title: H3K18ac_NT_4hDMSO_r3

description: Library name: wz5196

value: DMSO 4h


title: DT1_CD69CD103CD8

status: Public on Jun 10 2025

type: SRA

city: Chicago

first: Qianli

last: Liu

state: IL

address: 303 E. Superior St. Simpson Querrey

country: USA

institute: Northwestern Univesity

library_source: transcriptomic

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)

molecule: total RNA

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)

tag: tissue

value: Lung

tag: cell type

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

tag: genotype

tag: treatment

value: Diphtheria toxin


title: H2BK120ub_NT_4hR1881_r1

city: Amsterdam

first: Wilbert

last: Zwart

state: Noord-Holland

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute

description: Library name: wz5206

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

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:
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.

value: prostate cancer

tag: cell line

value: LNCaP

tag: chip antibody

value: H2BK120ub (39623, Actife Motif)

value: tumor


title: Rotenone|0.8uM|DTXSID6021248|24h|S09_sample-06-rotenone-0p8-dose

city: Research Triangle Park

first: Imran

last: Shah

state: NC

address: Mail Code: D143-02

department: Office of Research and Development

institute: US Environmental Protection Agency

description:
Library name: S09_sample-06-rotenone-0p8-dose
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

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.

value: liver

value: HepaRG

value: differentiated HepaRG hepatocyte-like cells

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

tag: timeh

tag: chem name

value: Rotenone

tag: conc

tag: dtxsid

tag: batch


title: Troglitazone|0.001uM|DTXSID8023719|24h|S09_sample-07-troglitazone-0p001-dose

description:
Library name: S09_sample-07-troglitazone-0p001-dose
TempO-LINC

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

value: Troglitazone


title: H3K18ac_NT_4hR1881_r2

description: Library name: wz5198

value: H3K18ac (C15410139, Diagenode)


title: Rotenone|0.4uM|DTXSID6021248|24h|S09_sample-05-rotenone-0p4-dose

description:
Library name: S09_sample-05-rotenone-0p4-dose
TempO-LINC

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


title: H3K18ac_NT_4hDMSO_r2

description: Library name: wz5195

value: DMSO 4h


title: H3K18ac_NT_4hDMSO_r1

description: Library name: wz5194


title: AR_NT_24hR1881_r3

description: Library name: wz5193


title: Control6_CD69CD103CD8

value: Lung


title: AR_NT_24hR1881_r2

description: Library name: wz5192


title: Control5_CD8

value: CD8 T cells


title: Brefeldin A|0.001uM|DTXSID00880041|24h|S09_sample-09-brefeldina-0p001-dose

description:
Library name: S09_sample-09-brefeldina-0p001-dose
TempO-LINC

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

value: Brefeldin A


title: AR_NT_24hR1881_r1

description: Library name: wz5191

value: prostate cancer

value: LNCaP


title: AR_NT_4hR1881_r3

description: Library name: wz5190

value: tumor


title: AR_NT_4hR1881_r2

description: Library name: wz5189


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S09_sample-03-DMSO-0dose

description:
Library name: S09_sample-03-DMSO-0dose
TempO-LINC

value: liver

value: DMSO control 24h in HepaRG cells

value: Dimethyl sulfoxide


title: Rotenone|0.2uM|DTXSID6021248|24h|S09_sample-04-rotenone-0p2-dose

description:
Library name: S09_sample-04-rotenone-0p2-dose
TempO-LINC

value: HepaRG

value: differentiated HepaRG hepatocyte-like cells

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


title: Control5_CD69CD8

value: CD8 T cells(CD69+CD8+)


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S09_sample-01-DMSO-0dose

description:
Library name: S09_sample-01-DMSO-0dose
TempO-LINC


title: Control6_CD69CD8


title: Control5_CD69CD103CD8

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


title: Control3_CD8


title: AR_NT_4hR1881_r1

description: Library name: wz5188


title: Etoposide|0.25uM|DTXSID5023035|24h|S08_sample-11-etopiside-0p25-dose

description:
Library name: S08_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|S08_sample-12-tuncamycin-0p001-dose

description:
Library name: S08_sample-12-tuncamycin-0p001-dose
TempO-LINC

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

value: Tunicamycin


title: Control3_CD69CD8

value: Lung


title: LNCaP_Input_paired_end

description: Library name: wz5038

value: Input paired-end


title: NT_mix_input

description: Library name: wz5183

value: prostate cancer

value: Input non-targeting


title: H3K9me3_LNCaP_24hR1881_r3

description: Library name: wz4921

value: LNCaP

value: H3K9me3 (ab8898, Abcam)

value: tumor


title: C2_mix_Input

description: Library name: wz5184

value: Input C2


title: AR_NT_4hDMSO_r1

description: Library name: wz5185

value: DMSO 4h


title: Control3_CD69CD103CD8


title: H3K9me3_LNCaP_24hR1881_r2

description: Library name: wz4920


title: Cycloheximide|0.2uM|DTXSID6024882|24h|S08_sample-10-cycloheximide-0p2-dose

description:
Library name: S08_sample-10-cycloheximide-0p2-dose
TempO-LINC

value: liver

value: HepaRG

value: differentiated HepaRG hepatocyte-like cells

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

value: Cycloheximide


title: H3K9me3_LNCaP_24hR1881_r1

description: Library name: wz4919


title: Control2_CD8

value: CD8 T cells


title: Dimethyl sulfoxide|0.0uM|nan|24h|S09_sample-02-DMSO-0dose

description:
Library name: S09_sample-02-DMSO-0dose
TempO-LINC

value: DMSO control 24h in HepaRG cells

value: Dimethyl sulfoxide


title: H3K9me3_LNCaP_4hR1881_r3

description: Library name: wz4918


title: H3K9me3_LNCaP_4hR1881_r2

description: Library name: wz4917


title: Brefeldin A|0.001uM|DTXSID00880041|24h|S08_sample-09-brefeldina-0p001-dose

description:
Library name: S08_sample-09-brefeldina-0p001-dose
TempO-LINC

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

value: Brefeldin A


title: AR_NT_4hDMSO_r3

description: Library name: wz5187

value: prostate cancer


title: Control2_CD69CD8

value: Lung

value: CD8 T cells(CD69+CD8+)


title: AR_NT_4hDMSO_r2

description: Library name: wz5186

value: LNCaP


title: Control2_CD69CD103CD8

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


title: Control1_CD8


title: Troglitazone|0.001uM|DTXSID8023719|24h|S08_sample-07-troglitazone-0p001-dose

description:
Library name: S08_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|S08_sample-06-rotenone-0p8-dose

description:
Library name: S08_sample-06-rotenone-0p8-dose
TempO-LINC

value: liver

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

value: Rotenone


title: Control1_CD69CD8


title: H3K9me3_LNCaP_4hDMSO_r1

description: Library name: wz4913

value: H3K9me3 (ab8898, Abcam)

value: tumor

value: DMSO 4h


title: H3K18ac_LNCaP_24hR1881_r1

description: Library name: wz4910

value: H3K18ac (C15410139, Diagenode)


title: H3K18ac_LNCaP_24hR1881_r2

description: Library name: wz4911


title: H3K18ac_LNCaP_4hR1881_r2

description: Library name: wz4908


title: H3K18ac_LNCaP_4hR1881_r3

description: Library name: wz4909


title: Rotenone|0.2uM|DTXSID6021248|24h|S08_sample-04-rotenone-0p2-dose

description:
Library name: S08_sample-04-rotenone-0p2-dose
TempO-LINC

value: HepaRG

value: differentiated HepaRG hepatocyte-like cells

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


title: Control1_CD69CD103CD8


title: Rotenone|0.4uM|DTXSID6021248|24h|S08_sample-05-rotenone-0p4-dose

description:
Library name: S08_sample-05-rotenone-0p4-dose
TempO-LINC

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


title: H3K18ac_LNCaP_4hR1881_r1

description: Library name: wz4907

value: prostate cancer


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S08_sample-03-DMSO-0dose

description:
Library name: S08_sample-03-DMSO-0dose
TempO-LINC

value: DMSO control 24h in HepaRG cells

value: Dimethyl sulfoxide


title: H3K18ac_LNCaP_4hDMSO_r2

description: Library name: wz4905

value: LNCaP


title: tert-Butylhydroquinone|3.0uM|DTXSID6020220|24h|S08_sample-08-tBHQ-3-dose

description:
Library name: S08_sample-08-tBHQ-3-dose
TempO-LINC

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

value: tert-Butylhydroquinone


title: H3K9me3_LNCaP_4hDMSO_r3

description: Library name: wz4915


title: H3K18ac_LNCaP_4hDMSO_r1

description: Library name: wz4904


title: H3K9me3_LNCaP_4hR1881_r1

description: Library name: wz4916


title: Dimethyl sulfoxide|0.0uM|nan|24h|S08_sample-02-DMSO-0dose

description:
Library name: S08_sample-02-DMSO-0dose
TempO-LINC

value: liver


title: H3K9me3_LNCaP_4hDMSO_r2

description: Library name: wz4914


title: Kelly_RCOR2-3xF_NT_Rep2

city: Bologna

first: Giorgio

last: Milazzo

address: Via F.Selmi 3

department: FaBiT

country: Italy

institute: University of Bologna

data_processing:
ChIP-seq reads were aligned to the GRCh38 reference genome using BWA version 0.7.17.
Read density track for each ChIP library were generated using deepTools bamCoverage function with RPGC as scale unit.
Peak calling was performed using MACS2. Mapping artifacts were removed by excluding regions listed in ENCODE exclusion list (ENCFF356LFX) and MYCN amplified region.
Assembly: hg38
Supplementary files format and content: bigWig and tab-delimited text file includes (BED files) including coordinates of peaks after the exclusion of regions listed in ENCODE blacklist (ENCFF356LFX) and MYCN amplified region.

source_name: Kelly

growth_protocol: Kelly adrenergic neuroblastoma cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cells were fixes with 1% formaldehyde for 10 min. After quenching, chromaitin was fragmented through sonication. Chromatin samples were immunoprecipitated overnight at 4°C. The complexes were immunoprecipitated with antibodies specific for RCoR1 (#EPR13825-ABCAM), RCoR3 (#ab76921-ABCAM), FLAG (#F3165-Sigma Aldrich) and LSD1 (#ab129195-ABCAM). The antibody/protein complexes were collected by Sepharose rec-Protein A or G (#101042 Invitrogen) and washed several times. The immune complexes were eluted with 1% SDS and 0.1 M NaHCO3 and samples were treated with proteinase K for 6h and DNA was purified by phenol/chloroform extraction, ethanol precipitation, and resuspended in H2O.
DNA libraries for ChIP-seq were prepared using Kapa Hyper Prep Library Prep Kit following manufacturer's instructions.

