title: Control_549

city: Wenzhou

first: Kejie

last: Chen

state: Zhejiang

address: Chashan

institute: Wenzhou Medical University

description: without Lespedeza bicolor root (5 µg/mL)

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm9

source_name: breast

growth_protocol: cells were incubated at 37 ℃ in 5% CO2 and maintained in DMEM medium with 10% FBS and 100 U/mL penicillin and streptomycin.

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

treatment_protocol: The control group was cultured in nomral medium. The treated group was challenged in Lespedeza bicolor root (5 µg/mL) for 48h.

value: breast

value: Human triple negative breast cancer cells BT549

value: Tumor cell

tag: genotype

value: WT

tag: treatment

value: Cultured in common medium


title: treated_549

status: Public on Mar 27 2024

type: SRA

country: China

description: with Lespedeza bicolor root (5 µg/mL)

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: cell type

value: Treated with Lespedeza bicolor root (5 ug/mL) for 48h


title: treated_231

description: with Lespedeza bicolor root (5 µg/mL)

value: Human triple negative breast cancer cells MDA-MB-231


title: Control_231


title: GPC3 CAR Expressed in T-cell (replicate 3)

city: HOUSTON

first: Xiaotong

last: Song

state: Texas

address: 2121 W. Holcombe Blvd

department: CIID

country: USA

institute: Texas A&M University

data_processing:
Raw FASTQ files were mapped to the human reference genome (hg38) using STAR (version 2.7.2b) RNASeq alignment tool. Biobambam (version 0.0.191) was used to mark duplicates and index raw files before alignment.
HTSeq (version 0.11.0) was utilized to extract raw read counts from STAR-aligned RNAseq files.
Assembly: hg38
Supplementary files format and content: CSV file include raw counts of human genes for each sample

source_name: PBMC

growth_protocol: Human peripheral blood mononuclear cells purchased from STEMCELL was stimulated by OKT-3 and CD28 mAb-coated plates. The cells were washed and replated in complete RPMI 1640 medium with 100 U/ml IL-2 48 hours later. The cells were then maintained in incubators at 37°C with 5% CO2 for expansion.

extract_protocol:
RNA was isolated using the RNeasy Plus mini kit (Qiagen).
Quality control measures were implemented for each sample before library construction to ensure data reliability. Potential RNA degradation and contamination were assessed through agarose gel electrophoresis. Poly-A selection was employed to remove rRNA from the samples. Following the QC procedures, mRNA was enriched from each sample using oligo(dT) beads. Initially, the mRNA underwent random fragmentation by adding a fragmentation buffer. Subsequently, cDNA synthesis was performed using the fragmented mRNA template and random hexamers as primers.Next, the double-stranded cDNA library was completed through a series of steps, including terminal repair, A-ligation, sequencing adaptor ligation, size selection, and PCR enrichment.

value: PBMC

value: Primary

value: GPC3 CAR Expressed in T-cell


title: DMSO_326_MED_H_R4

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

library_source: other

data_processing:
Base calling was performed by bcl2fastq v 2.20.422
Quality trimming was performed using fastp v0.23.2
Alignment was performed using STAR v2.7.10b
Gene counts were performed with qCount in the QuasR R package v1.38.0
Normalization was performed with DESeq2 v1.38.0
Assembly: Biospyder Human Whole Transcriptome Gene Set
Supplementary files format and content: count_table.tsv is a genes by samples count matrix of raw counts from the TempO-Seq data alignments.
Library strategy: TempO-Seq

molecule: other

source_name: liver tumor associated with chronic hepatitis C

growth_protocol: Cryopreserved differentiated HepaRGTM cells (Biopredic International, Saint-Grégoire, France) were cultivated according to the manufacturer’s protocol. Differentiated HepaRGTM cells were thawed and seeded into collagen-coated wells at a density of approximately 0.072 x 106 viable cells per well (i.e. 100 μL of the cell suspension per well) in 96-well plates, using HepaRGTM Thawing/Plating/General Purpose Medium 670 (ADD670C, Biopredic International, Saint-Grégoire, France). After 24h, the media were changed to HepaRGTM Maintenance Medium 620 (ADD620C, Biopredic International, Saint-Grégoire, France) for cell maintenance. Cells were incubated for 7 days at 37°C, 5% CO2 and saturating humidity.

