:
Library name: hc73787
snm3C v1


title: tert-Butylhydroquinone|300.0uM|DTXSID6020220|24h|S21_S20-tBHQ-300-24-1

description:
Library name: S21_S20-tBHQ-300-24-1
TempO-LINC

value: tert-Butylhydroquinone


title: Tunicamycin|0.01uM|DTXSID8036730|24h|S21_S18-tuncamycin-0.01-24-1

description:
Library name: S21_S18-tuncamycin-0.01-24-1
TempO-LINC


title: Troglitazone|0.1uM|DTXSID8023719|24h|S21_S19-troglitazone-0.1-24-1

description:
Library name: S21_S19-troglitazone-0.1-24-1
TempO-LINC

value: Troglitazone


title: Etoposide|2.5uM|DTXSID5023035|24h|S21_S17-etopiside-2.5-24-1

description:
Library name: S21_S17-etopiside-2.5-24-1
TempO-LINC

value: liver

value: Etoposide|2.5uM|DTXSID5023035 for 24h in HepaRG cells


title: hc69984

description:
Library name: hc69984
snm3C v2


title: hc6052

description:
Library name: hc6052
snm3C v1


title: hc935

description:
Library name: hc935
snm3C v1


title: hc5614

description:
Library name: hc5614
snm3C v1


title: Cycloheximide|2.0uM|DTXSID6024882|24h|S21_S16-cycloheximide-2-24-1

description:
Library name: S21_S16-cycloheximide-2-24-1
TempO-LINC

value: Cycloheximide|2.0uM|DTXSID6024882 for 24h in HepaRG cells

value: Cycloheximide


title: hc6021

description:
Library name: hc6021
snm3C v1


title: Brefeldin A|0.01uM|DTXSID00880041|24h|S21_S15-brefeldin-a-0.01-24-1

description:
Library name: S21_S15-brefeldin-a-0.01-24-1
TempO-LINC

value: HepaRG

value: Brefeldin A|0.01uM|DTXSID00880041 for 24h in HepaRG cells

value: Brefeldin A


title: Brefeldin A|0.01uM|DTXSID00880041|24h|S22_S15-brefeldin-a-0.01-24-1

description:
Library name: S22_S15-brefeldin-a-0.01-24-1
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells


title: hc5610

description:
Library name: hc5610
snm3C v1

value: female


title: Troglitazone|0.01uM|DTXSID8023719|24h|S21_S13-troglitazone-0.01-24-1

description:
Library name: S21_S13-troglitazone-0.01-24-1
TempO-LINC

value: Troglitazone|0.01uM|DTXSID8023719 for 24h in HepaRG cells


title: tert-Butylhydroquinone|30.0uM|DTXSID6020220|24h|S21_S14-tBHQ-30-24-1

description:
Library name: S21_S14-tBHQ-30-24-1
TempO-LINC

value: tert-Butylhydroquinone|30.0uM|DTXSID6020220 for 24h in HepaRG cells


title: Troglitazone|0.01uM|DTXSID8023719|24h|S22_S13-troglitazone-0.01-24-1

description:
Library name: S22_S13-troglitazone-0.01-24-1
TempO-LINC


title: hc5579

description:
Library name: hc5579
snm3C v1

value: hippocampus


title: hc5276

description:
Library name: hc5276
snm3C v1


title: Tunicamycin|0.001uM|DTXSID8036730|24h|S20_sample-12-tuncamycin-0p001-dose

description:
Library name: S20_sample-12-tuncamycin-0p001-dose
TempO-LINC

value: Tunicamycin|0.001uM|DTXSID8036730 for 24h in HepaRG cells

value: Tunicamycin


title: Etoposide|0.25uM|DTXSID5023035|24h|S20_sample-11-etopiside-0p25-dose

description:
Library name: S20_sample-11-etopiside-0p25-dose
TempO-LINC

value: Etoposide|0.25uM|DTXSID5023035 for 24h in HepaRG cells

value: Etoposide


title: Cycloheximide|0.2uM|DTXSID6024882|24h|S20_sample-10-cycloheximide-0p2-dose

description:
Library name: S20_sample-10-cycloheximide-0p2-dose
TempO-LINC

value: Cycloheximide|0.2uM|DTXSID6024882 for 24h in HepaRG cells


title: hc5087

description:
Library name: hc5087
snm3C v1

value: male


title: hc73

description:
Library name: hc73
snm3C v1


title: tert-Butylhydroquinone|3.0uM|DTXSID6020220|24h|S20_sample-08-tBHQ-3-dose

description:
Library name: S20_sample-08-tBHQ-3-dose
TempO-LINC

value: liver

value: tert-Butylhydroquinone|3.0uM|DTXSID6020220 for 24h in HepaRG cells

value: tert-Butylhydroquinone


title: hc4781

description:
Library name: hc4781
snm3C v1


title: hc46426

description:
Library name: hc46426
snm3C v1


title: Rotenone|0.8uM|DTXSID6021248|24h|S20_sample-06-rotenone-0p8-dose

description:
Library name: S20_sample-06-rotenone-0p8-dose
TempO-LINC

value: HepaRG

value: Rotenone|0.8uM|DTXSID6021248 for 24h in HepaRG cells

value: Rotenone


title: Troglitazone|0.001uM|DTXSID8023719|24h|S20_sample-07-troglitazone-0p001-dose

description:
Library name: S20_sample-07-troglitazone-0p001-dose
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells

value: Troglitazone|0.001uM|DTXSID8023719 for 24h in HepaRG cells

value: Troglitazone


title: hc40

description:
Library name: hc40
snm3C v1

value: female


title: Rotenone|0.4uM|DTXSID6021248|24h|S20_sample-05-rotenone-0p4-dose

description:
Library name: S20_sample-05-rotenone-0p4-dose
TempO-LINC

value: Rotenone|0.4uM|DTXSID6021248 for 24h in HepaRG cells


title: Rotenone|0.2uM|DTXSID6021248|24h|S20_sample-04-rotenone-0p2-dose

description:
Library name: S20_sample-04-rotenone-0p2-dose
TempO-LINC

value: Rotenone|0.2uM|DTXSID6021248 for 24h in HepaRG cells


title: hc29

description:
Library name: hc29
snm3C v1

value: hippocampus


title: hc26

description:
Library name: hc26
snm3C v1


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S20_sample-03-DMSO-0dose

description:
Library name: S20_sample-03-DMSO-0dose
TempO-LINC

value: DMSO control 24h in HepaRG cells

value: Dimethyl sulfoxide


title: hc5551

description:
Library name: hc5551
snm3C v1


title: hc212191

description:
Library name: hc212191
snm3C v1


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S20_sample-01-DMSO-0dose

description:
Library name: S20_sample-01-DMSO-0dose
TempO-LINC


title: Tunicamycin|0.001uM|DTXSID8036730|24h|S19_sample-12-tuncamycin-0p001-dose

description:
Library name: S19_sample-12-tuncamycin-0p001-dose
TempO-LINC

value: Tunicamycin|0.001uM|DTXSID8036730 for 24h in HepaRG cells

value: Tunicamycin


title: Etoposide|0.25uM|DTXSID5023035|24h|S19_sample-11-etopiside-0p25-dose

description:
Library name: S19_sample-11-etopiside-0p25-dose
TempO-LINC

value: liver

value: Etoposide|0.25uM|DTXSID5023035 for 24h in HepaRG cells

value: Etoposide


title: hc13414

description:
Library name: hc13414
snm3C v1

value: male


title: hc1745

description:
Library name: hc1745
snm3C v1


title: hc19

description:
Library name: hc19
snm3C v1


title: Cycloheximide|0.2uM|DTXSID6024882|24h|S19_sample-10-cycloheximide-0p2-dose

description:
Library name: S19_sample-10-cycloheximide-0p2-dose
TempO-LINC

value: HepaRG

value: Cycloheximide|0.2uM|DTXSID6024882 for 24h in HepaRG cells

value: Cycloheximide


title: hc13394

description:
Library name: hc13394
snm3C v1


title: tert-Butylhydroquinone|30.0uM|DTXSID6020220|24h|S23_S14-tBHQ-30-24-1

description:
Library name: S23_S14-tBHQ-30-24-1
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells

value: tert-Butylhydroquinone|30.0uM|DTXSID6020220 for 24h in HepaRG cells

value: tert-Butylhydroquinone


title: hc5021

description:
Library name: hc5021
snm3C v1

value: female


title: tert-Butylhydroquinone|3.0uM|DTXSID6020220|24h|S19_sample-08-tBHQ-3-dose

description:
Library name: S19_sample-08-tBHQ-3-dose
TempO-LINC

value: tert-Butylhydroquinone|3.0uM|DTXSID6020220 for 24h in HepaRG cells


title: Brefeldin A|0.001uM|DTXSID00880041|24h|S19_sample-09-brefeldina-0p001-dose

description:
Library name: S19_sample-09-brefeldina-0p001-dose
TempO-LINC

value: Brefeldin A|0.001uM|DTXSID00880041 for 24h in HepaRG cells

value: Brefeldin A


title: Rotenone|0.8uM|DTXSID6021248|24h|S19_sample-06-rotenone-0p8-dose

description:
Library name: S19_sample-06-rotenone-0p8-dose
TempO-LINC

value: Rotenone|0.8uM|DTXSID6021248 for 24h in HepaRG cells

value: Rotenone


title: hc13344

description:
Library name: hc13344
snm3C v1

value: hippocampus


title: hc1271

description:
Library name: hc1271
snm3C v1


title: hc1216

description:
Library name: hc1216
snm3C v2


title: Rotenone|0.4uM|DTXSID6021248|24h|S19_sample-05-rotenone-0p4-dose

description:
Library name: S19_sample-05-rotenone-0p4-dose
TempO-LINC

value: liver

value: Rotenone|0.4uM|DTXSID6021248 for 24h in HepaRG cells


title: hc1203

description:
Library name: hc1203
snm3C v1


title: hc1265

description:
Library name: hc1265
snm3C v1


title: Dimethyl sulfoxide|0.0uM|nan|24h|S20_sample-02-DMSO-0dose

description:
Library name: S20_sample-02-DMSO-0dose
TempO-LINC

value: DMSO control 24h in HepaRG cells

value: Dimethyl sulfoxide


title: hc12

description:
Library name: hc12
snm3C v1

value: male


title: Rotenone|0.2uM|DTXSID6021248|24h|S19_sample-04-rotenone-0p2-dose

description:
Library name: S19_sample-04-rotenone-0p2-dose
TempO-LINC

value: HepaRG

value: Rotenone|0.2uM|DTXSID6021248 for 24h in HepaRG cells


title: hc35

description:
Library name: hc35
snm3C v1


title: Dimethyl sulfoxide|0.0uM|nan|24h|S19_sample-02-DMSO-0dose

description:
Library name: S19_sample-02-DMSO-0dose
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells


title: hc1153

description:
Library name: hc1153
snm3C v1


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S19_sample-03-DMSO-0dose

description:
Library name: S19_sample-03-DMSO-0dose
TempO-LINC


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S19_sample-01-DMSO-0dose

description:
Library name: S19_sample-01-DMSO-0dose
TempO-LINC


title: hc1134

description:
Library name: hc1134
snm3C v1


title: Tunicamycin|0.001uM|DTXSID8036730|24h|S18_sample-12-tuncamycin-0p001-dose

description:
Library name: S18_sample-12-tuncamycin-0p001-dose
TempO-LINC

value: Tunicamycin|0.001uM|DTXSID8036730 for 24h in HepaRG cells

value: Tunicamycin


title: SW480 cell line, D3, Combination

city: Changchun

first: Can

last: Wang

state: Jilin

address: Ziqiang Street

country: China

institute: the second hospital of Jilin university

description: Library name: D3

library_source: transcriptomic

data_processing:
MAJORBIO Cloud Platform Processing Flow
Assembly: GRCh38
Supplementary files format and content: txt for gene and transcript both count and TPM with anno

source_name: colon

extract_protocol:
The sequencing experiment used the Illumina TruseqTM RNA sample prep Kit method to construct the library
The sequencing experiment used the Illumina TruseqTM RNA sample prep Kit method to construct the library

value: colon

value: colorectal cancer cell line

tag: genotype

value: WT

value: Combination


title: SW480 cell line, D2, Combination

description: Library name: D2


title: SW480 cell line, D1, Combination

description: Library name: D1


title: hc11

description:
Library name: hc11
snm3C v1


title: Cycloheximide|0.2uM|DTXSID6024882|24h|S18_sample-10-cycloheximide-0p2-dose

description:
Library name: S18_sample-10-cycloheximide-0p2-dose
TempO-LINC

value: Cycloheximide|0.2uM|DTXSID6024882 for 24h in HepaRG cells

value: Cycloheximide


title: Troglitazone|0.001uM|DTXSID8023719|24h|S19_sample-07-troglitazone-0p001-dose

description:
Library name: S19_sample-07-troglitazone-0p001-dose
TempO-LINC

value: Troglitazone|0.001uM|DTXSID8023719 for 24h in HepaRG cells

value: Troglitazone


title: tert-Butylhydroquinone|3.0uM|DTXSID6020220|24h|S18_sample-08-tBHQ-3-dose

description:
Library name: S18_sample-08-tBHQ-3-dose
TempO-LINC

value: liver

value: tert-Butylhydroquinone|3.0uM|DTXSID6020220 for 24h in HepaRG cells

value: tert-Butylhydroquinone


title: Troglitazone|0.001uM|DTXSID8023719|24h|S18_sample-07-troglitazone-0p001-dose

description:
Library name: S18_sample-07-troglitazone-0p001-dose
TempO-LINC


title: SW480 cell line, C1, 5uM 5-FU

description: Library name: C1

value: 5uM 5-FU


title: SW480 cell line, C2, 5uM 5-FU

description: Library name: C2


title: SW480 cell line, B3, 2.5uM SAL

description: Library name: B3

value: 2.5uM salinomycin


title: SW480 cell line, B1, 2.5uM SAL

description: Library name: B1


title: Rotenone|0.8uM|DTXSID6021248|24h|S18_sample-06-rotenone-0p8-dose

description:
Library name: S18_sample-06-rotenone-0p8-dose
TempO-LINC

value: HepaRG

value: Rotenone|0.8uM|DTXSID6021248 for 24h in HepaRG cells

value: Rotenone


title: SW480 cell line, A3, 0.1% DMSO

description: Library name: A3

value: 0.1% DMSO


title: Rotenone|0.4uM|DTXSID6021248|24h|S18_sample-05-rotenone-0p4-dose

description:
Library name: S18_sample-05-rotenone-0p4-dose
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells

value: Rotenone|0.4uM|DTXSID6021248 for 24h in HepaRG cells


title: Rotenone|0.2uM|DTXSID6021248|24h|S18_sample-04-rotenone-0p2-dose

description:
Library name: S18_sample-04-rotenone-0p2-dose
TempO-LINC

value: Rotenone|0.2uM|DTXSID6021248 for 24h in HepaRG cells


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S18_sample-03-DMSO-0dose

description:
Library name: S18_sample-03-DMSO-0dose
TempO-LINC

value: DMSO control 24h in HepaRG cells

value: Dimethyl sulfoxide


title: SW480 cell line, A1, 0.1% DMSO

description: Library name: A1

value: colon

value: colorectal cancer cell line

value: WT


title: Dimethyl sulfoxide|0.0uM|nan|24h|S18_sample-02-DMSO-0dose

description:
Library name: S18_sample-02-DMSO-0dose
TempO-LINC

value: liver


title: RNA_LS_023_D14_83y_7c

city: Lausanne

first: kevin

last: perez

address: rue du Bugnon 27

country: Switzerland

institute: University of Lausanne

description:
Library name: RNA_LS_023
RNA_LS_023_D14_83y_7c

data_processing:
Raw FASTQ files were assessed for quality, adapter content and duplication rates with FastQC.
Reads were aligned to the Human genome (GRCh38) using the STAR aligner (v2.7.9a) with '--sjdbOverhang 100' (Dobin et al, 2013).
Number of reads per gene was quantified using the featureCounts function in the subread package (Liao et al, 2013).
Ensembl transcripts were mapped to gene symbols using the mapIds function in the AnnotationDbi package (Pagès et al, 2022) with the org.Hs.eg.db reference package (Carlson, 2019).
Assembly: Human genome (GRCh38)
Supplementary files format and content: LogCPM: Raw counts were normalized by library size and converted to counts per million (CPM) for downstream analysis

source_name: Skin

growth_protocol: Human dermal fibroblasts were freshly extracted using Collagenase I (Sigma, C0130) and Dispase II (Sigma, D4693) and cultured in DMEM (Gibco, 11960085) containing non-essential amino acids (Gibco, 11140035), GlutaMax (Gibco, 35050061), Sodium Pyruvate (Gibco, 11360039) and 10% fetal bovine serum (FBS, Hyclone, SH30088.03) at 37°C in hypoxic conditions (3% O2).

extract_protocol:
Total RNA was extracted using Monarch Total RNA Miniprep Kit (New England Biolabs, T2010S) according to manufacturer’s instructions with DNase treatment (Qiagen, 79254) for 15 minutes (1:8 in DNase buffer
RNA-Seq library preparation and sequencing was performed by Novogene (UK) Company Limited on an Illumina NovaSeq 6000 in 150 bp paired-end mode.

value: Skin

value: Human dermal fibroblast

tag: time


title: RNA_LS_024_D14_83y_2c

description:
Library name: RNA_LS_024
RNA_LS_024_D14_83y_2c


title: Etoposide|0.25uM|DTXSID5023035|24h|S17_sample-11-etopiside-0p25-dose

description:
Library name: S17_sample-11-etopiside-0p25-dose
TempO-LINC

value: Etoposide|0.25uM|DTXSID5023035 for 24h in HepaRG cells

value: Etoposide


title: Tunicamycin|0.001uM|DTXSID8036730|24h|S17_sample-12-tuncamycin-0p001-dose

description:
Library name: S17_sample-12-tuncamycin-0p001-dose
TempO-LINC

value: HepaRG

value: Tunicamycin|0.001uM|DTXSID8036730 for 24h in HepaRG cells

value: Tunicamycin


title: Cycloheximide|0.2uM|DTXSID6024882|24h|S17_sample-10-cycloheximide-0p2-dose

description:
Library name: S17_sample-10-cycloheximide-0p2-dose
TempO-LINC

value: Cycloheximide|0.2uM|DTXSID6024882 for 24h in HepaRG cells

value: Cycloheximide


title: Etoposide|0.25uM|DTXSID5023035|24h|S18_sample-11-etopiside-0p25-dose

description:
Library name: S18_sample-11-etopiside-0p25-dose
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells


title: RNA_LS_022_D14_83y_DMSO

description:
Library name: RNA_LS_022
RNA_LS_022_D14_83y_DMSO

value: DMSO


title: RNA_LS_021_D14_23y_DMSO

description:
Library name: RNA_LS_021
RNA_LS_021_D14_23y_DMSO


title: SW480 cell line, C3, 5uM 5-FU

description: Library name: C3

value: 5uM 5-FU


title: RNA_LS_020_D14_56y_2c

description:
Library name: RNA_LS_020
RNA_LS_020_D14_56y_2c


title: tert-Butylhydroquinone|3.0uM|DTXSID6020220|24h|S17_sample-08-tBHQ-3-dose

description:
Library name: S17_sample-08-tBHQ-3-dose
TempO-LINC

value: tert-Butylhydroquinone|3.0uM|DTXSID6020220 for 24h in HepaRG cells

value: tert-Butylhydroquinone


title: Brefeldin A|0.001uM|DTXSID00880041|24h|S18_sample-09-brefeldina-0p001-dose

description:
Library name: S18_sample-09-brefeldina-0p001-dose
TempO-LINC

value: Brefeldin A|0.001uM|DTXSID00880041 for 24h in HepaRG cells

value: Brefeldin A


title: Brefeldin A|0.001uM|DTXSID00880041|24h|S17_sample-09-brefeldina-0p001-dose

description:
Library name: S17_sample-09-brefeldina-0p001-dose
TempO-LINC

value: liver


title: RNA_LS_019_D14_56y_7c

description:
Library name: RNA_LS_019
RNA_LS_019_D14_56y_7c

value: Skin


title: SW480 cell line, B2, 2.5uM SAL

description: Library name: B2

value: colon

value: colorectal cancer cell line

value: WT

value: 2.5uM salinomycin


title: RNA_LS_018_D14_56y_DMSO

description:
Library name: RNA_LS_018
RNA_LS_018_D14_56y_DMSO

value: Human dermal fibroblast


title: Rotenone|0.8uM|DTXSID6021248|24h|S17_sample-06-rotenone-0p8-dose

description:
Library name: S17_sample-06-rotenone-0p8-dose
TempO-LINC

value: HepaRG

value: Rotenone|0.8uM|DTXSID6021248 for 24h in HepaRG cells

value: Rotenone


title: RNA_LS_017_D14_22y_DMSO

description:
Library name: RNA_LS_017
RNA_LS_017_D14_22y_DMSO


title: Troglitazone|0.001uM|DTXSID8023719|24h|S17_sample-07-troglitazone-0p001-dose

description:
Library name: S17_sample-07-troglitazone-0p001-dose
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells

value: Troglitazone|0.001uM|DTXSID8023719 for 24h in HepaRG cells

value: Troglitazone


title: Rotenone|0.4uM|DTXSID6021248|24h|S17_sample-05-rotenone-0p4-dose

description:
Library name: S17_sample-05-rotenone-0p4-dose
TempO-LINC

value: Rotenone|0.4uM|DTXSID6021248 for 24h in HepaRG cells


title: SW480 cell line, A2, 0.1% DMSO

description: Library name: A2

value: 0.1% DMSO


title: RNA_LS_016_D14_56y_2c

description:
Library name: RNA_LS_016
RNA_LS_016_D14_56y_2c


title: RNA_LS_015_D14_56y_7c

description:
Library name: RNA_LS_015
RNA_LS_015_D14_56y_7c


title: Rotenone|0.2uM|DTXSID6021248|24h|S17_sample-04-rotenone-0p2-dose

description:
Library name: S17_sample-04-rotenone-0p2-dose
TempO-LINC

value: Rotenone|0.2uM|DTXSID6021248 for 24h in HepaRG cells


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S17_sample-03-DMSO-0dose

description:
Library name: S17_sample-03-DMSO-0dose
TempO-LINC

value: DMSO control 24h in HepaRG cells

value: Dimethyl sulfoxide


title: Dimethyl sulfoxide|0.0uM|nan|24h|S17_sample-02-DMSO-0dose

description:
Library name: S17_sample-02-DMSO-0dose
TempO-LINC

value: liver


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S18_sample-01-DMSO-0dose

description:
Library name: S18_sample-01-DMSO-0dose
TempO-LINC


title: RNA_LS_013_D14_22y_DMSO

description:
Library name: RNA_LS_013
RNA_LS_013_D14_22y_DMSO

value: Skin

value: DMSO


title: Tunicamycin|0.001uM|DTXSID8036730|24h|S16_sample-12-tuncamycin-0p001-dose

description:
Library name: S16_sample-12-tuncamycin-0p001-dose
TempO-LINC

value: Tunicamycin|0.001uM|DTXSID8036730 for 24h in HepaRG cells

value: Tunicamycin


title: RNA_LS_012_D6_83y_2c

description:
Library name: RNA_LS_012
RNA_LS_012_D6_83y_2c

value: Human dermal fibroblast


title: RNA_LS_011_D6_83y_7c

description:
Library name: RNA_LS_011
RNA_LS_011_D6_83y_7c


title: RNA_LS_010_D6_83y_DMSO

description:
Library name: RNA_LS_010
RNA_LS_010_D6_83y_DMSO


title: Cycloheximide|0.2uM|DTXSID6024882|24h|S16_sample-10-cycloheximide-0p2-dose

description:
Library name: S16_sample-10-cycloheximide-0p2-dose
TempO-LINC

value: HepaRG

value: Cycloheximide|0.2uM|DTXSID6024882 for 24h in HepaRG cells

value: Cycloheximide


title: Brefeldin A|0.001uM|DTXSID00880041|24h|S16_sample-09-brefeldina-0p001-dose

description:
Library name: S16_sample-09-brefeldina-0p001-dose
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells

value: Brefeldin A|0.001uM|DTXSID00880041 for 24h in HepaRG cells

value: Brefeldin A


title: RNA_LS_008_D6_56y_2c

description:
Library name: RNA_LS_008
RNA_LS_008_D6_56y_2c


title: tert-Butylhydroquinone|3.0uM|DTXSID6020220|24h|S16_sample-08-tBHQ-3-dose

description:
Library name: S16_sample-08-tBHQ-3-dose
TempO-LINC

value: tert-Butylhydroquinone|3.0uM|DTXSID6020220 for 24h in HepaRG cells

value: tert-Butylhydroquinone


title: RNA_LS_007_D6_56y_7c

description:
Library name: RNA_LS_007
RNA_LS_007_D6_56y_7c


title: Troglitazone|0.001uM|DTXSID8023719|24h|S16_sample-07-troglitazone-0p001-dose

description:
Library name: S16_sample-07-troglitazone-0p001-dose
TempO-LINC

value: Troglitazone|0.001uM|DTXSID8023719 for 24h in HepaRG cells

value: Troglitazone


title: Rotenone|0.8uM|DTXSID6021248|24h|S16_sample-06-rotenone-0p8-dose

description:
Library name: S16_sample-06-rotenone-0p8-dose
TempO-LINC

value: Rotenone|0.8uM|DTXSID6021248 for 24h in HepaRG cells

value: Rotenone


title: RNA_LS_005_D6_22y_DMSO

description:
Library name: RNA_LS_005
RNA_LS_005_D6_22y_DMSO

value: Skin


title: Rotenone|0.4uM|DTXSID6021248|24h|S16_sample-05-rotenone-0p4-dose

description:
Library name: S16_sample-05-rotenone-0p4-dose
TempO-LINC

value: liver

value: Rotenone|0.4uM|DTXSID6021248 for 24h in HepaRG cells


title: Rotenone|0.2uM|DTXSID6021248|24h|S16_sample-04-rotenone-0p2-dose

description:
Library name: S16_sample-04-rotenone-0p2-dose
TempO-LINC

value: Rotenone|0.2uM|DTXSID6021248 for 24h in HepaRG cells


title: RNA_LS_003_D6_56y_7c

description:
Library name: RNA_LS_003
RNA_LS_003_D6_56y_7c

value: Human dermal fibroblast


title: RNA_LS_002_D6_56y_DMSO

description:
Library name: RNA_LS_002
RNA_LS_002_D6_56y_DMSO

value: DMSO


title: RNA_LS_014_D14_56y_DMSO

description:
Library name: RNA_LS_014
RNA_LS_014_D14_56y_DMSO


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S16_sample-03-DMSO-0dose

description:
Library name: S16_sample-03-DMSO-0dose
TempO-LINC

value: HepaRG

value: DMSO control 24h in HepaRG cells

value: Dimethyl sulfoxide


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S17_sample-01-DMSO-0dose

description:
Library name: S17_sample-01-DMSO-0dose
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells


title: RNA_LS_001_D6_22y_DMSO

description:
Library name: RNA_LS_001
RNA_LS_001_D6_22y_DMSO


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S16_sample-01-DMSO-0dose

description:
Library name: S16_sample-01-DMSO-0dose
TempO-LINC


title: Tunicamycin|0.001uM|DTXSID8036730|24h|S15_sample-12-tuncamycin-0p001-dose

description:
Library name: S15_sample-12-tuncamycin-0p001-dose
TempO-LINC

value: Tunicamycin|0.001uM|DTXSID8036730 for 24h in HepaRG cells

value: Tunicamycin


title: Xenograft_PC_treated_2

city: Boston

first: Raghav

last: Joshi

state: MA

address: 800 Washington Street

institute: Tufts Medical Center

description:
Library name: PCX_treated_2
column name in PCX_counts.tsv: A2

data_processing:
nfcore RNAseq pipeline
Assembly: GRCH38
Supplementary files format and content: tab delimited file with counts for each sample

source_name: Tumor

growth_protocol: Cell lines were maintained under standard conditions.  Cancer cell xenografts experiments were performed in nude mice.  See paper for full methods.

extract_protocol:
Total RNA was extracted from samples and assessed for quality using an Agilent TapeStation
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit.

treatment_protocol: In vitro: 10ug/mL antibody for 48h; in vivo: 10mg/kg once a week

value: Tumor

value: prostate

value: WT


title: Etoposide|0.25uM|DTXSID5023035|24h|S16_sample-11-etopiside-0p25-dose

description:
Library name: S16_sample-11-etopiside-0p25-dose
TempO-LINC

value: Etoposide|0.25uM|DTXSID5023035 for 24h in HepaRG cells

value: Etoposide


title: Xenograft_PC_treated_1

description:
Library name: PCX_treated_1
column name in PCX_counts.tsv: A1


title: RNA_LS_009_D6_23y_DMSO

description:
Library name: RNA_LS_009
RNA_LS_009_D6_23y_DMSO

value: Skin


title: Xenograft_PC_control_1

description:
Library name: PCX_control_1
column name in PCX_counts.tsv: A4

value: Control


title: Xenograft_DU_treated_2

description:
Library name: DUX_treated_2
column name in DUX_counts.tsv: B2


title: Etoposide|0.25uM|DTXSID5023035|24h|S15_sample-11-etopiside-0p25-dose

description:
Library name: S15_sample-11-etopiside-0p25-dose
TempO-LINC

value: liver


title: Xenograft_DU_treated_1

description:
Library name: DUX_treated_1
column name in DUX_counts.tsv: B1


title: tert-Butylhydroquinone|3.0uM|DTXSID6020220|24h|S15_sample-08-tBHQ-3-dose

description:
Library name: S15_sample-08-tBHQ-3-dose
TempO-LINC

value: tert-Butylhydroquinone|3.0uM|DTXSID6020220 for 24h in HepaRG cells

value: tert-Butylhydroquinone


title: RNA_LS_006_D6_56y_DMSO

description:
Library name: RNA_LS_006
RNA_LS_006_D6_56y_DMSO

value: Human dermal fibroblast

value: DMSO


title: Brefeldin A|0.001uM|DTXSID00880041|24h|S15_sample-09-brefeldina-0p001-dose

description:
Library name: S15_sample-09-brefeldina-0p001-dose
TempO-LINC

value: HepaRG

value: Brefeldin A|0.001uM|DTXSID00880041 for 24h in HepaRG cells

value: Brefeldin A


title: Troglitazone|0.001uM|DTXSID8023719|24h|S15_sample-07-troglitazone-0p001-dose

description:
Library name: S15_sample-07-troglitazone-0p001-dose
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells

value: Troglitazone|0.001uM|DTXSID8023719 for 24h in HepaRG cells

value: Troglitazone


title: Rotenone|0.8uM|DTXSID6021248|24h|S15_sample-06-rotenone-0p8-dose

description:
Library name: S15_sample-06-rotenone-0p8-dose
TempO-LINC

value: Rotenone|0.8uM|DTXSID6021248 for 24h in HepaRG cells

value: Rotenone


title: Xenograft_DU_control_2

description:
Library name: DUX_control_2
column name in DUX_counts.tsv A2

value: Tumor

value: prostate

value: WT


title: RNA_LS_004_D6_56y_2c

description:
Library name: RNA_LS_004
RNA_LS_004_D6_56y_2c

value: Skin


title: Xenograft_DU_control_1

description:
Library name: DUX_control_1
column name in DUX_counts.tsv: A1

value: Control


title: Rotenone|0.4uM|DTXSID6021248|24h|S15_sample-05-rotenone-0p4-dose

description:
Library name: S15_sample-05-rotenone-0p4-dose
TempO-LINC

value: liver

value: Rotenone|0.4uM|DTXSID6021248 for 24h in HepaRG cells


title: Cell_line_C4_treated_1

description:
Library name: C4_treated_1
column name in C4_counts.tsv: B1

source_name: Cell line

value: Cell line


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S15_sample-03-DMSO-0dose

description:
Library name: S15_sample-03-DMSO-0dose
TempO-LINC

value: DMSO control 24h in HepaRG cells

value: Dimethyl sulfoxide


title: Cell_line_C4_control_2

description:
Library name: C4_control_2
column name in C4_counts.tsv: A2


title: Dimethyl sulfoxide|0.0uM|nan|24h|S16_sample-02-DMSO-0dose

description:
Library name: S16_sample-02-DMSO-0dose
TempO-LINC

value: HepaRG


title: Dimethyl sulfoxide|0.0uM|nan|24h|S15_sample-02-DMSO-0dose

description:
Library name: S15_sample-02-DMSO-0dose
TempO-LINC


title: Cell_line_C4_control_1

description:
Library name: C4_control_1
column name in C4_counts.tsv: A1


title: Cell_line_DM_treated_2

description:
Library name: DM_treated_2
column name in DM_counts.tsv: C2

value: DU-145 PTEN-mt

value: PTEN-MT


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S15_sample-01-DMSO-0dose

description:
Library name: S15_sample-01-DMSO-0dose
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells


title: Cell_line_DM_treated_1

description:
Library name: DM_treated_1
column name in DM_counts.tsv: C1


title: Cycloheximide|0.2uM|DTXSID6024882|24h|S15_sample-10-cycloheximide-0p2-dose

description:
Library name: S15_sample-10-cycloheximide-0p2-dose
TempO-LINC

value: Cycloheximide|0.2uM|DTXSID6024882 for 24h in HepaRG cells

value: Cycloheximide


title: Etoposide|0.25uM|DTXSID5023035|24h|S14_sample-11-etopiside-0p25-dose

description:
Library name: S14_sample-11-etopiside-0p25-dose
TempO-LINC

value: Etoposide|0.25uM|DTXSID5023035 for 24h in HepaRG cells

value: Etoposide


title: Cell_line_DM_control_2

description:
Library name: DM_control_2
column name in DM_counts.tsv: B2

value: prostate


title: Cell_line_DM_control_1

description:
Library name: DM_control_1
column name in DM_counts.tsv: B1


title: Cycloheximide|0.2uM|DTXSID6024882|24h|S14_sample-10-cycloheximide-0p2-dose

description:
Library name: S14_sample-10-cycloheximide-0p2-dose
TempO-LINC


title: Rotenone|0.2uM|DTXSID6021248|24h|S15_sample-04-rotenone-0p2-dose

description:
Library name: S15_sample-04-rotenone-0p2-dose
TempO-LINC

value: Rotenone|0.2uM|DTXSID6021248 for 24h in HepaRG cells

value: Rotenone


title: Rotenone|0.8uM|DTXSID6021248|24h|S14_sample-06-rotenone-0p8-dose

description:
Library name: S14_sample-06-rotenone-0p8-dose
TempO-LINC

value: Rotenone|0.8uM|DTXSID6021248 for 24h in HepaRG cells


title: Brefeldin A|0.001uM|DTXSID00880041|24h|S14_sample-09-brefeldina-0p001-dose

description:
Library name: S14_sample-09-brefeldina-0p001-dose
TempO-LINC

value: liver

value: Brefeldin A|0.001uM|DTXSID00880041 for 24h in HepaRG cells

value: Brefeldin A


title: Troglitazone|0.001uM|DTXSID8023719|24h|S14_sample-07-troglitazone-0p001-dose

description:
Library name: S14_sample-07-troglitazone-0p001-dose
TempO-LINC

value: Troglitazone|0.001uM|DTXSID8023719 for 24h in HepaRG cells

value: Troglitazone


title: Cell_line_PC_treated_2

description:
Library name: PC_treated_2
column name in PC_counts.txt: E2

value: Cell line

value: WT


title: Cell_line_PC_control_1

description:
Library name: PC_control_1
column name in PC_counts.txt: A1

value: Control


title: tert-Butylhydroquinone|3.0uM|DTXSID6020220|24h|S14_sample-08-tBHQ-3-dose

description:
Library name: S14_sample-08-tBHQ-3-dose
TempO-LINC

value: HepaRG

value: differentiated HepaRG hepatocyte-like cells

value: tert-Butylhydroquinone|3.0uM|DTXSID6020220 for 24h in HepaRG cells

value: tert-Butylhydroquinone


title: Cell_line_PC_treated_1

description:
Library name: PC_treated_1
column name in PC_counts.txt: E1


title: Cell_line_PC_control_2

description:
Library name: PC_control_2
column name in PC_counts.txt: A2


title: Rotenone|0.4uM|DTXSID6021248|24h|S14_sample-05-rotenone-0p4-dose

description:
Library name: S14_sample-05-rotenone-0p4-dose
TempO-LINC

value: Rotenone|0.4uM|DTXSID6021248 for 24h in HepaRG cells


title: Rotenone|0.2uM|DTXSID6021248|24h|S14_sample-04-rotenone-0p2-dose

description:
Library name: S14_sample-04-rotenone-0p2-dose
TempO-LINC


title: Cell_line_DU_treated_2

description:
Library name: DU_treated_2
column name in DUP_counts.txt: E2

value: prostate


title: Cell_line_C4_treated_2

description:
Library name: C4_treated_2
column name in C4_counts.tsv: B2


title: Cell_line_DU_treated_1

description:
Library name: DU_treated_1
column name in DUP_counts.txt: E1


title: Cell_line_DU_control_2

description:
Library name: DU_control_2
column name in DUP_counts.txt: A2


title: Dimethyl sulfoxide|0.0uM|nan|24h|S14_sample-02-DMSO-0dose

description:
Library name: S14_sample-02-DMSO-0dose
TempO-LINC

value: DMSO control 24h in HepaRG cells

value: Dimethyl sulfoxide


title: Cell_line_DU_control_1

description:
Library name: DU_control_1
column name in DUP_counts.txt: A1


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S14_sample-03-DMSO-0dose

description:
Library name: S14_sample-03-DMSO-0dose
TempO-LINC


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S14_sample-01-DMSO-0dose

description:
Library name: S14_sample-01-DMSO-0dose
TempO-LINC


title: Pooled Bulk RNA-seq human bronchial ALI

city: Vienna

first: Max

middle: J

last: Kellner

address: Dr Bohr Gasse 3

country: Austria

institute: IMBA

description:
Library name: Pooled_BulkRNASeq_HBEC
Pooled 3'-end Bulk RNA-seq

data_processing:
Raw FASTQ processing: For single-cell RNA-sequencing data, 10x Cellranger count (version 7.1) was run using a custom genome index of Rousettus aegyptiacus (Assembly mRouAeg1.p) or human (Assembly GRCh38.90), or a custom genome index of the Rousettus aegyptiacus (Assembly mRouAeg1.p) and human (Assembly GRCh38.90) reference genomes for mixed identity samples. For pooled 3'end bulk RNA-sequencing: Cutadapt was used to trim read1 to 25nt reads required for BRB-seq tools, read2 was aligned to the Rousettus aegyptiacus (Assembly mRouAeg1.p) or human (Assembly GRCh38.90) reference genomes, BRB-seq tools CreateDGEMatrix was used to create UMI count matrices from aligned read2 and trimmed read1 files. A sample sheet containing  barcodes for sample-demultiplexing is provided for each pooled sample. For further details, please see the associated manuscript.
For scRNA-Seq 10x data: To remove artefacts and noise, Cellbender remove-background was run with the raw_feature_bc_matrix.h5 file from Cellranger count (see methods in associated publication) to create a UMI count matrix.
For scRNA-Seq 10x data: For mixed samples (pooled cells form individual bats and human cultures), the souporcell pipeline (souporcell_pipeline.py) was further used to derive SNPs and assign individual sample identities to each cells (listed in barcodes.tsv file and further explained in the Processed_Data_Information_Readme.txt file) to samples from aligned reads (10x Cellranger count output: possorted_genome_bam.bam) using the following options (-k X, whereas X is the number of expected samples; -t 8 --skip_remap True --ignore True).
For scRNA-Seq 10x data: The output files from Cellbender (filtered UMI count matrix), Cellranger (gem_classification files containing species identity for mixed samples), Souporcell (Cluster information to separate individual bat samples) were then used for downstream analysis in R using Seuratv4 (version 4.2.1). Details to the full analysis can be found in the associated manuscript.
For 3'-end pooled bulk RNA-sequencing: CreateDGEMatrix was used to create a UMI count matrix with the trimmed read1 file containing UMI and sample-barcode information (-p BU -UMI 12), the STAR-aligned read2 bam file (STAR index made from Rousettus aegyptiacus (Assembly mRouAeg1.p) or human genomes (Assembly GRCh38.90) ), the sample barcode sheet for demultiplexing and a gtf annotation file from the the respective genome assembly for gene-level read  quantification.
Assembly: Rousettus aegyptiacus (Assembly mRouAeg1.p) and human (Assembly GRCh38.90)
Supplementary files format and content: *.h5 files contain single cell RNA-sequencing gene expression matrices from Cellbender
Supplementary files format and content: *gem_classification.csv files contain the Cellranger cell droplet species information for mixed samples
Supplementary files format and content: *_Souporcell_clusters.tsv contains the souporcell output that determines singlets or multiples based on SNP information and was used for separation of mixed identifiy single cell RNA-sequencing samples
Supplementary files format and content: *.rds contains Seurat R objects for analysed single cell RNA-sequencing data as presented in the associated publication
Supplementary files format and content: *_Demultiplex_Sample_Sheet.txt contains the sample-barcode information used in BRB-seq tools CreateDGEMatrix for Pooled 3'-end Bulk RNA-seq libraries
Supplementary files format and content: *_UMI_Counts.txt contains UMI count matrix output from BRB-seq tools CreateDGEMatrix for Pooled 3'-end Bulk RNA-seq libraries

source_name: Lung epithelium

growth_protocol: Organoids were grown in expansion or differentiation medium (see methods of associated publication)

extract_protocol:
Single cell suspension were obtained by enzymatic digestion of tissue (collagenase from Clostridium histolyticum and Dispase) or organoids (TrypLE Express) followed by AnnexinV magnetic bead-based selection of viable cells (STEMCELL technologies). Cells were resuspended in DMEM/F12 and submitted to an on-campus facility for 10x library preparation. For bulk RNA sequencing, total RNA was extracted using a magnetic bead-based semi-automatic purification system (Kingfisher).
Single cell RNA-sequencing Libraries were generated according to the 10x Chromium Single Cell 3' Reagent Kit v3 and v4 kit manual instructions. Pooled 3'-end bulk RNA-sequencing libraries were prepared using an in-house protocol that adheres to the PLATE-seq (PMID: 28740083; modified to include UMIs and optimized steps for library generation) and BRB-seq (PMID: 30999927; for bioinformatic tools) methodologies (see methods of associated publication).