value: Kelly

value: MYCN-amplified neuroblastoma

value: Non-treated

tag: time

value: Monoclonal ANTI-FLAG M2_F3165-Sigma Aldrich


title: Kelly_RCOR2-3xF_NT_Rep1


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S08_sample-01-DMSO-0dose

description:
Library name: S08_sample-01-DMSO-0dose
TempO-LINC


title: Kelly_RCOR2-3xF_DOX_Rep2

value: 2 ug/mL Doxycycline


title: H3K18ac_LNCaP_24hR1881_r3

description: Library name: wz4912

value: H3K18ac (C15410139, Diagenode)

value: tumor


title: Kelly_RCOR2-3xF_DOX_Rep1


title: H3K18ac_LNCaP_4hDMSO_r3

description: Library name: wz4906

value: DMSO 4h


title: LAN5_shRCOR1_H3K27ac_NT

data_processing:
ChIP-seq reads were aligned to the GRCh38 reference genome using BWA version 0.7.17.
Read density track for each ChIP library were generated using deepTools bamCoverage function with RPGC as scale unit and using spike-in normalization factors as scaling factors.
Peak calling was performed using MACS2. Mapping artifacts were removed by excluding regions listed in ENCODE exclusion list (ENCFF356LFX).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes (BED files) including coordinates of peaks after the exclusion of regions listed in ENCODE blacklist (ENCFF356LFX) and MYCN amplified region.

extract_protocol:
Cells were fixes with 1% formaldehyde for 10 min. After quenching, cells were digested to achieve chromatin fragmented to a range of 150–900 bp using Micrococcal Nuclease. Chromatin samples were immunoprecipitated overnight at 4°C.
DNA libraries for ChIP-seq were prepared using NEBNext Ultra II DNA kit following manufacturer's instructions.

treatment_protocol: shRNA expression was induced by treating cells with 2 μg/mL doxycycline for 48h.

value: MABE647 - Millipore


title: LAN5_shRCOR1_H3K27ac_DOX


title: Tunicamycin|0.001uM|DTXSID8036730|24h|S07_sample-12-tuncamycin-0p001-dose

description:
Library name: S07_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: Etoposide|0.25uM|DTXSID5023035|24h|S07_sample-11-etopiside-0p25-dose

description:
Library name: S07_sample-11-etopiside-0p25-dose
TempO-LINC

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

value: Etoposide


title: LAN5_shRCOR2_H3K27ac_NT


title: Kelly_shRCOR2_H3K4me2_DOX

value: 9725S - Cell Signaling


title: Kelly_shRCOR2_H3K4me2_NT


title: WT_Cold1h.2

type: RNA

city: Freiburg

first: Wolfgang

middle: R.

last: Hess

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

country: Germany

institute: University of Freiburg

description:
WTCold/1
Gene expression in WT after 1h in cold conditions

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505C US90900275, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09 for Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. Median signal intensities were normexp background substracted (offset=50) and quantile normalized.

organism: Synechocystis sp. PCC 6803

label_protocol: DNase-treated RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol. Further details of the labeling and hybridization protocol were published in:  Voß,B. and Hess,W.R. (2014) The identification of bacterial non-coding RNAs through complementary approaches. In Handbook of RNA Biochemistry. WILEY-VCH, Weinheim, Germany, Vol. 2, pp. 787–800.

growth_protocol: Liquid cultures in TES-buffered BG11 media (pH 7.5) at 30°C under constant light with an intensity of 50 µmol photons m-2 s-1 and shaking.

extract_protocol: RNA was prepared using a hot phenol-based protocol.

treatment_protocol: To test the acclimation responses of the Δrbp2Δrbp3 double mutant and wild type to downshifts in temperature or to upshifts in light intensity, cultures were transferred from 30°C to 20°C, or from a light intensity of 50 to 250 µmol photons m-2 s-1.  Following the shift, the cultures were sampled for the transcriptome analysis by filtration after 30 min (HL experiment) or 1 h (cold experiment).

value: bacterial cell

value: WT

value: 1h in cold conditions


title: Mut_Cold1h.1

description:
MutCold/1
Gene expression in Δrbp2Δrbp3 after 1h in cold conditions


title: Kelly_shRCOR1_H3K4me2_DOX

value: Kelly

value: MYCN-amplified neuroblastoma


title: Mut_Cold1h.2


title: Kelly_shRCOR1_H3K4me2_NT

value: Non-treated


title: Brefeldin A|0.001uM|DTXSID00880041|24h|S07_sample-09-brefeldina-0p001-dose

description:
Library name: S07_sample-09-brefeldina-0p001-dose
TempO-LINC

value: liver

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

value: Brefeldin A


title: tert-Butylhydroquinone|3.0uM|DTXSID6020220|24h|S07_sample-08-tBHQ-3-dose

description:
Library name: S07_sample-08-tBHQ-3-dose
TempO-LINC

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

value: tert-Butylhydroquinone


title: LAN5_shRCOR2_H3K27ac_DOX

value: 2 ug/mL Doxycycline

value: MABE647 - Millipore


title: WT_Cold0h.2

description:
WTCold/0
Gene expression in WT under standard conditions

value: standard conditions


title: Troglitazone|0.001uM|DTXSID8023719|24h|S07_sample-07-troglitazone-0p001-dose

description:
Library name: S07_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: Kelly_shRCOR1_H3K27ac_DOX


title: Kelly_shRCOR2_H3K27ac_DOX


title: Kelly_shRCOR2_H3K27ac_NT


title: Mut_Cold0h.2

description:
MutCold/0
Gene expression in Δrbp2Δrbp3 under standard conditions

value: bacterial cell


title: Kelly_shRCOR2_Pol2_DOX

value: CTD4H8, sc-47701 - Santa Cruz Biotechnology


title: Kelly_shRCOR1_H3K27ac_NT

value: Kelly


title: WT_Cold1h.1

value: WT

value: 1h in cold conditions


title: WT_Cold0h.1


title: Rotenone|0.4uM|DTXSID6021248|24h|S07_sample-05-rotenone-0p4-dose

description:
Library name: S07_sample-05-rotenone-0p4-dose
TempO-LINC

value: liver

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

value: Rotenone


title: Rotenone|0.8uM|DTXSID6021248|24h|S07_sample-06-rotenone-0p8-dose

description:
Library name: S07_sample-06-rotenone-0p8-dose
TempO-LINC

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


title: Mut_Cold0h.1


title: Mut_HL_30m.2

description:
MutHL/30
Gene expression in Δrbp2Δrbp3 after 30 min at HL

value: 30 min at HL


title: Kelly_shRCOR2_DOX_Pol2

data_processing:
HiChIP reads were aligned to the human (hg38) or mouse (mm10) reference genome using Bowtie2.
Downstream analysis was performed following HiC-Pro pipeline (Servant et al. 2015).
HiChIP-reads were filtered for read pairs with contact range >1000bp.
Assembly: hg38
Supplementary files format and content: hic files are provided at chromosome level.
Library strategy: HiChIP

extract_protocol:
HiChIP was performed using the Dovetail MNase-HiChIP kit (#21007, Dovetail Genomics) following manufacturer’s instruction. 10x10^6 Kelly cells were collected and snap-frozen at -80C for at least 30 minutes. Cells were then crosslinked with disuccinimidyl glutarate (DSG, #A35392, Thermo Fisher) and 37% formaldehyde. Chromatin lysates extracted from C2C12 mouse cells were used as spike-in for AQuA-normalization and chromatin immunoprecipitation of H3K27ac (MABE647, Millipore) or Pol2 (CTD4H8, sc-47701 - Santa Cruz Biotechnology) was performed overnight.
HiChIP libraries were prepared using the Dovetail MNase-HiChIP kit following manifacturer's instruction.

value: MYCN-amplified neuroblastoma

value: 2 ug/mL Doxycycline


title: Rotenone|0.2uM|DTXSID6021248|24h|S07_sample-04-rotenone-0p2-dose

description:
Library name: S07_sample-04-rotenone-0p2-dose
TempO-LINC

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


title: Mut_HL_30m.1


title: Cycloheximide|0.2uM|DTXSID6024882|24h|S07_sample-10-cycloheximide-0p2-dose

description:
Library name: S07_sample-10-cycloheximide-0p2-dose
TempO-LINC

value: HepaRG

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

value: Cycloheximide


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S07_sample-03-DMSO-0dose

description:
Library name: S07_sample-03-DMSO-0dose
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells

value: DMSO control 24h in HepaRG cells

value: Dimethyl sulfoxide


title: Kelly_shRCOR2_NT_Pol2

value: Kelly

value: Non-treated

value: CTD4H8, sc-47701 - Santa Cruz Biotechnology


title: Kelly_shRCOR1_DOX

data_processing:
ATAC-seq reads were analyzed using Nextflof nf-core/atacseq pipeline (v2.1.2) with default settings and GRCh38 human genome reference.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
ATAC-seq sample were prepared from 5x104 cells that were resuspended in 50 μl cold ATAC-Resuspension Buffer (RSB) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin and incubated on ice for 3 minutes. The suspension was then diluted with 1 ml of cold ATAC-RSB containing 0.1% Tween-20 but no NP40 or digitonin. Nuclei were pelleted at 500g for 10 min at 4°C in a fixed angle centrifuge and resuspended in 50 μl of transposition mix (25 μl 2x TD buffer, 2.5 μl transposase (100nM final), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, 5 μl H2O) and incubated at 37°C for 30 minutes in a thermomixer with 1000 rpm mixing. DNA was purified using a Zymo DNA Clean Kit and eluted in 20 μl.
DNA libraries for ATAC-seq were prepared amplifying the DNA for a proper number of cycles using NEBNext 2x MasterMix.