extract_protocol:
Cell lysates were used directly for TempO-Seq library building
TempO-Seq® gene expression analysis was conducted on exposed and control HepaRGTM cell lysates. Libraries were prepared in a 96-well plate format using the TempO-Seq® Human Whole Transcriptome Panel reagent kit (BioSpyder Technologies, Carlsbad, CA, USA), following the manufacturer’s protocol. Human Brain Total RNA and qPCR Human Reference Total RNA (Takara Bio, CA, USA) were included as positive assay controls and a no-lysate control (1X TempO-Seq® R Lysis Buffer only) was included as a negative assay control (two replicates per control). In brief, 2 µl cell lysates were hybridized with the targeted detector oligo (DO) probe mix in 1X TempO-Seq® R Lysis Buffer for 10 min at 70oC followed by a temperature gradient with a ramp rate of 0.5oC/min to 45oC over a 50 min period, followed by a nuclease digestion at 37oC for 90 min to remove excess, unbound, or incorrectly bound DOs enzymatically. Ligation of the DO pairs bound to adjacent target sequences was then completed with a 60 min incubation at 37oC, immediately followed with a 15 min enzyme denaturation at 80oC to generate a pool of amplification templates. All amplification templates (i.e., 10 µl of ligated DOs) were transferred to its corresponding well of the 96-well PCR Pre-Mix and Primers plate. Amplification proceeded with a CFX96 Real-Time PCR Detection System (Bio-Rad, Mississauga, ON, Canada) to attach a unique sequence tag and the sequencing adaptors to each sample using the following PCR program settings: 37oC for 10 min, 95oC for 2 min; 6 cycles of 95oC for 30 sec, 54oC for 30 sec, 72oC for 120 sec; 16 cycles of 95oC for 30 sec; 72oC for 2 min; 72oC for 1 min. The TempO-Seq® libraries were pooled (5 µl of all 96 samples) and purified using the Macherey-Nagel NucleoSpin® Gel and PCR Clean-Up kit (Clontech Laboratories Inc., Bethlehem, PA, USA), according to the manufacturer’s instructions for PCR cleanup with three modifications outlined in the TempO-Seq® Assay User Guide. The pooled, purified TempO-Seq® libraries were sequenced using a NextSeq® 2000 High Output flow cell (v2 kit, 75 cycles) on an Illumina NextSeq® 2000 Sequencing platform (Illumina, San Diego, CA, USA).

treatment_protocol: At day 7, cells were exposed in triplicate to 5 concentrations of test chemical and refreshed with test chemical in HepaRGTM Induction Medium 640 (ADD640C, Biopredic International, Saint-Grégoire, France) daily for 72 hours (i.e., 3-day repeat exposures; 0 h, 24 h, 48 h). Cells were exposed to  glycidol (97, 291, 873, 1200 and 1402µM), methyl methanesulfonate (27, 81, 243.3, 400 and 500 µM) and nitrosodimethylamine (80, 240, 720, 2160 and 5454 µM). After 72 h exposure, cells were used to generate cell lysates for gene expression analysis (n = 3 per treatment group per assay for TempO-Seq®).

value: HepaRGTM

value: liver progenitor cells

tag: chemical short_form

value: DMSO

tag: chemical long_name

value: dimethylsulfoxide

tag: dose

tag: batch nr_heparg

tag: plate

value: Plate 1 index H

tag: well

tag: dose group

value: MED

value: H

tag: index

value: ACCTGAGGC

value: AGCTAGACC

tag: group

value: DMSO H

tag: replicate

tag: solvent control

value: T

tag: reference rna

value: F

tag: technical control

tag: chemical type

value: control

tag: cas-nr


title: Brain, 30 Months, Rep3

city: Kiel

first: Lena

last: Best

address: Michaelis-Straße 5

department: Institute of Experimental Medicine

country: Germany

institute: Christian-Albrechts-University Kiel

description:
30M.N3
Brain_30M_N3
brain_RNA_gene_counts.tsv.gz

data_processing:
Illumina TruSeq adapter sequences were trimmed from forward and reverse reads using Cutadapt (1.12) with minimum sequence overlap of 3 bp, at most 10% mismatches allowed and minimum read length filter for 20 bp, as well as a 3’-end quality trimming for a phred-score >=30.
An additional quality filter was applied with Prinseq lite (0.20.4) for at most 8 unknown nucleotides (‘N’) per read, an overall mean read quality of at least phred-score 15 and a minimum quality trim also from the 5’-end of the read for a minimum phred-score of 12.
Filtered reads were then mapped against Mus musculus reference genome (GRCm38.p6, mm10) via Hisat2 (2.1.0) with RNA strandedness set to FR, employing non-deterministic random seeds and suppressing the mixed alignments of read pairs. Only primary alignments for each read were kept, via a filtering step (-F 256) with Samtools (1.9).
Gene counts were extracted using HTSeq count (0.6.1) with reverse stranded information in union mode.
Assembly: GRCm38.p6 (mm10)
Supplementary files format and content: Tabular delimited matrix text files of read counts per GRCm38 gene (rows) and sample (columns).