treatment_protocol: Untreated, virus infected and interferon stimulated organoids were analysed

value: Lung epithelium

value: Bronchial epithelial cell-derived ALI

value: Epithelial cells


title: Pooled Bulk RNA-seq human small intestinal organoids

description:
Library name: Pooled_BulkRNASeq_HuSi
Pooled 3'-end Bulk RNA-seq

source_name: Small Intestine

value: Small Intestine

value: Small intestinal organoids


title: Xenograft_PC_control_2

description:
Library name: PCX_control_2
column name in PCX_counts.tsv A5

value: Tumor


title: Cycloheximide|0.2uM|DTXSID6024882|24h|S13_sample-10-cycloheximide-0p2-dose

description:
Library name: S13_sample-10-cycloheximide-0p2-dose
TempO-LINC

value: liver

value: Cycloheximide|0.2uM|DTXSID6024882 for 24h in HepaRG cells

value: Cycloheximide


title: e5

city: Beijing

first: Wei

last: Ge

state: State...

address: 5 Dong Dan San Tiao, Dongcheng District

department: Department of Immunology

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences

description: Library name: e5

data_processing:
We use in-house script to perform basic statistics of raw data, and evaluate the data quality and GC content along the sequencing cycles. Raw FASTQ files and histology images were processed by sample with the Space Ranger (version spaceranger-1.2.0, 10X Genomics) software with default parameters. The filtered gene-spots matrix and the fiducial-aligned low-resolution image was used for down-streaming data analyses (Seurat).
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: hd5 file for each Sample

source_name: Cornea

extract_protocol:
The Visium Spatial Tissue Optimization workflow includes placing tissue sections on 7 Capture Areas on a Visium Tissue Optimization slide. The sections are fixed, stained, and then permeabilized for different times. mRNA released during permeabilization binds to oligonucleotides on the Capture Areas. Fluorescent cDNA is synthesized on the slide and imaged. The permeabilization time that results in maximum fluorescence signal with the lowest signal diffusion is optimal. If the signal is the same at two time points, the longer permeabilization time is considered optimal.
The Visium Spatial Gene Expression Slide & Reagent kit (10X Genomics) was used to construct sequencing libraries according to the Visium Spatial Gene Expression User Guide (CG000239 , 10X Genomics). A 10um frozen tissue section was placed on one of the Visium gene expression slide capture areas in a slide. After tissue Hematoxylin and Eosin (H&E) staining, bright-field images were acquired as described in the Spatial Transcriptomics procedure. Tissue permeabilization was performed for a optimal minutes, as established in the TO procedure. Then reverse transcription experiment was conducted and sequencing libraries were prepared following the manufacturer’s protocol.

value: Cornea

value: Keratoconus (KC)


title: e4

description: Library name: e4


title: Brefeldin A|0.001uM|DTXSID00880041|24h|S13_sample-09-brefeldina-0p001-dose

description:
Library name: S13_sample-09-brefeldina-0p001-dose
TempO-LINC

value: HepaRG

value: differentiated HepaRG hepatocyte-like cells

value: Brefeldin A|0.001uM|DTXSID00880041 for 24h in HepaRG cells

value: Brefeldin A


title: Troglitazone|0.001uM|DTXSID8023719|24h|S13_sample-07-troglitazone-0p001-dose

description:
Library name: S13_sample-07-troglitazone-0p001-dose
TempO-LINC

value: Troglitazone|0.001uM|DTXSID8023719 for 24h in HepaRG cells

value: Troglitazone


title: e2

description: Library name: e2


title: tert-Butylhydroquinone|3.0uM|DTXSID6020220|24h|S13_sample-08-tBHQ-3-dose

description:
Library name: S13_sample-08-tBHQ-3-dose
TempO-LINC

value: tert-Butylhydroquinone|3.0uM|DTXSID6020220 for 24h in HepaRG cells

value: tert-Butylhydroquinone


title: e1

description: Library name: e1


title: Rotenone|0.8uM|DTXSID6021248|24h|S13_sample-06-rotenone-0p8-dose

description:
Library name: S13_sample-06-rotenone-0p8-dose
TempO-LINC

value: Rotenone|0.8uM|DTXSID6021248 for 24h in HepaRG cells

value: Rotenone


title: Rotenone|0.4uM|DTXSID6021248|24h|S13_sample-05-rotenone-0p4-dose

description:
Library name: S13_sample-05-rotenone-0p4-dose
TempO-LINC

value: Rotenone|0.4uM|DTXSID6021248 for 24h in HepaRG cells


title: c2

description: Library name: c2

value: Control


title: c3

description: Library name: c3


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S13_sample-03-DMSO-0dose

description:
Library name: S13_sample-03-DMSO-0dose
TempO-LINC

value: liver

value: DMSO control 24h in HepaRG cells

value: Dimethyl sulfoxide


title: Dimethyl sulfoxide|0.0uM|nan|24h|S13_sample-02-DMSO-0dose

description:
Library name: S13_sample-02-DMSO-0dose
TempO-LINC


title: Rotenone|0.2uM|DTXSID6021248|24h|S13_sample-04-rotenone-0p2-dose

description:
Library name: S13_sample-04-rotenone-0p2-dose
TempO-LINC

value: Rotenone|0.2uM|DTXSID6021248 for 24h in HepaRG cells


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S13_sample-01-DMSO-0dose

description:
Library name: S13_sample-01-DMSO-0dose
TempO-LINC


title: 42D_sgT33-5_6hR1881_RNA-seq_rep3

city: Amsterdam

first: Wilbert

last: Zwart

state: Noord-Holland

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute

description: Library name: wz5010

data_processing:
Fastq files have been demultiplexed by Cutadapt
Read were mapped on Hg38/GRCh38 genome assembly using HISAT2 (v2.1.0) using the following parameters: --wrapper basic-0 --min-intronlen 20 --max-intronlen 500000 --rna-strandness FR -k 5 --minins 0 --maxins 500 --fr --new-summary
HISAT2 (v2.1.0) was used to generate raw gene counts
Assembly: Hg38/GRCh38
Supplementary files format and content: raw gene counts (.txt) for all samples

molecule: polyA RNA

source_name: prostate cancer

growth_protocol: LNCaP prostate cancer cell line was cultured in RPMI-1640 (Gibco), supplemented with 10% Fetal Bovine Serum (FBS-12A, Capricorn Scientific) and penicillin/streptomycin (100μg/mL, Gibco).

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen) following manufacture instructions. Quality of the RNA extraction was assessed using the 2100 Bioanalzer (Agilent, RNA 6000 Nano Kit) and selecting samples with a RNA Integrity Number (RIN) above 9.
PolyA+ stranded RNA library was prepared using the Illumina Stranded mRNA Prep kit and quality was assessed by using the 2100 Bioanalyzer (Agilent, DNA 7500 kit). RNA-seq libraries have been pooled equimolarly and sequenced using NovaSeq6000 (Illumina) sequencer with a 51bp Paired-End reads setup.

treatment_protocol: For hormone stimulation, cells were pre-cultured for 3 days in RPMI-1640 (Gibco) supplied with 5% dextran-coated charcoal (DCC) stripped FBS), and penicillin/streptomycin (100μg/mL, Gibco), then cells were stimulated with 5nM R1881 or DMSO for 6 hours.

value: prostate cancer

value: tumor


title: 42D_sgT33-5_6hR1881_RNA-seq_rep1

description: Library name: wz5008


title: Tunicamycin|0.001uM|DTXSID8036730|24h|S13_sample-12-tuncamycin-0p001-dose

description:
Library name: S13_sample-12-tuncamycin-0p001-dose
TempO-LINC

value: HepaRG

value: differentiated HepaRG hepatocyte-like cells

value: Tunicamycin|0.001uM|DTXSID8036730 for 24h in HepaRG cells

value: Tunicamycin


title: Tunicamycin|0.001uM|DTXSID8036730|24h|S14_sample-12-tuncamycin-0p001-dose

description:
Library name: S14_sample-12-tuncamycin-0p001-dose
TempO-LINC


title: 42D_sgT33-5_6hR1881_RNA-seq_rep2

description: Library name: wz5009


title: Etoposide|0.25uM|DTXSID5023035|24h|S12_sample-11-etopiside-0p25-dose

description:
Library name: S12_sample-11-etopiside-0p25-dose
TempO-LINC

value: Etoposide|0.25uM|DTXSID5023035 for 24h in HepaRG cells

value: Etoposide


title: Tunicamycin|0.001uM|DTXSID8036730|24h|S12_sample-12-tuncamycin-0p001-dose

description:
Library name: S12_sample-12-tuncamycin-0p001-dose
TempO-LINC


title: Etoposide|0.25uM|DTXSID5023035|24h|S13_sample-11-etopiside-0p25-dose

description:
Library name: S13_sample-11-etopiside-0p25-dose
TempO-LINC


title: 42D_sgT33-5_DMSO_RNA-seq_rep3

description: Library name: wz5007

value: 6h DMSO


title: 42D_sgT33-5_DMSO_RNA-seq_rep1

description: Library name: wz5005


title: Cycloheximide|0.2uM|DTXSID6024882|24h|S12_sample-10-cycloheximide-0p2-dose

description:
Library name: S12_sample-10-cycloheximide-0p2-dose
TempO-LINC

value: Cycloheximide|0.2uM|DTXSID6024882 for 24h in HepaRG cells

value: Cycloheximide


title: Brefeldin A|0.001uM|DTXSID00880041|24h|S12_sample-09-brefeldina-0p001-dose

description:
Library name: S12_sample-09-brefeldina-0p001-dose
TempO-LINC

value: Brefeldin A|0.001uM|DTXSID00880041 for 24h in HepaRG cells

value: Brefeldin A


title: 42D_sgT33-5_DMSO_RNA-seq_rep2

description: Library name: wz5006


title: tert-Butylhydroquinone|3.0uM|DTXSID6020220|24h|S12_sample-08-tBHQ-3-dose

description:
Library name: S12_sample-08-tBHQ-3-dose
TempO-LINC

value: liver

value: tert-Butylhydroquinone|3.0uM|DTXSID6020220 for 24h in HepaRG cells

value: tert-Butylhydroquinone


title: 42D_NT3_6hR1881_RNA-seq_rep3

description: Library name: wz5004


title: Troglitazone|0.001uM|DTXSID8023719|24h|S12_sample-07-troglitazone-0p001-dose

description:
Library name: S12_sample-07-troglitazone-0p001-dose
TempO-LINC

value: Troglitazone|0.001uM|DTXSID8023719 for 24h in HepaRG cells

value: Troglitazone


title: 42D_NT3_6hR1881_RNA-seq_rep2

description: Library name: wz5003

value: prostate cancer

value: tumor


title: 42D_NT3_DMSO_RNA-seq_rep3

description: Library name: wz5001


title: Rotenone|0.8uM|DTXSID6021248|24h|S12_sample-06-rotenone-0p8-dose

description:
Library name: S12_sample-06-rotenone-0p8-dose
TempO-LINC

value: HepaRG

value: differentiated HepaRG hepatocyte-like cells

value: Rotenone|0.8uM|DTXSID6021248 for 24h in HepaRG cells

value: Rotenone


title: e3

description: Library name: e3

value: Cornea

value: Keratoconus (KC)