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S07_sample-01-DMSO-0dose

description:
Library name: S07_sample-01-DMSO-0dose
TempO-LINC

value: liver


title: Kelly_shRCOR2_NT_H3K27ac

value: MABE647 - Millipore


title: Kelly_shRCOR2_DOX


title: Tunicamycin|0.001uM|DTXSID8036730|24h|S06_sample-12-tuncamycin-0p001-dose

description:
Library name: S06_sample-12-tuncamycin-0p001-dose
TempO-LINC

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

value: Tunicamycin


title: Kelly_shRCOR1_Pol2_NT


title: Kelly_shRCOR2_Pol2_NT


title: Dimethyl sulfoxide|0.0uM|nan|24h|S07_sample-02-DMSO-0dose

description:
Library name: S07_sample-02-DMSO-0dose
TempO-LINC


title: Kelly_shRCOR1_NT


title: WT_HL_30m.2

description:
WTHL/30
Gene expression in WT after 30 min at HL

value: bacterial cell

value: WT

value: 30 min at HL


title: WT_HL_30m.1


title: C04_MNC

city: Atlanta

first: Edwin

last: Horwitz

state: Georgia

address: 1570 Haygood Drive NE

institute: Emory University

description: 10x Genomics

data_processing:
Data were processed with Cell Ranger v7.1.0 (force_cells=10000 for EOS)
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab delimited barcode and features, counts matrix

source_name: Blood

extract_protocol:
The Miltenyi Whole Blood Eosinophil Isolation Kit was used to quickly isolate untouched eosinophils without prior density gradient centrifugation. Following erythrocyte removal, non-eosinophils were gently removed by magnetic depletion
10x Chromium Next GEM Single Cell 3' kit was used to generate sequencing libraries

value: Blood

value: Mononuclear cells

tag: condition

value: Healthy


title: Kelly_shRCOR1_Pol2_DOX

value: MYCN-amplified neuroblastoma

value: 2 ug/mL Doxycycline


title: Mut_HL_0h.2

description:
MutHL/0
Gene expression in Δrbp2Δrbp3 under standard conditions

value: standard conditions


title: C03_MNC

description: 10x Genomics


title: Mut_HL_0h.1


title: Kelly_shRCOR2_NT


title: Shear stress 3

city: Bangkok

first: Hnin

middle: Yu

last: Lwin

address: Henridunant

country: Thailand

institute: Chulalorngkorn University

description: Library name: Sample 6

data_processing:
Genome assembly via software Hisat2 (v2.0.1)
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Single-ended sequencing was conducted on an Illumina Nextseq platform with 75 cycles.
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
GOSeq(v1.34.1) was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant padj less than 0.05. And topGO was used to plot DAG.
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances (http://en.wikipedia.org/wiki/KEGG). We used scripts in house to enrich significant differential expression gene in KEGG pathways.
After assembling a transcriptome from one or more samples, Cuffcompare, a tool of Cufflinks v2.2.1, compared assembly to known transcripts. Then, novel transcripts can be predicted via results of Cuffcompare.
rMATs v4.1.0 is a computational tool to detect differential alternative splicing events from RNA-Seq data. And resulting bam files of aligner HISAT2 had been used as input during the analysis.
Samtools v0.1.19 with command mpileup and Bcftools v0.1.19 were used to do SNV calling.
Assembly: GRCh38.107
Supplementary files format and content: fpkm

source_name: Pulp tissue

extract_protocol:
extracted using Ribospin II (GeneAll, Seoul, South Korea) after being stimulated with shear stress for 24 hours. 1µg of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using Qubit RNA HS assay kit according to manufacturer's instructions.

value: Pulp tissue

value: Primary

value: Human dental pulp stem cells


title: Etoposide|0.25uM|DTXSID5023035|24h|S06_sample-11-etopiside-0p25-dose

description:
Library name: S06_sample-11-etopiside-0p25-dose
TempO-LINC

value: HepaRG

value: differentiated HepaRG hepatocyte-like cells

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

value: Etoposide


title: C04_EOS

description: 10x Genomics

value: Eosinophil


title: WT_HL_0h.2

description:
WTHL/0
Gene expression in WT under standard conditions

value: bacterial cell


title: Control 3

description: Library name: Sample 5


title: Brefeldin A|0.001uM|DTXSID00880041|24h|S06_sample-09-brefeldina-0p001-dose

description:
Library name: S06_sample-09-brefeldina-0p001-dose
TempO-LINC

value: liver

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

value: Brefeldin A


title: Cycloheximide|0.2uM|DTXSID6024882|24h|S06_sample-10-cycloheximide-0p2-dose

description:
Library name: S06_sample-10-cycloheximide-0p2-dose
TempO-LINC

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

value: Cycloheximide


title: C03_EOS

description: 10x Genomics

value: Blood

value: Healthy


title: A06_EOS

description: 10x Genomics

value: Moderate asthma


title: C01_EOS

description: 10x Genomics


title: Shear stress 1

description: Library name: Sample 2

value: Pulp tissue


title: C02_EOS

description: 10x Genomics


title: C02_MNC

description: 10x Genomics

value: Mononuclear cells


title: tert-Butylhydroquinone|3.0uM|DTXSID6020220|24h|S06_sample-08-tBHQ-3-dose

description:
Library name: S06_sample-08-tBHQ-3-dose
TempO-LINC

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

value: tert-Butylhydroquinone


title: Rotenone|0.8uM|DTXSID6021248|24h|S06_sample-06-rotenone-0p8-dose

description:
Library name: S06_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: B05_EOS

description: 10x Genomics

value: Eosinophil

value: Severe asthma


title: B02_EOS

description: 10x Genomics


title: Control 2

description: Library name: Sample 3

value: Primary

value: Human dental pulp stem cells


title: Troglitazone|0.001uM|DTXSID8023719|24h|S06_sample-07-troglitazone-0p001-dose

description:
Library name: S06_sample-07-troglitazone-0p001-dose
TempO-LINC

value: liver

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

value: Troglitazone


title: A03_EOS

description: 10x Genomics

value: Blood


title: B03_EOS

description: 10x Genomics


title: Rotenone|0.4uM|DTXSID6021248|24h|S06_sample-05-rotenone-0p4-dose

description:
Library name: S06_sample-05-rotenone-0p4-dose
TempO-LINC

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


title: Shear stress 2

description: Library name: Sample 4

value: Pulp tissue


title: A02_EOS

description: 10x Genomics

value: Moderate asthma


title: A04_EOS

description: 10x Genomics


title: Confined Treated Replicate 3

city: Barcelona

first: Ritobrata

last: Ghose

address: Carrer del Doctor Aiguader, 88, CRG 5th Floor Reception

country: Spain

institute: Center for Genomic Regulation

description: Oligomycin A (1 µM) treated Confined

data_processing:
50 base-pairs paired-end reads, were subjected to alignment against the hg19 human genome using Bowtie2 aligner (v 2.5.1) after removal of adaptors with TrimGalore (v. 0.6.10). The alignment was carried out with default parameters, except for the utilization of the "very-sensitive 2000" option. To ensure the quality of aligned reads, those with a quality score below 30 were filtered out using Samtools 1.16.1. Mitochondrial reads were excluded from further analysis followed by removal of duplicated reads by using Picard (v 2.23.8). The alignment of reads was adjusted to account for Tn5 transposase insertions with deepTools (v 3.5.1). Peaks were identified using MACS2 (v 2.2.8) with false discovery rate (FDR) threshold of less than 0.01. Regions designated as blacklisted were filtered out from further analysis (blacklist v2). Peak intersection between replicates and union between conditions was done using the GenomicRanges package in R (V4.2). Differentially accessible (DA) regions were quantified utilizing the csaw R package with Trimmed Mean of M-values (TMM) normalization on binned counts followed by edgeR for DA analysis, employing a significance threshold of log-fold change > 0.5 and FDR < 0.1.
Assembly: hg19
Supplementary files format and content: txt file containing differential accessible genomic windows for respective comparisons
Supplementary files format and content: csv file containing differential accessibility peak mapping for respective comparisons
Supplementary files format and content: csv file containing collapsed regions for differential accessibility peak mapping for for respective comparisons

source_name: HeLa

extract_protocol:
50,000 cells for two biological replicates, for each treated condition, was collected and treated with transposase Tn5 (Nextera Tn5 Transposase; Illumina Cat #FC-121-1030). DNA was purified using AMPure XP beads to remove large fragments (0.5 × beads; >1kb) and small fragments (1.5 × beads; < 100bp).
Samples were then amplified using NEBNext high-Fidelity 2x PCR Master Mix (New England Labs #M0541) with primers containing a barcode to generate the libraries, as previously described. Each condition was amplified using a combination of the P7 forward primer and a P5 reverse primers containing multiplexing adaptors, and sequenced accordingly to allow for segregation of reads. The number of cycles of library amplification was calculated as previously described. DNA was purified using a MinElute PCR Purification Kit (Qiagen), and samples were sequenced using an Illumina NextSeq2000 at the CRG Genomics Core Facility.

value: HeLa


title: WT_HL_0h.1

value: bacterial cell

value: WT

value: standard conditions


title: Unconfined Treated Replicate 3

description: Oligomycin A (1 µM) treated Suspension


title: H97-1RP

city: Boston

first: Heng

last: Du

address: 45 Francis St

institute: Brigham and Women's Hospital

data_processing:
Raw data (raw reads) of FASTQ format were firstly filterd and examed.
Burrows-Wheeler Aligner (BWA) was utilized to map the paired-end clean reads to the mouse reference genome
Single nucleotide polymorphisms (SNPs), also known as single nucleotide variants (SNVs), constitute the largest class of genome variants in genome.
Small insertions and deletions (InDels) that are less than 50bp in length constitute another class of genomic variants in reference genome.
muTect to detect somatic SNPs, and the tool Strelka to detect somatic InDels.
Assembly: mm10/hg38
Supplementary files format and content: VCF
Library strategy: whole exon sequencing

growth_protocol: Cells were maintained in DMEM medium supplemented with 10% fetal bovine serum (FBS), 100 units/ml of penicillin and streptomycin, and incubated at 37℃ in 5% CO2.

extract_protocol:
Genomic DNA was extracted using a QIAGEN kit
A total amount of 1.0μg genomic DNA per sample was used as input material for the DNA sample preparation.Sequencing libraries were generated using Agilent SureSelectXT Mouse All Exon kit (Agilent Technologies, CA, USA)

treatment_protocol: Cells were treated with DMSO, or 500 nM rapamycin for more than 3 months (duplicates or triplicates per condition).