molecule: polyA RNA

organism: Mus musculus

source_name: Brain

growth_protocol: All the mice were kept solely for aging in a controlled environment and  a controlled health status.

extract_protocol:
RNA was extracted from tissue samples of liver, colon and left brain hemisphere with the phenol-chloroform extraction method using for each tissue 1ml Qiazol Lysis Reagent (Qiagen, Hilden, Germany).
RNA was reverse transcripted into Illumina shotgun sequencing libraries at Competence Centre for Genomic Analysis (CCGA, Kiel Germany) with TruSeq RNA stranded kit (Illumina, San Diego, CA) with polyA enrichment according to the manufacturer’s instructions and sequenced for 2x75 cycles (2x100 for colon) in paired end mode with ~13 samples per lane on a HiSeq4000 machine. Demultiplexing was done with zero mismatches allowed in the barcodes.

tag: tissue

value: Brain

tag: strain

tag: Sex

value: Male

tag: age

value: 30 Months

tag: library batch

value: Run 1


title: Caco-2_pCDNA_3_1-Siglec12_2_S78

city: La Jolla, CA 92093

first: Pradipta

last: Ghosh

state: CA

address: 9500 Gilman Drive (MC 0651)

department: Departments of Medicine and Cellular and Molecular Medicine

institute: University of California San Diego

data_processing:
RNASeq data was processed using kallisto (version 0.45.0). Gene-level TPM values and gene annotations were computed using a custom Perl Script.
Assembly: Homo sapiens genome build hsGRCh38_94
Supplementary files format and content: tab-delimited text file includes log2 of TPM values

extract_protocol:
RNA extraction was done  using a commertial kit as per manufacturer’s protocol
RNA sequencing libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, except modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) Paired End (PE100) to a depth of approximately 25-40 million reads per sample on an Illumina NovaSeq 6000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).

tag: cell line

tag: treatment


title: Caco-2_pCDNA_3_1-Empty_Vector_4_S76

value: Control


title: Caco-2_pCDNA_3_1-Siglec12_4_S80


title: Caco-2_pCDNA_3_1-Siglec12_3_S79


title: Caco-2_pCDNA_3_1-Siglec12_1_S77


title: DMSO_303_MED_H_R3

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

tag: cell type

value: liver progenitor cells

tag: chemical short_form

tag: chemical long_name

tag: dose

tag: batch nr_heparg

tag: plate

tag: well

value: TAGCGACAA

value: TAAGTTACG


title: Caco-2_pCDNA_3_1-Empty_Vector_3_S75


title: Brain, 30 Months, Rep2

description:
30M.N2
Brain_30M_N2
brain_RNA_gene_counts.tsv.gz


title: Caco-2_pCDNA_3_1-Empty_Vector_2_S74


title: DMSO_330_MED_H_R3

value: DMSO

value: dimethylsulfoxide

value: Plate 1 index H

tag: dose group

value: MED

value: H

tag: index

value: ATTGGTTGC

tag: group

tag: replicate

tag: solvent control

tag: reference rna

tag: technical control


title: Caco-2_pCDNA_3_1-Empty_Vector_1_S73


title: DMSO_303_MED_H_R2

tag: tissue

value: ACCTGAGGC

value: TGCCGGTAT

value: DMSO H

value: T

value: F

tag: chemical type

value: control

tag: cas-nr


title: FT33, Replicate 2, Hi-ChIP

city: Los Angeles

first: Michelle

middle: Renee

last: Jones

address: 8720 Alden Dv

department: Biomedical Sciences

institute: Cedars-Sinai Medical Center

library_source: genomic

data_processing:
Sequencing reads from HiChIP libraries were filtered and the adapters were removed using cutadapt and mapped to the GRCh37 genome using HiC-Pro v2.11.0.  Replicates were merged together and the HiCPro output files were used for QC metrics and subsequent input for FitHiChIP.  FitHiChIP was used to call peaks from Hi-C Pro with default settings. This tool uses all reads from dangling ends, re-ligation and self-circle pairs and also all reads with Washington Epigenome browser
Assembly: GRCh37
Supplementary files format and content: allValidPairs
Library strategy: Hi-ChIP

molecule: genomic DNA

growth_protocol: Cells were grown to 80% confluency, detached with trypsin, strained through a 40 micron filter. The cell pellet was crosslinked with 1% formaldehyde (Sigma) that was freshly made for 10 minutes at room temperature with rotation and quenched with 125 mM of ice-cold glycine. Cells were pelleted, washed in PBS, flash frozen in liquid nitrogen and stored at -80°C.