title: 42D_NT3_6hR1881_RNA-seq_rep1

description: Library name: wz5002


title: LNCaP_sgT33-5_MC_F2_6hR1881_RNA-seq_rep3

description: Library name: wz4998

value: LNCaP


title: Rotenone|0.2uM|DTXSID6021248|24h|S12_sample-04-rotenone-0p2-dose

description:
Library name: S12_sample-04-rotenone-0p2-dose
TempO-LINC

value: Rotenone|0.2uM|DTXSID6021248 for 24h in HepaRG cells


title: ChAR-seq K562 replicate 2-2

city: Stanford

first: Kelsey

last: Fryer

address: 279 Campus Drive

department: Biochemistry

institute: Stanford University

description:
Library name: ChAR-seq K562 replicate 2-2
combined in K562 rep2
K562rep2_cenDNAxcenRNA.class.exons.E.resid.tsv.gz
K562rep2_cenDNAxalignRNA.class.exons.E.resid.tsv.gz
K562rep2_cenDNAxcenRNA.reptype.exons.E.resid.tsv.gz
K562rep2_dna_class_counts.tsv
K562rep2_rna_class_counts.tsv

library_source: other

data_processing:
Demultiplexed fastq files from the ChAR-seq data were processed using a custom Snakemake pipeline (https://github.com/straightlab/charseq-pipelines), outputting pairs files containing the RNA and DNA coordinates of each RNA(cDNA)-DNA chimeric read and relevant annotations for each RNA-DNA contact.
Repeat derived reads were classified using CASK (classification of ambivalent sequences using k-mers). First, repeat sequence kmer databases are generated from sequences extracted from genome fasta (in this case T2T CHM13v2) according to repeat bed coordinates using KMC. k-mers present in the rest of the genome (everything outside of the provided repeat coordinates) were subtracted from repeat k-mer databases and remaining k-mers were annotated with a unique identifier. ChAR-seq reads (DNA side or both sides depending on the analysis) containing repeat k-mers were annotated with the unique identifier using BBDuk. Reads were then classified into ambivalence groups based on k-mer content. Reads were then counted for each RNA-DNA pair. Non-repetitive RNA reads were annotated according to their alignment to hg38 and non-repetitive DNA reads were annotated with a genomic bin identifier. Centromere only analysis incorporated repeat sequences from censat.bed file from https://github.com/marbl/CHM13.
To quantify RNA contacts at repetitive regions, we calculated an enrichment (E score) for each RNA-DNA contact as the number of times that RNA-DNA combination was observed in the dataset normalized by the number of DpnII restriction sites in the DNA contact domain. To account for the fact that more highly expressed RNAs and larger DNA domains will make more contacts, these counts were also normalized by the total number of times that RNA was found contacting anywhere in the genome, and the length of the contact domain. The background contact behavior of RNAs non specifically interacting with the genome was established using a generalized additive model of all trans contacting protein coding RNAs. For each RNA-DNA contact, a predicted enrichment score was calculated based on the background model specific for the contact chromosome which includes all protein coding RNAs contacting that chromosome and transcribed from any other chromosome (trans contacting). For DNA contacts including ambivalence groups, the background model included all trans contacting protein coding RNAs for all chromosomes in the ambivalence group. Predicted enrichment scores for each RNA-DNA were then subtracted from observed enrichment scores to generate a residual score (R score). The top 5% of residual scores were considered significantly enriched and plotted in heat maps.
Assembly: RNA Alignment: hg38; Centromere classification: T2T CHM13v2
Supplementary files format and content: Processed files ending in .E.resid.tsv.gz contain counts for each RNA-DNA contact, all metrics used in E score calculation, and predicted E score based on background model described above.  cenDNAxalignRNA contain all counts for hg38 transcriptome aligned RNAs contacting centromeric DNA domains. cenDNAxcenRNA files containg all counts for centromeric RNAs contacting centromeric DNA domains. All files contain counts for RNAs contacting non-centromere regions that aligned to the genome and were sorted into 100kb bins. These files were used to generate heatmaps of residual scores.
Supplementary files format and content: Processed files ending in rna_class_counts.tsv include counts for ChAR-seq RNA side reads that were classified as centromeric. Files ending in rna_class_counts.tsv  include counts for all ChAR-seq DNA side reads that were classified as centromeric. All files include all factors that were used to normalize read counts such as domain length and number of DpnII sites in that domain. These files were used to generate logCPM plots of RNA and DNA read counts.

molecule: other

growth_protocol: Human K562 cells were grown in RPMI 1640 media in 5% CO2 at 37°C

extract_protocol:
Cell extraction is described in detail in Limouse, C. et al in RNA-Chromatin Interactions: Methods Mol Biol. 2020;2161:115-142. doi:10.1007/978-1-0716-0680-3_10.
Library preparation is described in detail in Limouse, C. et al in RNA-Chromatin Interactions: Methods Mol Biol. 2020;2161:115-142. doi:10.1007/978-1-0716-0680-3_10.

value: lymphoblast


title: 42D_NT3_DMSO_RNA-seq_rep2

description: Library name: wz5000

value: 6h DMSO


title: Dimethyl sulfoxide|0.0uM|nan|24h|S12_sample-02-DMSO-0dose

description:
Library name: S12_sample-02-DMSO-0dose
TempO-LINC

value: liver

value: DMSO control 24h in HepaRG cells

value: Dimethyl sulfoxide


title: 42D_NT3_DMSO_RNA-seq_rep1

description: Library name: wz4999


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S12_sample-03-DMSO-0dose

description:
Library name: S12_sample-03-DMSO-0dose
TempO-LINC


title: c1

description: Library name: c1

value: Control


title: Rotenone|0.4uM|DTXSID6021248|24h|S12_sample-05-rotenone-0p4-dose

description:
Library name: S12_sample-05-rotenone-0p4-dose
TempO-LINC

value: Rotenone|0.4uM|DTXSID6021248 for 24h in HepaRG cells


title: LNCaP_sgT33-5_MC_F2_DMSO_RNA-seq_rep3

description: Library name: wz4995

value: prostate cancer


title: LNCaP_sgT33-5_MC_F2_6hR1881_RNA-seq_rep2

description: Library name: wz4997

value: tumor


title: ChAR-seq K562 replicate 2-1

description:
Library name: ChAR-seq K562 replicate 2-1
combined in K562 rep2
K562rep2_cenDNAxcenRNA.class.exons.E.resid.tsv.gz
K562rep2_cenDNAxalignRNA.class.exons.E.resid.tsv.gz
K562rep2_cenDNAxcenRNA.reptype.exons.E.resid.tsv.gz
K562rep2_dna_class_counts.tsv
K562rep2_rna_class_counts.tsv


title: LNCaP_sgT33-5_MC_F2_DMSO_RNA-seq_rep2

description: Library name: wz4994


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S12_sample-01-DMSO-0dose

description:
Library name: S12_sample-01-DMSO-0dose
TempO-LINC

value: HepaRG


title: ChAR-seq K562 replicate 1-3

description:
Library name: ChAR-seq K562 replicate 1-3
combined in K562 rep1
K562rep1_cenDNAxcenRNA.class.exons.E.resid.tsv.gz
K562rep1_cenDNAxalignRNA.class.exons.E.resid.tsv.gz
K562rep1_cenDNAxcenRNA.reptype.exons.E.resid.tsv.gz
K562rep1_dna_class_counts.tsv
K562rep1_rna_class_counts.tsv


title: LNCaP_sgT33-5_MC_F2_DMSO_RNA-seq_rep1

description: Library name: wz4993


title: LNCaP_sgT33-5_MC_F2_6hR1881_RNA-seq_rep1

description: Library name: wz4996


title: ChAR-seq K562 replicate 1-2

description:
Library name: ChAR-seq K562 replicate 1-2
combined in K562 rep1
K562rep1_cenDNAxcenRNA.class.exons.E.resid.tsv.gz
K562rep1_cenDNAxalignRNA.class.exons.E.resid.tsv.gz
K562rep1_cenDNAxcenRNA.reptype.exons.E.resid.tsv.gz
K562rep1_dna_class_counts.tsv
K562rep1_rna_class_counts.tsv


title: Tunicamycin|0.001uM|DTXSID8036730|24h|S11_sample-12-tuncamycin-0p001-dose

description:
Library name: S11_sample-12-tuncamycin-0p001-dose
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells

value: Tunicamycin|0.001uM|DTXSID8036730 for 24h in HepaRG cells

value: Tunicamycin


title: LNCaP_sgT33-5_MC_C2_6hR1881_RNA-seq_rep2

description: Library name: wz4991


title: LNCaP_sgT33-5_MC_C2_6hR1881_RNA-seq_rep1

description: Library name: wz4990


title: LNCaP_sgT33-5_MC_C2_6hR1881_RNA-seq_rep3

description: Library name: wz4992


title: Etoposide|0.25uM|DTXSID5023035|24h|S11_sample-11-etopiside-0p25-dose

description:
Library name: S11_sample-11-etopiside-0p25-dose
TempO-LINC

value: Etoposide|0.25uM|DTXSID5023035 for 24h in HepaRG cells

value: Etoposide


title: ChAR-seq K562 replicate 1-1

description:
Library name: ChAR-seq K562 replicate 1-1
combined in K562 rep1
K562rep1_cenDNAxcenRNA.class.exons.E.resid.tsv.gz
K562rep1_cenDNAxalignRNA.class.exons.E.resid.tsv.gz
K562rep1_cenDNAxcenRNA.reptype.exons.E.resid.tsv.gz
K562rep1_dna_class_counts.tsv
K562rep1_rna_class_counts.tsv


title: Cycloheximide|0.2uM|DTXSID6024882|24h|S11_sample-10-cycloheximide-0p2-dose

description:
Library name: S11_sample-10-cycloheximide-0p2-dose
TempO-LINC

value: Cycloheximide|0.2uM|DTXSID6024882 for 24h in HepaRG cells

value: Cycloheximide


title: LNCaP_sgT33-5_MC_C2_DMSO_RNA-seq_rep3

description: Library name: wz4989

value: LNCaP


title: LNCaP_sgT33-5_MC_C2_DMSO_RNA-seq_rep2

description: Library name: wz4988

value: 6h DMSO


title: Brefeldin A|0.001uM|DTXSID00880041|24h|S11_sample-09-brefeldina-0p001-dose

description:
Library name: S11_sample-09-brefeldina-0p001-dose
TempO-LINC

value: liver

value: Brefeldin A|0.001uM|DTXSID00880041 for 24h in HepaRG cells

value: Brefeldin A


title: LNCaP_sgT33-5_MC_C2_DMSO_RNA-seq_rep1

description: Library name: wz4987


title: LNCaP_sgT33-5_6hR1881_RNA-seq_rep3

description: Library name: wz4986


title: LNCaP_sgT33-5_6hR1881_RNA-seq_rep2

description: Library name: wz4985


title: ES-2_Control_3rd_Rep

city: Dresden

first: Gina

last: Dimari

address: Arnoldstrasse 18

department: Physics of Life

country: Germany

institute: Dresden University of Technology

description:
Library name: Sample11
column name in RNAseq_ES2_miR200c141.txt: Control_3rd_Rep