value: rapamycin persistant Bladder cancer

value: TSC1 null

value: 500 nM Rapamycin


title: H97-1

value: Bladder cancer

value: DMSO


title: Confined Control Replicate 3

description: Control Confined


title: Rotenone|0.2uM|DTXSID6021248|24h|S06_sample-04-rotenone-0p2-dose

description:
Library name: S06_sample-04-rotenone-0p2-dose
TempO-LINC

value: HepaRG

value: differentiated HepaRG hepatocyte-like cells

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

value: Rotenone


title: Control 1

description: Library name: Sample 1

value: Primary

value: Human dental pulp stem cells


title: RT4RP


title: A05_EOS

description: 10x Genomics

value: Blood

value: Eosinophil


title: RT4


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S06_sample-03-DMSO-0dose

description:
Library name: S06_sample-03-DMSO-0dose
TempO-LINC

value: liver

value: DMSO control 24h in HepaRG cells

value: Dimethyl sulfoxide


title: Unconfined Control Replicate 3

description: Control Suspension

value: HeLa


title: Donor 1362, WT

city: Philadelphia

first: Italo

last: Tempera

address: 3601 Spruce Street

institute: The Wistar Institute

data_processing:
RNA-seq data was aligned using STAR against hg19 version of the Human genome and all unaligned reads were then aligned against NC_007605.1 version of EBV genome and featureCounts software was used to estimate raw read counts for Human and EBV genes. DESeq2 was used to perform differential analysis
deepTools was used for data visualization
Assembly: hg19
Supplementary files format and content: tab delimited text file with raw counts per gene

growth_protocol: Cell lines were maintained in a humidified incubator containing 5% CO2 at 37°C. EBNA-LP WT and KO cell lines were cultured in RPMI 1640 supplemented with Fetal Bovine Serum at a concentration of 15%, supplemented with 1% penicillin-streptomycin and plasmocin at a concentration 1:500

extract_protocol:
Total RNA from EBNA-LP WT and KO cell lines was isolated from 2 million cells using a Direct-zol RNA Kit
SENSE mRNA-Seq Library Prep Kit V2 was used to generate Illumina-compatible sequencing libraries according to the manufacturer’s instructions

value: Lymphoblastoid Cell Line


title: PDXRP_2

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp.
clean data (clean reads) were obtained by removing reads containing adapter and poly-N. Q20, Q30 and GC content of the clean data were calculated
sequences and reads with low quality from raw data
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
FeatureCounts was used to count the read numbers mapped of each gene.
Assembly: mm10/hg38
Supplementary files format and content: tab-delimited text file including raw counts
Supplementary files format and content: tab-delimited text file including RPKM values

source_name: BLCA PDX after tumor regrowth

extract_protocol:
Total RNA was extracted using a RNeasy mini kit (Qiagen, #74104).
1 μg RNA per sample was used for cDNA library preparation using the NEBNextÒ UltraTM RNA Library Prep Kit for Illumina (NEB, USA)

treatment_protocol: Cells were treated with DMSO, Rapamycin (10 nM), or RMC-6272 (3 nM) for 24h (triplicates per condition).

value: BLCA PDX after tumor regrowth

value: rapamycin persistant Bladder cancer PDX

value: TSC1 null

value: Rapamycin

tag: concentration

value: 3 mg/kg

value: 4 weeks


title: Donor 1362, KO


title: A01_EOS

description: 10x Genomics

value: Moderate asthma


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S06_sample-01-DMSO-0dose

description:
Library name: S06_sample-01-DMSO-0dose
TempO-LINC

value: HepaRG

value: differentiated HepaRG hepatocyte-like cells


title: Dimethyl sulfoxide|0.0uM|nan|24h|S06_sample-02-DMSO-0dose

description:
Library name: S06_sample-02-DMSO-0dose
TempO-LINC


title: HCV29RP

value: rapamycin persistant Bladder cancer

value: 500 nM Rapamycin


title: PDXRP_1


title: Tunicamycin|0.001uM|DTXSID8036730|24h|S05_sample-12-tuncamycin-0p001-dose

description:
Library name: S05_sample-12-tuncamycin-0p001-dose
TempO-LINC

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

value: Tunicamycin


title: H101RP_2

value: rapamycin persistant angiomyolipoma

value: TSC2 null

value: > 3 months


title: Donor 1301, WT

value: Blood

value: Lymphoblastoid Cell Line


title: PDX_2

source_name: BLCA PDX

value: BLCA PDX

value: Bladder cancer PDX

value: DMSO


title: Etoposide|0.25uM|DTXSID5023035|24h|S05_sample-11-etopiside-0p25-dose

description:
Library name: S05_sample-11-etopiside-0p25-dose
TempO-LINC

value: liver

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

value: Etoposide


title: H101RP_1

value: Rapamycin


title: PDX_1

value: TSC1 null


title: Donor 1301, KO


title: H101C_2

value: angiomyolipoma


title: HCV29RP_3

value: rapamycin persistant Bladder cancer


title: Cycloheximide|0.2uM|DTXSID6024882|24h|S05_sample-10-cycloheximide-0p2-dose

description:
Library name: S05_sample-10-cycloheximide-0p2-dose
TempO-LINC

value: HepaRG

value: differentiated HepaRG hepatocyte-like cells

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

value: Cycloheximide


title: Brefeldin A|0.001uM|DTXSID00880041|24h|S05_sample-09-brefeldina-0p001-dose

description:
Library name: S05_sample-09-brefeldina-0p001-dose
TempO-LINC

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

value: Brefeldin A


title: H101C_1

value: TSC2 null


title: HCV29RP_2

value: > 3 months


title: LCL, YY1, rep1

data_processing:
Data was preprocessed using HiC-Pro v2.10.0 pipeline with default settings using a combined version of hg19 and EBV NC_007605.1 genomes at 5kb resolution
hichipper software was used to perform restriction site bias modeling and interaction identification using YY1 ChIP-seq peaks
Assembly: hg19
Supplementary files format and content: tab delimited text file with all called loops
Library strategy: HiChIP

growth_protocol: Cell lines were maintained in a humidified incubator containing 5% CO2 at 37°C. LCL cells, EBNA-LP WT and KO cell lines were cultured in RPMI 1640 supplemented with Fetal Bovine Serum at a concentration of 15%, supplemented with 1% penicillin-streptomycin and plasmocin at a concentration 1:500

extract_protocol:
25 million cells per condition were fixed with 1% formaldehyde for 10 min and then quenched with 0.125 M glycine for 5 min at RT. Ligation products were immunoprecipitated with 50 µg YY1 antibody. 5 μL of Streptavidin C-1 beads were used for biotin pull-down
After the last wash with Tween Wash Buffer bead-bound DNA was used to prepare libraries with Ultralow Library Systems V2

value: Blood

value: Lymphoblastoid Cell Line

value: YY1 (Active Motif 61779)


title: HCV29

value: Bladder cancer

value: DMSO


title: H101RP_ATAC_Rep2

data_processing:
Raw reads were filtered and aligned to hg38 or mm10 using bowtie2.
peaks were called using MACS3 with the cut-off q < = 0.01
bw files were generated using deepTools 3.5
Assembly: hg38/mm10
Supplementary files format and content: peak files and bw files

extract_protocol:
CUT&RUN was performed using a CUTANA ChIC/CUT&RUN Kit (EpiCypher, #14-1048) per manufacture’s protocol.  ATAC-seq was performed using ATAC-Seq Kit (Active Motif, #53150) per manufacture’s protocol.
For each sample, 5 ng of the purified CUT$RUN chromatin was subjected to library preparation with a NEB Ultra II DNA Library Prep Kit, followed by sequencing

value: rapamycin persistant angiomyolipoma

value: 500 nM rapamycin


title: HCV29RP_1

value: TSC1 null

value: Rapamycin


title: H101RP_ATAC_Rep1


title: Donor 1362, WT, YY1


title: tert-Butylhydroquinone|3.0uM|DTXSID6020220|24h|S05_sample-08-tBHQ-3-dose

description:
Library name: S05_sample-08-tBHQ-3-dose
TempO-LINC

value: liver

value: HepaRG

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

value: tert-Butylhydroquinone


title: H101_ATAC_Rep2

value: angiomyolipoma


title: Troglitazone|0.001uM|DTXSID8023719|24h|S05_sample-07-troglitazone-0p001-dose

description:
Library name: S05_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: H101_ATAC_Rep1

value: TSC2 null


title: Donor 1301, WT, YY1

value: Blood

value: Lymphoblastoid Cell Line


title: H101RP_H3K27ac_Rep1

data_processing:
Raw reads were filtered and aligned to hg38 or mm10 using bowtie2.
peaks were called using MACS3 with the cut-off q < = 0.01
bw files were generated using deepTools 3.5
Assembly: hg38/mm10
Supplementary files format and content: peak files and bw files
Library strategy: CUT&RUN


title: Donor 1362, KO, YY1

value: YY1 (Active Motif 61779)


title: Rotenone|0.8uM|DTXSID6021248|24h|S05_sample-06-rotenone-0p8-dose

description:
Library name: S05_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|S05_sample-05-rotenone-0p4-dose

description:
Library name: S05_sample-05-rotenone-0p4-dose
TempO-LINC

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


title: H101RP_H3K27ac_Rep2

value: rapamycin persistant angiomyolipoma

value: 500 nM rapamycin


title: Donor 1301, KO, YY1


title: Rotenone|0.2uM|DTXSID6021248|24h|S05_sample-04-rotenone-0p2-dose

description:
Library name: S05_sample-04-rotenone-0p2-dose
TempO-LINC

value: liver

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


title: H101_H3K27ac_Rep2


title: Donor 1362, WT, LCL, HiC

data_processing:
HiC data was preprocessed using HiC-Pro v2.10.0 pipeline with default settings using hg19 human genome. HiC matrices for the same condition were combined to get 600M reads per condition and HiCcompare was used to estimate significance of differential contact based on raw count matrix files at 150kb resolution.
Assembly: hg19
Supplementary files format and content: tab delimited text file with loop coordinates, hic files with raw and KR-normalized HiC matrices

extract_protocol:
5 million cells per condition were collected for in-situ Hi-C
Libraries of total ligation products were produced using Ultralow Library Systems V2


title: H101RP_MYC_Rep2


title: H101_H3K27ac_Rep1


title: H101RP_MYC_Rep1


title: LCL, YY1, rep2


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S05_sample-03-DMSO-0dose

description:
Library name: S05_sample-03-DMSO-0dose
TempO-LINC

value: HepaRG

value: DMSO control 24h in HepaRG cells

value: Dimethyl sulfoxide


title: H101_MYC_Rep1

value: angiomyolipoma


title: Dimethyl sulfoxide|0.0uM|nan|24h|S05_sample-02-DMSO-0dose

description:
Library name: S05_sample-02-DMSO-0dose
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells


title: H101_MYC_Rep2


title: Donor 1362, KO, LCL, HiC


title: Donor 1301, WT, LCL, HiC


title: 22_0547_3D

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

institute: Tigem

description:
patient, biological rep10
202401250620_BT-8

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a The expression levels of genes were determined with HTseq-counts 0.9.1
Assembly: Hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files including raw counts

source_name: Multicellular spheroids

growth_protocol: Multicellular spheroids grown 48h were harvested and pooled in 1,5ml tubes. After two PBS washes the spheroids were incubated for 30’ at room temperature with LBE buffer and then frozen over night at -80°C.