extract_protocol:
HiChIP libraries were generated utilizing the Mumbach et al. protocol with the following modifications. All samples were processed as technical replicates. Cells were digested with MBoI for 4 hours and mixed intermittently.  After digestion, overhangs were filled in with DNA polymerase I, large Klenow fragment for 1 hour at 37 °C.  Samples were ligated using a T4 DNA ligase for 4 hours at room temperature, nuclei were lysed using Lysis buffer (PBS pH 7.4, 0.1% SDS, 0.137 M NaCl, 0.5% Na-deoxycholic acid, 1% NP-40) with protease inhibitor, and chromatin was sonicated for 5 minutes on a Covaris E220.  Sonicated chromatin was precleared in a mixture of protein A and G Dynabeads (Thermo Fisher A: 10002D, G: 10004D) and the remaining chromatin incubated in 5.6 µug of H3K27ac antibody (Diagenode C15410196) overnight.  Chromatin was then purified using a NucleoSpin PCR clean-up kit (Machery-Nagel 740609) and tagmented with Tn5 enzyme (Illumina 15027865) when captured with streptavidin beads and eluted.  Libraries were generated by PCR with a Phusion HF 2x Mastermix (BioLabs MO536S) using Nextera custom oligos.  A two-sided size selection with Ampure XP beads (Beckman Coulter, A63881) captured fragments between 300-700 bp.  Libraries were pooled and assessed by a shallow depth 2x150 bp paired-end sequencing run on an Illumina Miniseq, generating 1-5 million reads per replicate.  Full depth sequencing of the HiChIP pool was performed on the Illumina Novaseq at 2X150 bp, generating 300-400 million paired-end reads per sample.
All FT lines were cultured in DMEM:F12  (Corning, Cellgro) with 10% fetal bovine serum (FBS). Kuramochi cells were grown in RPMI 1640 (Gibco) with 10% FBS added.  UWB1.289 cells were grown in a 1:1 mixture of MEGM (DMEM:F12, 5% Horse Serum, 20 ng/mL epidermal growth factor, 0.5 mg/mL hydrocortisone, 100 ng/mL cholera toxin, 10 ug/mL insulin) and RPMI 1640.

tag: cell line

tag: cell type

value: Precursor


title: Brain, 30 Months, Rep1

description:
30M.N1
Brain_30M_N1
brain_RNA_gene_counts.tsv.gz

value: Brain

tag: strain

tag: Sex

value: Male

tag: age

value: 30 Months

tag: library batch

value: Run 2


title: FT33, Replicate 1, Hi-ChIP


title: FT246, Replicate 2, Hi-ChIP


title: DMSO_303_MED_H_R1

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

value: liver progenitor cells

tag: chemical short_form

value: DMSO

tag: chemical long_name

tag: dose

tag: batch nr_heparg

tag: plate

tag: well

value: AGCCGATTA

value: AACACAATC


title: FT246, Replicate 1, Hi-ChIP


title: PDO10_ZT12

city: Chicago

first: Deepak

last: Sharma

state: Illinois

address: 1653 W Congress Pkwy #12

institute: Rush University Medical Center

data_processing:
Reads from the RNA-Sequencing data were aligned to the Homo Sapiens genome assembly GRCh38 (mm10) using the STAR software
Duplicated aligned reads were marked and removed using the Picardtools software
The gene expression count data were extracted using the HTseq software
The raw count data were normalized, followed by log2 transformation. We filtered out genes with mean read counts < 6. All data preprocessing was performed using R software.
Assembly: hg38
Supplementary files format and content: tab-delimited txt files with feature counts per gene

source_name: Patient derived organoids of pancreatic cancer

growth_protocol: Pancreas cancer tissue was collected from untreated patients undergoing tissue biopsy at Rush University Medical Center. Immediately following the tissue acquisition, the samples were processed as previously described. Briefly, after digestion with collagenase-II, dispase-II, and DNase-I, biopsy tissues were washed several times and then plated in 50 µL Matrigel domes on a 24-welled plate supplemented with 500 µL organoid medium.