data_processing:
quality control assessment of raw reads was performed using FastQC, followed by Trimmomatic trimming to remove low-quality sequences. The trimmed reads were then aligned to the reference genome using STAR version 2.7.9a. To facilitate the mapping process, a genome reference index was constructed using either GRCh37.fa (hg19) or GRCh38.108.gtf (hg38) as the reference. During the alignment step, specific parameters were employed to ensure accurate and reliable alignment results. These parameters included: alignIntronMax (maximum intron size) set to 500000; alignMatesGapMax (maximum gap between paired mates) 500000; outFilterMultimapNmax (maximum number of multiple alignments allowed) 100; outFilterMismatchNoverLmax (maximum ratio of mismatches allowed) 0.05; chimSegmentMin (minimum length of chimeric segment) 15; chimScoreMin (minimum chimeric score) 1; chimJunctionOverhangMin (minimum overhang for chimeric junctions) 15; chimSegmentReadGapMax (maximum gap in reads within a chimeric segment) 3; and alignSJstitchMismatchNmax (maximum mismatch in stitched junctions) set to 5 -1 5 5. The output was converted to sorted BAM files with SAMtools.
Assembly: GRCh38.108.gtf
Supplementary files format and content: The first column contains the gene ID, columnes 2-7 contained the 3 biological replicates with 2 samples each (control and induced) alternated. The first row has the identifiers, on the second row the total number of counts for each sample are shown. The rest of the rows show the number of reads of each gene ID for each sample.

source_name: Ovarium

growth_protocol: Cultured in DMEM enriched with 1% Penicillin/Streptomycin and 5% FBS

extract_protocol:
RNA was extracted from cell pellets containing (at least) 0.5 × 106 cells using the RNeasy Plus kit (#74134, Qiagen) following the manufacturer’s protocol
RNA sequencing (RNA-seq) libraries were prepared using the Stranded mRNA Prep, Ligation Kit (Illumina) according to the manufacturer’s instructions. Briefly, mRNA was purified from 1 µg total RNA using oligo(dT) beads, poly(A)+ RNA was fragmented to 150 bp and converted into cDNA, and cDNA fragments were end-repaired, adenylated on the 3’ end, adapter-ligated, and amplified with 12 cycles of PCR. The final libraries were validated using a Qubit 2.0 Fluorometer (Life Technologies) and a Bioanalyzer 2100 system. All barcoded libraries were pooled and sequenced 2x75bp paired-end on an Illumina NextSeq550 platform to obtain a minimum of 10 Mio reads per sample.

treatment_protocol: MDA-MB-231 cells stably transfected with the construct pINDUCER13 miR-200c-141 were cultured on DMEM with 10% Fetal Bovine Serum (#10270106, Thermofisher), 1% Pen/Strep (#15140122, Thermofisher) and 0.5 µg/mL Puromycin at 37 °C with 5% CO2. ES-2 cells stably transfected with the construct pINDUCER13 miR-200c-141 were cultured on DMEM with 10% Fetal Bovine Serum (#10270106, Thermofisher), 1% Pen/Strep (#15140122, Thermofisher) and 1 µg/mL Puromycin at 37 °C with 5% CO2

value: Ovarium

value: mesenchymal ovarian cancer cell

value: pINDUCER13 miR-200c-141

value: control


title: LNCaP_sgT33-5_6hR1881_RNA-seq_rep1

description: Library name: wz4984

value: prostate cancer

value: tumor


title: ES-2_MET-induced_2nd_Rep

description:
Library name: Sample10
column name in RNAseq_ES2_miR200c141.txt: MET-induced_2nd_Rep

value: 2 ug/mL doxycycline 4 days


title: Troglitazone|0.001uM|DTXSID8023719|24h|S11_sample-07-troglitazone-0p001-dose

description:
Library name: S11_sample-07-troglitazone-0p001-dose
TempO-LINC

value: HepaRG

value: differentiated HepaRG hepatocyte-like cells

value: Troglitazone|0.001uM|DTXSID8023719 for 24h in HepaRG cells

value: Troglitazone


title: tert-Butylhydroquinone|3.0uM|DTXSID6020220|24h|S11_sample-08-tBHQ-3-dose

description:
Library name: S11_sample-08-tBHQ-3-dose
TempO-LINC

value: tert-Butylhydroquinone|3.0uM|DTXSID6020220 for 24h in HepaRG cells

value: tert-Butylhydroquinone


title: LNCaP_sgT33-5_DMSO_RNA-seq_rep2

description: Library name: wz4982

value: LNCaP

value: 6h DMSO


title: LNCaP_sgT33-5_DMSO_RNA-seq_rep1

description: Library name: wz4981


title: LNCaP_sgT33-5_DMSO_RNA-seq_rep3

description: Library name: wz4983


title: ES-2_MET-induced_1st_rep

description:
Library name: Sample8
column name in RNAseq_ES2_miR200c141.txt: MET-induced_1st_rep


title: Rotenone|0.8uM|DTXSID6021248|24h|S11_sample-06-rotenone-0p8-dose

description:
Library name: S11_sample-06-rotenone-0p8-dose
TempO-LINC

value: liver

value: Rotenone|0.8uM|DTXSID6021248 for 24h in HepaRG cells

value: Rotenone


title: ES-2_Control_2nd_Rep

description:
Library name: Sample9
column name in RNAseq_ES2_miR200c141.txt: Control_2nd_Rep

value: Ovarium

value: mesenchymal ovarian cancer cell


title: LNCaP_NT3_6hR1881_RNA-seq_rep2

description: Library name: wz4979


title: Rotenone|0.4uM|DTXSID6021248|24h|S11_sample-05-rotenone-0p4-dose

description:
Library name: S11_sample-05-rotenone-0p4-dose
TempO-LINC

value: Rotenone|0.4uM|DTXSID6021248 for 24h in HepaRG cells


title: LNCaP_NT3_6hR1881_RNA-seq_rep1

description: Library name: wz4978

value: prostate cancer


title: ES-2_Control_1st_Rep

description:
Library name: Sample7
column name in RNAseq_ES2_miR200c141.txt: Control_1st_Rep

value: pINDUCER13 miR-200c-141

value: control


title: Rotenone|0.2uM|DTXSID6021248|24h|S11_sample-04-rotenone-0p2-dose

description:
Library name: S11_sample-04-rotenone-0p2-dose
TempO-LINC

value: HepaRG

value: Rotenone|0.2uM|DTXSID6021248 for 24h in HepaRG cells


title: MDA-MB-231_MET-induced_3rd_Rep

description:
Library name: Sample6
column name in RNAseq_MDAMB231_miR200c141.txt: MET-induced_3rd_Rep

source_name: Breast epithelium

value: Breast epithelium

value: mesenchymal breast cancer cell

value: pINDUCER13 miR-200c-146

value: 2 ug/mL doxycycline 4 days


title: LNCaP_NT3_DMSO_RNA-seq_rep2

description: Library name: wz4976

value: LNCaP

value: tumor


title: LNCaP_NT3_DMSO_RNA-seq_rep3

description: Library name: wz4977

value: 6h DMSO


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S11_sample-03-DMSO-0dose

description:
Library name: S11_sample-03-DMSO-0dose
TempO-LINC

value: liver

value: differentiated HepaRG hepatocyte-like cells

value: DMSO control 24h in HepaRG cells

value: Dimethyl sulfoxide


title: LNCaP_NT3_DMSO_RNA-seq_rep1

description: Library name: wz4975


title: H2BK120ub_C2_24hR1881_r3

description: Library name: wz5237

data_processing:
Reads were aligned to the human genome build Hg38/GRCh38 using BWA 0.5.9-r26-dev
Duplicates have been marked using GATK markdupoplicates (UMI-aware)
Reads with a mapping quality (MAPQ) < 20 were removed from further analysis
bamCoverage (from deeptools) was used to generate RPGC normalized bigwigs
Assembly: Hg38/GRCh38
Supplementary files format and content: .narrowPeak
Supplementary files format and content: .bw

extract_protocol:
Chromatin Immunoprecipitations of proteins of interest were performed as previously described (A.A. Singh, et al., Life Sci. Alliance; 2019) employing 1% formaldehyde to perform the crosslinking. At least 2 biological replicates are provided
Illumina kit, Paired-End 51bp, Novaseq6000 Illumina Kit, single-end, 65bp (trimmed), HiSeq4000

treatment_protocol: For hormone stimulation, cells were pre-cultured for 3 days in RPMI-1640 (Gibco) supplied with 5% dextran-coated charcoal (DCC) stripped FBS), and penicillin/streptomycin (100μg/mL, Gibco), then cells were stimulated with 10nM R1881 or DMSO for 4h or 24h hours.

tag: chip antibody

value: H2BK120ub (39623, Actife Motif)


title: MDA-MB-231_Control_3rd_Rep

description:
Library name: Sample5
column name in RNAseq_MDAMB231_miR200c141.txt: Control_3rd_Rep

value: pINDUCER13 miR-200c-145


title: ES-2_MET-induced_3rd_Rep

description:
Library name: Sample12
column name in RNAseq_ES2_miR200c141.txt: MET-induced_3rd_Rep

value: Ovarium

value: mesenchymal ovarian cancer cell

value: pINDUCER13 miR-200c-141


title: H2BK120ub_C2_24hR1881_r2

description: Library name: wz5236

value: prostate cancer


title: Dimethyl sulfoxide|0.0uM|nan|24h|S11_sample-02-DMSO-0dose

description:
Library name: S11_sample-02-DMSO-0dose
TempO-LINC

value: HepaRG


title: MDA-MB-231_MET-induced_2nd_Rep

description:
Library name: Sample4
column name in RNAseq_MDAMB231_miR200c141.txt: MET-induced_2nd_Rep

value: Breast epithelium

value: mesenchymal breast cancer cell

value: pINDUCER13 miR-200c-144


title: H2BK120ub_C2_4hR1881_r3

description: Library name: wz5234

value: LNCaP


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S11_sample-01-DMSO-0dose

description:
Library name: S11_sample-01-DMSO-0dose
TempO-LINC


title: H2BK120ub_C2_24hR1881_r1

description: Library name: wz5235

value: tumor


title: H2BK120ub_C2_4hR1881_r2

description: Library name: wz5233


title: LNCaP_NT3_6hR1881_RNA-seq_rep3

description: Library name: wz4980


title: MDA-MB-231_Control_2nd_Rep

description:
Library name: Sample3
column name in RNAseq_MDAMB231_miR200c141.txt: Control_2nd_Rep