extract_protocol:
The RNAs were extacted with RNAdvance Cell v2 as per manufacturer protocol (Beckman Coulter).  After quantification at the spectrophotometer, all the extracted RNA samples have been delivered to NEXT GENERATION DIAGNOSTICS S.r.l for library preparation and sequencing.Total RNA was quantified using the Qubit 4.0 fluorimetric Assay (Thermo Fisher Scientific). RNA extracted was precisely quantified and mixed at 10ng/µL.
NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostic srl)

value: Multicellular spheroids

value: EDS patient

value: Transcriptome profile of EDS patient, biological rep10


title: 20_3154_3D

description:
patient, biological rep9
202401250620_BT-7

value: Transcriptome profile of EDS patient, biological rep9


title: Donor 1301, KO, LCL, HiC

value: Blood

value: Lymphoblastoid Cell Line


title: 20_3156_3D

description:
patient, biological rep8
202401250620_BT-6

value: Transcriptome profile of EDS patient, biological rep8


title: Tunicamycin|0.001uM|DTXSID8036730|24h|S04_sample-12-tuncamycin-0p001-dose

description:
Library name: S04_sample-12-tuncamycin-0p001-dose
TempO-LINC

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

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

value: Tunicamycin


title: 20_4456_3D

description:
patient, biological rep6
202401250620_BT-4

value: Transcriptome profile of EDS patient, biological rep6


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S05_sample-01-DMSO-0dose

description:
Library name: S05_sample-01-DMSO-0dose
TempO-LINC

value: liver


title: Donor ND539, T0, HiC


title: Etoposide|0.25uM|DTXSID5023035|24h|S04_sample-11-etopiside-0p25-dose

description:
Library name: S04_sample-11-etopiside-0p25-dose
TempO-LINC

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

value: Etoposide


title: SF_3D

description:
patient, biological rep4
202401250620_BT-2

value: Transcriptome profile of EDS patient, biological rep4


title: 22_0548_3D

description:
patient, biological rep5
202401250620_BT-3

value: Transcriptome profile of EDS patient, biological rep5


title: Donor ND539, LCL, HiC


title: Cycloheximide|0.2uM|DTXSID6024882|24h|S04_sample-10-cycloheximide-0p2-dose

description:
Library name: S04_sample-10-cycloheximide-0p2-dose
TempO-LINC

value: HepaRG

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

value: Cycloheximide


title: 19_1597_3D

description:
patient, biological rep3
202401250620_BT-1

value: Multicellular spheroids

value: EDS patient

value: Transcriptome profile of EDS patient, biological rep3


title: VL_3D

description:
patient, biological rep2
202401250620_BT-13

value: Transcriptome profile of EDS patient, biological rep2


title: Donor ND307, T0, HiC

value: Blood

value: Lymphoblastoid Cell Line


title: GAU_3D

description:
patient, biological rep1
202401250620_BT-12

value: Transcriptome profile of EDS patient, biological rep1


title: Brefeldin A|0.001uM|DTXSID00880041|24h|S04_sample-09-brefeldina-0p001-dose

description:
Library name: S04_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: RR_3D

description:
Control, biological rep4
202401250620_BT-14

value: healthy control

value: Transcriptome profile of control , biological rep4


title: C3B_3D

description:
Control, biological rep3
202401250620_BT-11

value: Transcriptome profile of control , biological rep3


title: Mutu1, IgG, rep2

data_processing:
Reads were mapped against the hg19 version of the human genome and the human gammaherpesvirus 4 (HHV4) NC_007605.1 genome assembly using Burrows-Wheeler Aligner. MACS2 software package was used to call peaks using input samples as control. deepTools was used for data visualization
For comparisons, alignment files were read-depth normalized and replicates were merged for visualization purposes using samtools
Assembly: hg19
Supplementary files format and content: tab delimited text file with peak coordinates and bigwig files for read-depth/spike-in normalized aligned reads
Library strategy: Cut&Run

growth_protocol: Cell lines were maintained in a humidified incubator containing 5% CO2 at 37°C. LCL cells, EBNA-LP WT and KO cell lines were cultured in RPMI 1640 supplemented with Fetal Bovine Serum at a concentration of 15%, supplemented with 1% penicillin-streptomycin and plasmocin at a concentration 1:500. Mutu1 cell lines where cultured under the same conditions using RPMI 1640 supplemented with Fetal Bovine Serum at a concentration of 10%. B cells were maintained in RPMI 1640 supplemented with HyCloneTM Fetal Bovine Serum at a concentration of 15% and infected with EBV (B95.8 strain)

extract_protocol:
500,000 cells per condition were crosslinked using 0.1% formaldehyde for 1 minute, then crosslinking was quenched using 0.125M glycine. Cells were spun down 600g 3 minutes, washed twice with XL Wash Buffer at RT. Activated ConA beads were added to the cells and incubated on nutator for 10 minutes. Beads were then collected on a magnet and 50uL/reaction of fresh ice-cold Antibody Buffer was added to the beads. 1ug of each antibody was added to the reaction and incubated o/n on a nutator at 4°C with cap elevated. Next day beads were collected on a magnet, washed twice with 200uL of ice-cold Digitonin Buffer, resuspended in 50 uL of the same buffer and 2.5 uL of pAG-MNase was added to each reaction. Samples were incubated for 10 minutes at RT on nutator with caps elevated. Beads were washed again twice with ice-cold Digitonin Buffer and resuspended in 50 uL of the same buffer. 1 uL of 100 mM CaCl2 was added to each sample on ice and samples were incubated for 2 hours on nutator at 4°C with caps elevated. Chromatin digestion with MNase was stopped using Stop Buffer at 37°C for 10 minutes in a thermocycler. Supernatant was incubated with 0.8 uL of SDS and 1 uL of Proteinase K o/n at 55°C in a thermocycler to revert crosslinking. DNA was then purified using 1.1X AMPure XP Beads and quantified using Qubit 1X dsDNA HS quantification kit
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit

tag: cut&run antibody

value: IgG antibody (CST 66362S)


title: tert-Butylhydroquinone|3.0uM|DTXSID6020220|24h|S04_sample-08-tBHQ-3-dose

description:
Library name: S04_sample-08-tBHQ-3-dose
TempO-LINC

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.

value: liver

value: HepaRG

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

value: tert-Butylhydroquinone


title: C2B_3D

description:
Control, biological rep2
202401250620_BT-10

value: Multicellular spheroids

value: Transcriptome profile of control , biological rep2


title: Donor ND307, LCL, HiC


title: C1A_3D

description:
Control, biological rep1
202401250620_BT-9

value: Transcriptome profile of control , biological rep1


title: 20-4222_pat

description:
patient, biological rep10
202212170310_BT-9

source_name: Transcriptome profile of EDS patient, biological rep10

extract_protocol:
For gene expression analyses, total RNA was extracted according to the manufacturer's instructions (RNeasy Mini Kit). Total RNA was quantified using the Qubit 4.0 fluorimetric Assay (Thermo Fisher Scientific). RNA extracted was precisely quantified and mixed at 10ng/µL.
NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostic srl)

value: fibroblast cell lines

tag: disease state

value: EDS patient


title: Troglitazone|0.001uM|DTXSID8023719|24h|S04_sample-07-troglitazone-0p001-dose

description:
Library name: S04_sample-07-troglitazone-0p001-dose
TempO-LINC

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

value: Troglitazone


title: 22-0548_pat

description:
patient, biological rep9
202212170310_BT-8

source_name: Transcriptome profile of EDS patient, biological rep9


title: Rotenone|0.8uM|DTXSID6021248|24h|S04_sample-06-rotenone-0p8-dose

description:
Library name: S04_sample-06-rotenone-0p8-dose
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells

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

value: Rotenone


title: 22-0547_pat

description:
patient, biological rep8
202212170310_BT-7

source_name: Transcriptome profile of EDS patient, biological rep8


title: 20_A222_3D

description:
patient, biological rep7
202401250620_BT-5

value: Transcriptome profile of EDS patient, biological rep7


title: Mutu1, IgG, rep1

value: Blood

value: Lymphoblastoid Cell Line


title: SF_pat

description:
patient, biological rep7
202212170310_BT-6

source_name: Transcriptome profile of EDS patient, biological rep7


title: Rotenone|0.4uM|DTXSID6021248|24h|S04_sample-05-rotenone-0p4-dose

description:
Library name: S04_sample-05-rotenone-0p4-dose
TempO-LINC

value: liver

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


title: GAU_pat

description:
patient, biological rep5
202212170310_BT-4

source_name: Transcriptome profile of EDS patient, biological rep5


title: Mutu1, H3K27ac, rep1

value: H3K27ac (Active Motif 39133)


title: Rotenone|0.2uM|DTXSID6021248|24h|S04_sample-04-rotenone-0p2-dose

description:
Library name: S04_sample-04-rotenone-0p2-dose
TempO-LINC

value: HepaRG

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


title: 19-1597_pat

description:
patient, biological rep6
202212170310_BT-5

source_name: Transcriptome profile of EDS patient, biological rep6


title: VL_pat

description:
patient, biological rep4
202212170310_BT-3

source_name: Transcriptome profile of EDS patient, biological rep4


title: 20-4456_pat

description:
patient, biological rep3
202212170310_BT-2

source_name: Transcriptome profile of EDS patient, biological rep3


title: 20-3156_pat

description:
patient, biological rep1
202212170310_BT-1

source_name: Transcriptome profile of EDS patient, biological rep1


title: Donor 1362, KO, CTCF

value: CTCF (Active Motif 61311)