extract_protocol:
For RNA extraction, cells and organoids were cultured in a 6-well plate followed by dexamethasone treatment. 24 h after the synchronization, cells were collected and lysed with RLT buffer containing 1% 2-mercaptoethanol (Bio-Rad, CA). According to the instructions, RNA was isolated using RNeasy® extraction kit (Qiagen, Germany).
RNA concentration was measured using a NanoDrop 2000c spectrophotometer (Thermo Scientific, MA). cDNA was prepared from the purified RNA using a cDNA Reverse Transcription Kit (Applied Biosystems, United States).

treatment_protocol: Human pancreatic cell line AsPC-1 (ATCC Cat# CRL-1682TM) was cultured in Roswell Park Memorial Institute medium (RPMI-1640 ATCC Cat# 30-2001), PANC-1 (ATCC Cat# CRL-1469TM) and MIA PaCa-2 1 (ATCC Cat# CRL-1420TM) were cultured in Dulbecco's Modified Eagle's Medium (DMEM), Capan-1 (ATCC Cat# HTB-79TM) was cultured in Iscove's Modified Dulbecco's Medium (IMDM) Cat# 30-2005TM. All the cell culture media were supplemented with 10% FBS (except 20% for IMDM), and 1% penicillin-streptomycin, and cells were incubated in a humidified incubator at 37 °C with 5% CO2.

tag: treatment

value: Dexamethasone treatment

tag: time


title: Brain, 24 Months, Rep9

description:
24M.N9
Brain_24M_N9
brain_RNA_gene_counts.tsv.gz

tag: tissue

value: 24 Months


title: Brain, 24 Months, Rep8

description:
24M.N8
Brain_24M_N8
brain_RNA_gene_counts.tsv.gz


title: Kuramochi, Replicate 2, Hi-ChIP

source_name: Kuramochi

value: Kuramochi

value: HGSOC


title: UWB1-289, Replicate 2, Hi-ChIP


title: DMSO_330_MED_H_R1

value: dimethylsulfoxide

value: Plate 1 index H

tag: dose group

value: MED

value: H

tag: index

value: TCAGCTAAT

tag: group

value: DMSO H

tag: replicate

tag: solvent control

value: T

tag: reference rna

value: F

tag: technical control

tag: chemical type


title: Kuramochi, Replicate 1, Hi-ChIP

tag: cell line

tag: cell type


title: Brain, 24 Months, Rep6

description:
24M.N6
Brain_24M_N6
brain_RNA_gene_counts.tsv.gz

value: Brain

tag: strain

tag: Sex

value: Male

tag: age

tag: library batch

value: Run 2


title: DMSO_326_MED_H_R3

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

value: liver progenitor cells

tag: chemical short_form

value: DMSO

tag: chemical long_name

tag: dose

tag: batch nr_heparg

tag: plate

tag: well

value: TGCTTATTC

value: AATAGGTGC

value: control

tag: cas-nr


title: PBMC Cells, Middle aged, Male, Unstim, 43

city: IRVINE

first: Anshu

last: Agrawal

address: C-380 MED/SCI

department: Medicine/immunology

institute: University of California Irvine

data_processing:
Aligned to reference genomes GRCh38 with Strand NGS 3.1
Reads filtered on duplicates to remove PCR artifacts
Normalization of reads was performed using De-Seq method in Strand NGS 3.1
Assembly: GRCh38
Supplementary files format and content: tab-delimited textfile that includes normalized DESeq data

growth_protocol: PBMCs were purified from the blood using ficoll dendity gradient centrifugation

extract_protocol:
RNA was extracted using Zymo research RNA/DNA extraction kit
The input was 400ng by Nanodrop concentrations with 2.5min of fragmentation and 9 cycles of PCR.
Illumina TruSeq mRNA Stranded Kit

treatment_protocol: PBMCs were activated with irradiated SARS-CoV-2 virus for 24h