value: pINDUCER13 miR-200c-143

value: control


title: MDA-MB-231_MET-induced_1st_rep

description:
Library name: Sample2
column name in RNAseq_MDAMB231_miR200c141.txt: MET-induced_1st_rep

value: pINDUCER13 miR-200c-142

value: 2 ug/mL doxycycline 4 days


title: Etoposide|0.25uM|DTXSID5023035|24h|S10_sample-11-etopiside-0p25-dose

description:
Library name: S10_sample-11-etopiside-0p25-dose
TempO-LINC

value: liver

value: differentiated HepaRG hepatocyte-like cells

value: Etoposide|0.25uM|DTXSID5023035 for 24h in HepaRG cells

value: Etoposide


title: MDA-MB-231_Control_1st_Rep

description:
Library name: Sample1
column name in RNAseq_MDAMB231_miR200c141.txt: Control_1st_Rep


title: H2BK120ub_C2_4hDMSO_r1

description: Library name: wz5229

value: H2BK120ub (39623, Actife Motif)

value: DMSO 4h


title: H2BK120ub_C2_4hDMSO_r3

description: Library name: wz5231

value: prostate cancer


title: H3K18ac_C2_24hR1881_r3

description: Library name: wz5228

value: H3K18ac (C15410139, Diagenode)


title: H2BK120ub_C2_4hDMSO_r2

description: Library name: wz5230


title: Cycloheximide|0.2uM|DTXSID6024882|24h|S10_sample-10-cycloheximide-0p2-dose

description:
Library name: S10_sample-10-cycloheximide-0p2-dose
TempO-LINC

value: HepaRG

value: Cycloheximide|0.2uM|DTXSID6024882 for 24h in HepaRG cells

value: Cycloheximide


title: DT5_CD8

city: Chicago

first: Qianli

last: Liu

state: IL

address: 303 E. Superior St. Simpson Querrey

institute: Northwestern Univesity

data_processing:
Basecalls performed using Illumina RTA2 software.
bcl2fastq v2.20 was used to convert bcl files to fastq files (default parameters).
FASTQ files were processed using the nf-core/RNA-seq pipeline1 v3.9 implemented in Nextflow v23.04.2 with Northwestern University Quest HPC (Genomic Nodes) configuration
Assembly: GRCm38/mm10
Supplementary files format and content: csv files including raw counts values for each sample was generated by nf-core/RNA-seq pipeline1 v3.9 (--aligner star_salmon)

organism: Mus musculus

source_name: Lung

extract_protocol:
RNA was extracted from FACSorted cells using the AllPrep DNA/RNA Micro Kit.
Next Ultra II RNA Kits (NEB)

value: Lung

value: CD8 T cells

value: Diphtheria toxin


title: H2BK120ub_C2_4hR1881_r1

description: Library name: wz5232

value: LNCaP

value: tumor


title: H3K18ac_C2_24hR1881_r2

description: Library name: wz5227


title: Brefeldin A|0.001uM|DTXSID00880041|24h|S10_sample-09-brefeldina-0p001-dose

description:
Library name: S10_sample-09-brefeldina-0p001-dose
TempO-LINC

value: Brefeldin A|0.001uM|DTXSID00880041 for 24h in HepaRG cells

value: Brefeldin A


title: DT5_CD69CD8

value: CD8 T cells(CD69+CD8+)


title: H3K18ac_C2_24hR1881_r1

description: Library name: wz5226


title: H3K18ac_C2_4hR1881_r2

description: Library name: wz5224


title: tert-Butylhydroquinone|3.0uM|DTXSID6020220|24h|S10_sample-08-tBHQ-3-dose

description:
Library name: S10_sample-08-tBHQ-3-dose
TempO-LINC

value: liver

value: differentiated HepaRG hepatocyte-like cells

value: tert-Butylhydroquinone|3.0uM|DTXSID6020220 for 24h in HepaRG cells

value: tert-Butylhydroquinone


title: Tunicamycin|0.001uM|DTXSID8036730|24h|S10_sample-12-tuncamycin-0p001-dose

description:
Library name: S10_sample-12-tuncamycin-0p001-dose
TempO-LINC

value: Tunicamycin|0.001uM|DTXSID8036730 for 24h in HepaRG cells

value: Tunicamycin


title: DT5_CD69CD103CD8

value: CD8 T cells(CD69+CD103+CD8+)


title: H3K18ac_C2_4hR1881_r3

description: Library name: wz5225

value: prostate cancer

value: H3K18ac (C15410139, Diagenode)


title: H3K18ac_C2_4hDMSO_r3

description: Library name: wz5222

value: DMSO 4h


title: Troglitazone|0.001uM|DTXSID8023719|24h|S10_sample-07-troglitazone-0p001-dose

description:
Library name: S10_sample-07-troglitazone-0p001-dose
TempO-LINC

value: HepaRG

value: Troglitazone|0.001uM|DTXSID8023719 for 24h in HepaRG cells

value: Troglitazone


title: DT4_CD8

value: Lung

value: CD8 T cells

value: Diphtheria toxin


title: H3K18ac_C2_4hDMSO_r2

description: Library name: wz5221

value: LNCaP

value: tumor


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S10_sample-03-DMSO-0dose

description:
Library name: S10_sample-03-DMSO-0dose
TempO-LINC

value: liver

value: differentiated HepaRG hepatocyte-like cells

value: DMSO control 24h in HepaRG cells

value: Dimethyl sulfoxide


title: Rotenone|0.4uM|DTXSID6021248|24h|S10_sample-05-rotenone-0p4-dose

description:
Library name: S10_sample-05-rotenone-0p4-dose
TempO-LINC

value: Rotenone|0.4uM|DTXSID6021248 for 24h in HepaRG cells

value: Rotenone


title: AR_C2_4hR1881_r2

description: Library name: wz5216

value: prostate cancer


title: Rotenone|0.2uM|DTXSID6021248|24h|S10_sample-04-rotenone-0p2-dose

description:
Library name: S10_sample-04-rotenone-0p2-dose
TempO-LINC

value: Rotenone|0.2uM|DTXSID6021248 for 24h in HepaRG cells


title: DT4_CD69CD103CD8

value: CD8 T cells(CD69+CD103+CD8+)


title: H2BK120ub_NT_24hR1881_r1

description: Library name: wz5209

value: H2BK120ub (39623, Actife Motif)


title: AR_C2_4hR1881_r1

description: Library name: wz5215


title: DT2_CD8


title: H2BK120ub_NT_24hR1881_r3

description: Library name: wz5211


title: AR_C2_4hDMSO_r3

description: Library name: wz5214

value: DMSO 4h


title: AR_C2_24hR1881_r3

description: Library name: wz5219


title: AR_C2_24hR1881_r1

description: Library name: wz5218


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S10_sample-01-DMSO-0dose

description:
Library name: S10_sample-01-DMSO-0dose
TempO-LINC

value: HepaRG


title: DT3_CD69CD8

value: Lung

value: CD8 T cells(CD69+CD8+)


title: H2BK120ub_NT_4hR1881_r2

description: Library name: wz5207


title: DT3_CD8

value: CD8 T cells

value: Diphtheria toxin


title: H2BK120ub_NT_24hR1881_r2

description: Library name: wz5210

value: LNCaP

value: tumor


title: AR_C2_4hR1881_r3

description: Library name: wz5217


title: Dimethyl sulfoxide|0.0uM|nan|24h|S10_sample-02-DMSO-0dose

description:
Library name: S10_sample-02-DMSO-0dose
TempO-LINC

value: liver

value: differentiated HepaRG hepatocyte-like cells


title: AR_C2_4hDMSO_r1

description: Library name: wz5212


title: DT4_CD69CD8


title: H2BK120ub_NT_4hR1881_r3

description: Library name: wz5208


title: DT3_CD69CD103CD8


title: H3K18ac_C2_4hR1881_r1

description: Library name: wz5223

value: H3K18ac (C15410139, Diagenode)


title: DT2_CD69CD8


title: Tunicamycin|0.001uM|DTXSID8036730|24h|S09_sample-12-tuncamycin-0p001-dose

description:
Library name: S09_sample-12-tuncamycin-0p001-dose
TempO-LINC

value: Tunicamycin|0.001uM|DTXSID8036730 for 24h in HepaRG cells

value: Tunicamycin


title: H3K18ac_C2_4hDMSO_r1

description: Library name: wz5220

value: prostate cancer


title: AR_C2_4hDMSO_r2

description: Library name: wz5213


title: Etoposide|0.25uM|DTXSID5023035|24h|S09_sample-11-etopiside-0p25-dose

description:
Library name: S09_sample-11-etopiside-0p25-dose
TempO-LINC

value: Etoposide|0.25uM|DTXSID5023035 for 24h in HepaRG cells

value: Etoposide


title: Rotenone|0.8uM|DTXSID6021248|24h|S10_sample-06-rotenone-0p8-dose

description:
Library name: S10_sample-06-rotenone-0p8-dose
TempO-LINC

value: Rotenone|0.8uM|DTXSID6021248 for 24h in HepaRG cells

value: Rotenone


title: H2BK120ub_NT_4hDMSO_r2

description: Library name: wz5204

value: H2BK120ub (39623, Actife Motif)

value: DMSO 4h


title: Cycloheximide|0.2uM|DTXSID6024882|24h|S09_sample-10-cycloheximide-0p2-dose

description:
Library name: S09_sample-10-cycloheximide-0p2-dose
TempO-LINC

value: HepaRG

value: Cycloheximide|0.2uM|DTXSID6024882 for 24h in HepaRG cells

value: Cycloheximide


title: H2BK120ub_NT_4hDMSO_r3

description: Library name: wz5205

value: LNCaP


title: DT2_CD69CD103CD8

value: Lung

value: CD8 T cells(CD69+CD103+CD8+)

value: Diphtheria toxin


title: H2BK120ub_NT_4hDMSO_r1

description: Library name: wz5203

value: tumor


title: DT1_CD69CD8

value: CD8 T cells(CD69+CD8+)


title: H3K18ac_NT_24hR1881_r3

description: Library name: wz5202

value: H3K18ac (C15410139, Diagenode)


title: DT1_CD8

value: CD8 T cells


title: tert-Butylhydroquinone|3.0uM|DTXSID6020220|24h|S09_sample-08-tBHQ-3-dose

description:
Library name: S09_sample-08-tBHQ-3-dose
TempO-LINC

value: liver

value: differentiated HepaRG hepatocyte-like cells

value: tert-Butylhydroquinone|3.0uM|DTXSID6020220 for 24h in HepaRG cells

value: tert-Butylhydroquinone


title: H3K18ac_NT_24hR1881_r2

description: Library name: wz5201

value: prostate cancer


title: H3K18ac_NT_4hR1881_r3

description: Library name: wz5199


title: Control6_CD8


title: H3K18ac_NT_4hR1881_r1

description: Library name: wz5197


title: H3K18ac_NT_24hR1881_r1

description: Library name: wz5200