title: 20-3154_pat

description:
patient, biological rep2
202212170310_BT-10

source_name: Transcriptome profile of EDS patient, biological rep2


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S04_sample-03-DMSO-0dose

description:
Library name: S04_sample-03-DMSO-0dose
TempO-LINC

source_name: liver

value: DMSO control 24h in HepaRG cells

value: Dimethyl sulfoxide


title: Donor 1362, WT, CTCF

source_name: Blood


title: C2B_healthy

description:
Control, biological rep2
202212170310_BT-12

source_name: Transcriptome profile of control , biological rep2

value: fibroblast cell lines

value: healthy control


title: C3B_healthy

description:
Control, biological rep1
202212170310_BT-11

source_name: Transcriptome profile of control , biological rep1


title: Dimethyl sulfoxide|0.0uM|nan|24h|S04_sample-02-DMSO-0dose

description:
Library name: S04_sample-02-DMSO-0dose
TempO-LINC


title: Donor 1301, WT, CTCF


title: Tunicamycin|0.001uM|DTXSID8036730|24h|S03_sample-12-tuncamycin-0p001-dose

description:
Library name: S03_sample-12-tuncamycin-0p001-dose
TempO-LINC

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

value: Tunicamycin


title: C1A_healthy

description:
Control, biological rep4
202212170310_BT-14

source_name: Transcriptome profile of control , biological rep4


title: Mutu1, H3K27ac, rep2


title: RR_healthy

description:
Control, biological rep3
202212170310_BT-13

source_name: Transcriptome profile of control , biological rep3


title: Single-cell_Multiome_Spleen_Male_Donor168

first: Golnaz

last: Vahedi

state: Pennsylvania

address: 421 Curie Boulevard

department: Genetics

institute: University of Pennsylvania

library_source: genomic single cell

data_processing:
Cell Ranger ARC, Seurat instructions
Assembly: Grch38
Supplementary files format and content: Cell Ranger ARC output

source_name: Spleen

extract_protocol:
Both RNA and ATAC libraries were made based on the 10x single-cell multiome protocol.
Library was made based on manufaturer protocol.
Single Cell Multiome ATAC + Gene Expression

value: Spleen

tag: Sex

value: Male

tag: donor


title: Donor 1301, KO, CTCF

tag: tissue


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S04_sample-01-DMSO-0dose

description:
Library name: S04_sample-01-DMSO-0dose
TempO-LINC

tag: cell type

value: differentiated HepaRG hepatocyte-like cells


title: Single-cell_Multiome_PLNH_Male_Donor167


title: Donor2, T0, H3K27ac

value: Blood


title: Single-cell_Multiome_PLNH_Male_Donor166


title: Donor2, T0, YY1

value: Lymphoblastoid Cell Line

value: YY1 (Active Motif 61779)


title: Single-cell_Multiome_Spleen_Male_Donor165


title: Etoposide|0.25uM|DTXSID5023035|24h|S03_sample-11-etopiside-0p25-dose

description:
Library name: S03_sample-11-etopiside-0p25-dose
TempO-LINC

value: liver

tag: treatment

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

value: Etoposide


title: Single-cell_Multiome_PLNT_Male_Donor164

source_name: PLNT

value: PLNT


title: Cycloheximide|0.2uM|DTXSID6024882|24h|S03_sample-10-cycloheximide-0p2-dose

description:
Library name: S03_sample-10-cycloheximide-0p2-dose
TempO-LINC

tag: cell line

value: HepaRG

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

value: Cycloheximide


title: Single-cell_TEA_Spleen_Male_Donor163


title: Donor2, LCL, YY1


title: Brefeldin A|0.001uM|DTXSID00880041|24h|S03_sample-09-brefeldina-0p001-dose

description:
Library name: S03_sample-09-brefeldina-0p001-dose
TempO-LINC

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

value: Brefeldin A


title: Single-cell_Multiome_PLNH_Male_Donor161

source_name: PLNH

value: PLNH


title: Donor2, LCL, H3K27ac

value: H3K27ac (Active Motif 39133)


title: Single-cell_Multiome_PLNT_Male_Donor162


title: Single-cell_Multiome_PLNH_Female_Donor160

value: Female


title: Single-cell_Multiome_Spleen_Male_Donor159

value: Male


title: Troglitazone|0.001uM|DTXSID8023719|24h|S03_sample-07-troglitazone-0p001-dose

description:
Library name: S03_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: Single-cell_Multiome_Spleen_Male_Donor158

value: Spleen


title: Donor1, T0, H3K27ac

value: Blood

value: Lymphoblastoid Cell Line


title: Single-cell_Multiome_PLNT_Male_Donor157


title: Single-cell_Multiome_PLNB_Male_Donor156

source_name: PLNB

value: PLNB


title: Rotenone|0.8uM|DTXSID6021248|24h|S03_sample-06-rotenone-0p8-dose

description:
Library name: S03_sample-06-rotenone-0p8-dose
TempO-LINC

value: liver

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

value: Rotenone


title: Donor1, LCL, H3K27ac


title: Rotenone|0.2uM|DTXSID6021248|24h|S03_sample-04-rotenone-0p2-dose

description:
Library name: S03_sample-04-rotenone-0p2-dose
TempO-LINC

value: HepaRG

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


title: Rotenone|0.4uM|DTXSID6021248|24h|S03_sample-05-rotenone-0p4-dose

description:
Library name: S03_sample-05-rotenone-0p4-dose
TempO-LINC

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


title: Single-cell_Multiome_Spleen_Female_Donor155


title: Single-cell_Multiome_Spleen_Female_Donor153


title: Single-cell_Multiome_Spleen_Male_Donor152


title: Mutu1, YY1, rep2

data_processing:
Reads were mapped against the hg19 version of the human genome and the human gammaherpesvirus 4 (HHV4) NC_007605.1 genome assembly using Burrows-Wheeler Aligner. MACS2 software package was used to call peaks using input samples as control. deepTools was used for data visualization
For comparisons, alignment files were read-depth normalized and replicates were merged for visualization purposes using samtools
DESeq2 was used for differential analysis of ChIP-seq peaks
Assembly: hg19
Supplementary files format and content: tab delimited text file with peak coordinates and bigwig files for read-depth normalized aligned reads

growth_protocol: Cell lines were maintained in a humidified incubator containing 5% CO2 at 37°C. LCL cells, EBNA-LP WT and KO cell lines were cultured in RPMI 1640 supplemented with Fetal Bovine Serum at a concentration of 15%, supplemented with 1% penicillin-streptomycin and plasmocin at a concentration 1:500. Mutu1 cell lines where cultured under the same conditions using RPMI 1640 supplemented with Fetal Bovine Serum at a concentration of 10%

extract_protocol:
Briefly, 50mln cells per immunoprecipitation were collected and fixed with 1% formaldehyde for 15 min and then quenched with 0.25 M glycine for 5 min on ice. After 3 washes with 1X PBS, pellets were resuspended in 10 mL each of a series of two lysis buffers and resuspended in 1mL of the third lysis buffer before fragmentation in Covaris ME220 Ultrasonicator to generate chromatin fragments roughly 200–500 bp in size. Chromatin was centrifuged to clear debris and a 1:20 of this cleared chromatin was kept as standard input for comparison against immunoprecipitations. Chromatin was incubated rotating at 4°C 1h with the specific antibody and chromatin–antibody complexes were precipitated using 250 µL of Dynabeads Protein A at 4°C overnight. DNA was purified using Zymo ChIP DNA Clean & Concentrator Kit
Libraries for sequencing were made using NEBNext Ultra II DNA Library Prep Kit

tag: chip antibody

value: YY1 (Active Motif 61779)


title: Single-cell_Multiome_PLNH_Male_Donor150

description: HPAP128_PLNH_CD45_Multiome_FC_combined_ATAC

value: PLNH


title: Single-cell_Multiome_PLNT_Male_Donor151

value: PLNT


title: Mutu1, YY1, rep1


title: Single-cell_Multiome_PLNB_Male_Donor149

value: Male


title: Single-cell_TEA_Spleen_Male_Donor148


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S03_sample-03-DMSO-0dose

description:
Library name: S03_sample-03-DMSO-0dose
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells

value: DMSO control 24h in HepaRG cells

tag: timeh

value: Dimethyl sulfoxide


title: Mutu1, Input, rep2


title: Dimethyl sulfoxide|0.0uM|nan|24h|S03_sample-02-DMSO-0dose

description:
Library name: S03_sample-02-DMSO-0dose
TempO-LINC

tag: chem name


title: tert-Butylhydroquinone|3.0uM|DTXSID6020220|24h|S03_sample-08-tBHQ-3-dose

description:
Library name: S03_sample-08-tBHQ-3-dose
TempO-LINC

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

value: tert-Butylhydroquinone

tag: conc


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S03_sample-01-DMSO-0dose

description:
Library name: S03_sample-01-DMSO-0dose
TempO-LINC

tag: dtxsid


title: Mutu1, Input, rep1

value: Blood

value: Lymphoblastoid Cell Line


title: Single-cell_Multiome_PLNT_Male_Donor147


title: Single-cell_Multiome_PLNH_Male_Donor146


title: Single-cell_Multiome_PLNB_Male_Donor145

value: PLNB


title: Donor1, T0, YY1


title: Tunicamycin|0.001uM|DTXSID8036730|24h|S02_sample-12-tuncamycin-0p001-dose

description:
Library name: S02_sample-12-tuncamycin-0p001-dose
TempO-LINC

value: liver

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

value: Tunicamycin

tag: batch


title: LCL, YY1, rep2


title: Donor1, LCL, YY1


title: Single-cell_Multiome_PLNH_Female_Donor154

value: Female


title: Etoposide|0.25uM|DTXSID5023035|24h|S02_sample-11-etopiside-0p25-dose

description:
Library name: S02_sample-11-etopiside-0p25-dose
TempO-LINC

value: HepaRG

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

value: Etoposide


title: Single-cell_Multiome_Spleen_Male_Donor143

value: Spleen


title: Single-cell_Multiome_PLNT_Male_Donor142

value: PLNT

value: Male


title: Single-cell_Multiome_PLNH_Male_Donor141

value: PLNH


title: Single-cell_Multiome_PLNB_Male_Donor140


title: LCL, Input, rep2


title: LCL, YY1, rep1

value: YY1 (Active Motif 61779)


title: Single-cell_TEA_Spleen_Female_Donor139


title: Brefeldin A|0.001uM|DTXSID00880041|24h|S02_sample-09-brefeldina-0p001-dose

description:
Library name: S02_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: Single-cell_Multiome_PLNH_Female_Donor138


title: LCL, Input, rep1

value: Blood

value: Lymphoblastoid Cell Line


title: tert-Butylhydroquinone|3.0uM|DTXSID6020220|24h|S02_sample-08-tBHQ-3-dose

description:
Library name: S02_sample-08-tBHQ-3-dose
TempO-LINC

value: liver

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

value: tert-Butylhydroquinone


title: Single-cell_TEA_Spleen_Female_Donor137

value: Female


title: Single-cell_Multiome_PLNH_Female_Donor136


title: Troglitazone|0.001uM|DTXSID8023719|24h|S02_sample-07-troglitazone-0p001-dose

description:
Library name: S02_sample-07-troglitazone-0p001-dose
TempO-LINC

value: HepaRG

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

value: Troglitazone


title: Donor 1362, WT, Pol2


title: Single-cell_TEA_Spleen_Male_Donor135


title: Single-cell_Multiome_Spleen_Male_Donor134

value: Spleen


title: Single-cell_Multiome_PLNT_Male_Donor133

value: PLNT


title: Rotenone|0.8uM|DTXSID6021248|24h|S02_sample-06-rotenone-0p8-dose

description:
Library name: S02_sample-06-rotenone-0p8-dose
TempO-LINC

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

value: Rotenone


title: Donor 1301, WT, Pol2


title: Single-cell_TEA_Spleen_Female_Donor131


title: Single-cell_Multiome_Spleen_Male_Donor144

value: Male


title: Rotenone|0.4uM|DTXSID6021248|24h|S02_sample-05-rotenone-0p4-dose

description:
Library name: S02_sample-05-rotenone-0p4-dose
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells

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


title: Single-cell_Multiome_PLNH_Male_Donor132

value: PLNH


title: Single-cell_Multiome_PLNT_Female_Donor130


title: Donor 1301, KO, Pol2

value: Blood


title: Rotenone|0.2uM|DTXSID6021248|24h|S02_sample-04-rotenone-0p2-dose

description:
Library name: S02_sample-04-rotenone-0p2-dose
TempO-LINC

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


title: Donor 1362, WT, YY1

value: Lymphoblastoid Cell Line

value: YY1 (Active Motif 61779)


title: Cycloheximide|0.2uM|DTXSID6024882|24h|S02_sample-10-cycloheximide-0p2-dose

description:
Library name: S02_sample-10-cycloheximide-0p2-dose
TempO-LINC

value: liver

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

value: Cycloheximide


title: Single-cell_Multiome_PLNB_Female_Donor128

value: PLNB

value: Female


title: Single-cell_Multiome_PLNH_Female_Donor129


title: Single-cell_TEA_Spleen_Female_Donor127


title: Single-cell_TEA_Spleen_Female_Donor126


title: Donor 1362, WT, Input


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S02_sample-03-DMSO-0dose

description:
Library name: S02_sample-03-DMSO-0dose
TempO-LINC

value: HepaRG

value: DMSO control 24h in HepaRG cells

value: Dimethyl sulfoxide


title: Single-cell_Multiome_PLNT_Female_Donor125

value: PLNT


title: Dimethyl sulfoxide|0.0uM|nan|24h|S02_sample-02-DMSO-0dose

description:
Library name: S02_sample-02-DMSO-0dose
TempO-LINC


title: Single-cell_Multiome_PLNH_Female_Donor124


title: Donor 1362, WT, H3K27ac

value: H3K27ac (Active Motif 39133)


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S02_sample-01-DMSO-0dose

description:
Library name: S02_sample-01-DMSO-0dose
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells


title: Single-cell_Multiome_Spleen_Male_Donor122

value: Spleen

value: Male


title: Donor 1362, KO, Pol2

value: Blood


title: Single-cell_Multiome_PLNT_Male_Donor121


title: Tunicamycin|0.001uM|DTXSID8036730|24h|S01_sample-12-tuncamycin-0p001-dose

description:
Library name: S01_sample-12-tuncamycin-0p001-dose
TempO-LINC

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

value: Tunicamycin


title: Single-cell_Multiome_PLNH_Male_Donor120

value: PLNH


title: Donor 1362, KO, H3K27ac

value: Lymphoblastoid Cell Line


title: Single-cell_Multiome_Spleen_Male_Donor117


title: Single-cell_Multiome_PLNs_Female_Donor118

source_name: PLNs

value: PLNs


title: Single-cell_Multiome_PLNH_Male_Donor116


title: Donor 1301, WT, YY1

value: YY1 (Active Motif 61779)


title: Donor 1362, KO, Input


title: Etoposide|0.25uM|DTXSID5023035|24h|S01_sample-11-etopiside-0p25-dose

description:
Library name: S01_sample-11-etopiside-0p25-dose
TempO-LINC

value: liver

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

value: Etoposide


title: Single-cell_Multiome_PLNT_Male_Donor114


title: Single-cell_Multiome_Spleen_Female_Donor113

value: Female


title: Brefeldin A|0.001uM|DTXSID00880041|24h|S01_sample-09-brefeldina-0p001-dose

description:
Library name: S01_sample-09-brefeldina-0p001-dose
TempO-LINC

value: HepaRG

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

value: Brefeldin A


title: Donor 1301, WT, Input


title: tert-Butylhydroquinone|3.0uM|DTXSID6020220|24h|S01_sample-08-tBHQ-3-dose

description:
Library name: S01_sample-08-tBHQ-3-dose
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells

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

value: tert-Butylhydroquinone


title: Single-cell_Multiome_Spleen_Female_Donor111

value: Spleen


title: Single-cell_TEA_Spleen_Male_Donor123

value: Male


title: Donor 1362, KO, YY1

value: Blood


title: Donor 1301, WT, H3K27ac

value: H3K27ac (Active Motif 39133)


title: Single-cell_Multiome_PLNs_Female_Donor110


title: Troglitazone|0.001uM|DTXSID8023719|24h|S01_sample-07-troglitazone-0p001-dose

description:
Library name: S01_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|S01_sample-06-rotenone-0p8-dose

description:
Library name: S01_sample-06-rotenone-0p8-dose
TempO-LINC

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

value: Rotenone


title: Single-cell_Multiome_PLNH_Female_Donor108

value: PLNH


title: Donor 1301, KO, YY1

value: Lymphoblastoid Cell Line

value: YY1 (Active Motif 61779)


title: Single-cell_Multiome_Spleen_Female_Donor107

value: Female


title: Donor 1301, KO, Input


title: Single-cell_Multiome_PLNH_Female_Donor106


title: Single-cell_Multiome_Spleen_Female_Donor119


title: Cycloheximide|0.2uM|DTXSID6024882|24h|S01_sample-10-cycloheximide-0p2-dose

description:
Library name: S01_sample-10-cycloheximide-0p2-dose
TempO-LINC

value: liver

value: HepaRG

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

value: Cycloheximide


title: Donor 1301, KO, H3K27ac


title: Single-cell_Multiome_Spleen_Male_Donor115


title: LCL, Donor 1362, WT

extract_protocol:
100,000 cells were spun down at 500g for 5 min at 4°C. Cell pellet was resuspended in 50 µL of fresh ice-cold ATAC-seq Lysis Buffer by pipetting up and down three times and incubated on ice for 3 min. Then, 1 mL of fresh ice-cold ATAC-seq Wash Buffer was added to dilute the lysis reagents and tubes inverted five times to mix. Nuclei were spun down at 500g for 10 min at 4 °C. Nuclei pellets were then resuspended in 50 µL of freshly made Transposition Mix by pipetting up and down six times and reactions were incubated at 37°C for 30 min in a thermomixer with 1,000 rpm mixing. The transposition reaction was terminated by adding 250 µL (five volumes) of DNA Binding Buffer from the DNA Clean and Concentrator-5 Kit and mixed well by inversion. Reactions were kept o/n at -20°C. The next day DNA was purified using the Zymo DNA Clean and Concentrator-5 Kit as per protocol
Each sample in the study was assigned to a unique combination of the Adapter 1 (Ad1) and Adapter 2 (Ad2) sequences. Each cleaned-up transposed DNA sample was transferred to a 200 µL PCR tube and mixed with 25 µL of NEBNext Ultra II Q5 2X Master Mix, 2.5 µL of the corresponding Ad1 and 2.5 µL of the corresponding Ad2


title: Single-cell_Multiome_Spleen_Male_Donor103


title: Rotenone|0.2uM|DTXSID6021248|24h|S01_sample-04-rotenone-0p2-dose

description:
Library name: S01_sample-04-rotenone-0p2-dose
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells

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


title: Single-cell_Multiome_PLNH_Female_Donor112


title: LCL, Donor 1362, KO


title: Single-cell_Multiome_PLNT_Male_Donor102

value: PLNT

value: Male


title: Dimethyl sulfoxide|0.0uM|nan|24h|S01_sample-02-DMSO-0dose

description:
Library name: S01_sample-02-DMSO-0dose
TempO-LINC

value: DMSO control 24h in HepaRG cells

value: Dimethyl sulfoxide


title: Single-cell_Multiome_PLNH_Male_Donor100


title: LCL, Donor 1301, WT

value: Blood


title: Single-cell_Multiome_PLNH_Female_Donor101


title: Single-cell_Multiome_Spleen_Female_Donor109

value: Spleen


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S01_sample-01-DMSO-0dose

description:
Library name: S01_sample-01-DMSO-0dose
TempO-LINC


title: Single-cell_Multiome_PLNH_Male_Donor98


title: LCL, Donor 1301, KO


title: Single-cell_Multiome_Spleen_Male_Donor97


title: Single-cell_Multiome_Spleen_Male_Donor99


title: CL_HEK293_SRRM4_HIGH_b

first: Manuel

last: Irimia

state: Barcelona

address: 88 Dr. Aiguader

department: MELIS

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

data_processing:
vast-tools was used to map the reads to a library of mRNAs using vast-tools align --expr, for -sp hg38. The libraries were analyzed using a pipeline described in Bonnal et al
Assembly: hg38
Supplementary files format and content: cRPKM files have raw read counts to each human gene annotated in vast-tools. They were generated using vast-tools align with --expr option.  TRUSTED_ASSOCIATIONS have the trusted barcode-variant associations. CORRECTED_COUNTS have PSI and different metrics for BARCODE-VARIANT association in each experimental condition. INCLUSION_TABLE have PSI and different metrics per VARIANT and experimental condition. enr_INPUT_COUNTS and enr_OUTPUT_COUNTS have CPM values.

molecule: polyA RNA

source_name: HEK 293 Flp-In T-Rex

growth_protocol: Described in Bonnal et al

extract_protocol:
Described in Bonnal et al
mRNA sequencing: RNA was isolated using the RNeasy Mini Qiagen kit and the RNA quality was checked using Bioanalyzer (Agilent). Libraries were prepared at the CRG Genomics Unit using the TruSeq stranded mRNA Library Prep (ref. 20020595, Illumina) according to the manufacturer's protocol. Briefly, 500 ng of total RNA were used for polyA-mRNA selection using Oligo-dT beads, and two rounds of purification were performed. During the second elution of the mRNA, this was fragmented under elevated temperature and primed with random hexamers for cDNA synthesis, that was performed using reverse transcriptase (SuperScript II; ref. 18064-014, Invitrogen). Then, a second strand cDNA was synthesized, incorporating dUTP in place of dTTP and generating blunt-ended ds cDNA. A single ‘A’ nucleotide was added to the 3′ ends of the blunt fragments (A-tailing) and immediately afterwards the Truseq adapter was ligated. Finally, PCR selectively enriched those DNA fragments that had adapter molecules on both ends. The PCR was performed using Unique Dual Indexes and the master mix provided with the kit. All purification steps were performed using AgenCourt AMPure XP beads (ref. A63882, Beckman Coulter). Final libraries were analyzed using Bioanalyzer DNA 1000 or Fragment Analyzer Standard Sensitivity (ref. 5067-1504 or ref. DNF-473, Agilent) to estimate the quantity and validate the size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit KK4835 (ref. 07960204001, Roche). Amplicon sequencing: Amplicons were checked using Bioanalyzer (Agilent) and the final steps amplification (consisting in the addition of the Illumina adaptors) were performed at CRG Genomics Unit. Both the input and output PCR products were deep sequenced. After quantification by qubit, amplification was performed by PCR using NEBNext Q5 Hot Start HiFi PCR Master Mix (ref. M0543L) and Index 1 (i7) and Index 2 (i5) primers containing Illumina's P5 and P7 sequences. Final libraries were analyzed using Agilent Bioanalyzer or Fragment analyzer High Sensitivity assay (ref. 5067‐4626 or ref. DNF‐474) to estimate the quantity and check size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit KK4835 (Ref. 07960204001, Roche).

treatment_protocol: Described in Bonnal et al

value: HEK 293 Flp-In T-Rex

value: humanembryonickidney

value: 4.8 ng/ml Doxycycline, 24 hours


title: Single-cell_Multiome_Spleen_Male_Donor95


title: Rotenone|0.4uM|DTXSID6021248|24h|S01_sample-05-rotenone-0p4-dose

description:
Library name: S01_sample-05-rotenone-0p4-dose
TempO-LINC

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

value: Rotenone


title: CL_HEK293_SRRM4_MID_b

value: 1.2 ng/ml Doxycycline, 24 hours


title: Unconfined Treated Replicate 2

description:
Oligomycin A (1 µM) treated Suspension
nucleosome_counts.csv
UT_vs_CT_csaw_DA_windows_all.txt
UT_vs_UU_csaw_DA_windows_all.txt

data_processing:
50 base-pairs paired-end reads, were subjected to alignment against the hg19 human genome using Bowtie2 aligner (v 2.5.1) after removal of adaptors with TrimGalore (v. 0.6.10). The alignment was carried out with default parameters, except for the utilization of the "very-sensitive 2000" option. To ensure the quality of aligned reads, those with a quality score below 30 were filtered out using Samtools 1.16.1. Mitochondrial reads were excluded from further analysis followed by removal of duplicated reads by using Picard (v 2.23.8). The alignment of reads was adjusted to account for Tn5 transposase insertions with deepTools (v 3.5.1). Peaks were identified using MACS2 (v 2.2.8) with false discovery rate (FDR) threshold of less than 0.01. Regions designated as blacklisted were filtered out from further analysis (blacklist v2). Peak intersection between replicates and union between conditions was done using the GenomicRanges package in R (V4.2). Differentially accessible (DA) regions were quantified utilizing the csaw R package with Trimmed Mean of M-values (TMM) normalization on binned counts followed by edgeR for DA analysis, employing a significance threshold of log-fold change > 0.5 and FDR < 0.1.
Assembly: hg19
Supplementary files format and content: csv file containing nucleosome counts
Supplementary files format and content: .txt file containing differentially accessible regions comparing between suspension and confined cells.
Supplementary files format and content: .txt file containing differentially accessible regions between suspensions (untreated vs treated) and confined (untreated vs treated) samples.

source_name: HeLa

value: HeLa


title: Single-cell_Multiome_PLNH_Male_Donor96

value: PLNH


title: Single-cell_Multiome_PLNH_Male_Donor94


title: Single-cell_Multiome_PLNH_Female_Donor104

value: Female


title: Single-cell_Multiome_Spleen_Female_Donor93


title: Dimethyl sulfoxide|0.0uM|DTXSID2021735|24h|S01_sample-03-DMSO-0dose

description:
Library name: S01_sample-03-DMSO-0dose
TempO-LINC

value: liver

value: HepaRG

value: differentiated HepaRG hepatocyte-like cells


title: CL_HEK293_SRRM4_LOW_b

value: 0,3 ng/ml Doxycycline, 24 hours


title: Single-cell_Multiome_PLNH_Female_Donor92


title: CL_HEK293_SRRM4_CONT_b

value: 0 ng/ml Doxycycline, 24 hours


title: Confined Control Replicate 2

description:
Control Confined
nucleosome_counts.csv
UU_vs_CU_csaw_DA_windows_all.txt
CT_vs_CU_csaw_DA_windows_all.txt


title: Single-cell_Multiome_PLNH_Male_Donor90

value: Male


title: Unconfined Control (UC) Replicate 2

description:
Control Suspension
nucleosome_counts.csv
UU_vs_CU_csaw_DA_windows_all.txt
UT_vs_UU_csaw_DA_windows_all.txt


title: Single-cell_Multiome_PLNH_Male_Donor88


title: Single-cell_Multiome_Spleen_Male_Donor89


title: CL_HEK293_SRRM4_HIGH_a


title: Single-cell_Multiome_Spleen_Female_Donor105


title: Confined Treated (CT) Replicate 1

description:
Oligomycin A (1 µM) treated Confined
nucleosome_counts.csv
UT_vs_CT_csaw_DA_windows_all.txt
CT_vs_CU_csaw_DA_windows_all.txt


title: Single-cell_Multiome_Spleen_Female_Donor86


title: Unconfined Treated (UT) Replicate 1


title: CL_HEK293_SRRM4_MID_a


title: Single-cell_Multiome_Spleen_Male_Donor84

molecule: nuclear RNA


title: CL_HEK293_SRRM4_LOW_a


title: Single-cell_Multiome_PLNH_Female_Donor85


title: Confined Control (CU) Replicate 1


title: Confined Treated Replicate 2


title: Single-cell_Multiome_PLNH_Male_Donor83


title: CL_HEK293_SRRM4_CONT_a


title: m27mo, scRNAseq

city: New Haven

first: Ruben

last: De Man

state: CT

address: 333 Cedar St

institute: Yale School of Medicine

description:
Library name: m27mo
10x Genomics

data_processing:
Raw sequencing reads were demultiplexed based on sample index adaptors, which were added during the last step of cDNA library preparation.
Possible adaptor and/or primer contamination were removed using Cutadapt.
Using the scRNA-seq implementation of STAR (STARsolo), reads were mapped to the murine reference genome GRCm38 release M22 (GRCm38.p6), collapsed and counted, and summarized to a gene expression matrix.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Proximal pulmonary artery

extract_protocol:
Proximal pulmonary arteries were excised with surrounding tissue. The arteries were mechanically chopped and placed in 1mg/ml collagenase (Roche) and 3 U/ml elastase (Worthington).
Following cellular dissociation, we barcoded unique mRNA molecules of each cell using our 10x Genomics Chromium platform (3’ v3.1 kit) and a droplet-based microfluidic system, then performed reverse transcription, cDNA amplification, fragmentation, adaptor ligation, and sample index PCR according to the manufacturer’s protocol.

value: Proximal pulmonary artery


title: Single-cell_Multiome_PLNH_Male_Donor82


title: Unconfined Control (UU) Replicate 1


title: Single-cell_Multiome_PLNT_Male_Donor80

value: PLNT


title: Single-cell_Multiome_Spleen_Male_Donor91

value: Spleen


title: Patient 17, Week 24

city: Matsumoto

first: Keita

last: Hirai

state: Nagano

address: 3-1-1 Asahi

department: Graduate School of Medicine

country: Japan

institute: Shinshu University

description:
Library name: B34
B34: Patient 17, Week 24

data_processing:
The sequence reads were trimmed for adapter sequences and low-quality reads using Trimmomatic (version 0.39), followed by quality verification using FastQC v0.11.9. Alignment of reads to the human reference genome (GRCh38 patch 13) was performed using the STAR alignment tool (version 2.7.5c) with gene annotation based on GENECODE release 39. Transcript counts were quantified using RSEM v1.3.1. The TCC R package (version 1.44.0) was utilized for count data normalization using the trimmed mean of M values (TMM) method, and differential gene expression analysis was conducted using edgeR (version 4.2.2).
Assembly: GRCh38
Supplementary files format and content: raw counts for each sample

source_name: Peripheral blood T cell

extract_protocol:
Total RNA was extracted from T cells using a miRNeasy kit (Qiagen)
Library preparation was conducted using the NEBNext Ultra II Directional RNA Library Prep Kit with NEBNext rRNA Depletion Kit (New England Biolabs), with 10 ng of total RNA used for each sample.

treatment_protocol: Following the collection of blood samples, T cells were immediately isolated by immunomagnetic negative selection using the EasySep Direct Human T Cell Isolation Kit (STEMCELL Technologies).

value: Peripheral blood T cell

tag: responder

value: Yes

tag: time

value: Week 24


title: Single-cell_TEA_Spleen_Male_Donor79


title: Single-cell_Multiome_PLNT_Male_Donor78


title: f3m, scRNAseq

description:
Library name: f3m
10x Genomics