value: PBMC

tag: treatment

value: Unstim


title: DMSO_326_MED_H_R2

tag: tissue

value: dimethylsulfoxide

value: Plate 1 index H

tag: dose group

value: MED

value: H

tag: index

value: ATTCGAATC

value: TGTAACGGC

tag: group

tag: replicate

tag: solvent control

tag: reference rna


title: Brain, 24 Months, Rep7

description:
24M.N7
Brain_24M_N7
brain_RNA_gene_counts.tsv.gz

value: Brain

tag: strain

tag: Sex

value: Male

tag: age

value: 24 Months


title: Brain, 24 Months, Rep5

description:
24M.N5
Brain_24M_N5
brain_RNA_gene_counts.tsv.gz

tag: library batch

value: Run 2


title: PBMC Cells, Young, Female, Covid stim, 37

description: Y8_Cov stim_37_F

tag: cell type

value: Female

value: Cov stim


title: PBMC Cells, Young, Female, Unstim, 37


title: PBMC Cells, Middle aged, Male, Unstim, 56


title: DMSO_326_MED_H_R1

value: liver tumor associated with chronic hepatitis C

tag: cell line

value: HepaRGTM

value: liver progenitor cells

tag: chemical short_form

value: DMSO

tag: chemical long_name

tag: dose

tag: batch nr_heparg

value: ATCGCGACT

value: GCTGCGTAT

value: DMSO H

value: T

value: F

tag: technical control

tag: chemical type


title: Brain, 24 Months, Rep10

description:
24M.N10
Brain_24M_N10
brain_RNA_gene_counts.tsv.gz

tag: tissue


title: Brain, 24 Months, Rep4

description:
24M.N4
Brain_24M_N4
brain_RNA_gene_counts.tsv.gz


title: PBMC Cells, Aged, Male, Covid stim, 73 (2)

description: A8_Cov stim_73_M

value: PBMC

tag: treatment


title: PBMC Cells, Aged, Male, Unstim, 73 (2)

value: Unstim


title: DMSO_303_MED_E_R3

value: dimethylsulfoxide

tag: plate

value: Plate 2 index E

tag: well

tag: dose group

value: MED

value: E

tag: index

value: TAAGGTAGC

value: GACGCGTTA

tag: group

value: DMSO E

tag: replicate

value: control

tag: cas-nr


title: DMSO_330_MED_H_R2

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

tag: cell type

value: liver progenitor cells

value: Plate 1 index H

value: H

value: TGATTAAGC

value: TGCCGGTAT

tag: solvent control

tag: reference rna


title: PBMC Cells, Middle aged, Female, Covid stim, 55

description: M18_Cov stim_55_F

value: PBMC

tag: Sex

value: Female

tag: age

value: Cov stim


title: Brain, 24 Months, Rep3

description:
24M.N3
Brain_24M_N3
brain_RNA_gene_counts.tsv.gz

value: Brain

tag: strain

value: Male

value: 24 Months

tag: library batch

value: Run 2


title: UWB1-289, Replicate 1, Hi-ChIP

tag: cell line

value: HGSOC


title: PBMC Cells, Middle aged, Female, Unstim, 55

value: Unstim


title: DMSO_330_MED_E_R3

tag: tissue

tag: chemical short_form

value: DMSO

tag: chemical long_name

value: dimethylsulfoxide

tag: dose

tag: batch nr_heparg

value: Plate 2 index E

value: MED

value: E

value: ATTCGCTCT

value: GACGCGTTA

value: DMSO E

value: T

value: F

tag: technical control

tag: chemical type

value: control


title: PBMC Cells, Middle aged, Female, Covid stim, 42

description: M16_Cov stim_42_F

value: PBMC

value: Female

tag: treatment

value: Cov stim


title: PBMC Cells, Middle aged, Male, Covid stim, 56

description: M20_Cov stim_56_M

value: Male


title: PBMC Cells, Middle aged, Female, Unstim, 42


title: Brain, 24 Months, Rep1

description:
24M.N1
Brain_24M_N1
brain_RNA_gene_counts.tsv.gz

value: Brain

value: 24 Months

value: Run 2


title: PBMC Cells, Young, Female, Unstim, 24

value: Unstim


title: PBMC Cells, Young, Female, Covid stim, 24

description: Y6_Cov stim_24_F


title: DMSO_303_MED_E_R2

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

value: liver progenitor cells

value: DMSO

value: dimethylsulfoxide

tag: plate

value: Plate 2 index E

tag: well

tag: dose group

tag: index

value: TGCATGACA

value: TGCATCTGC

tag: group

tag: replicate

tag: cas-nr


title: Brain, 24 Months, Rep2

description:
24M.N2
Brain_24M_N2
brain_RNA_gene_counts.tsv.gz

tag: strain

tag: Sex

tag: age

tag: library batch


title: DMSO_330_MED_E_R2

tag: tissue

tag: cell line

tag: cell type

tag: chemical short_form

tag: chemical long_name

value: MED

value: E

value: ACTCATGTA

value: DMSO E

tag: solvent control

value: T

tag: reference rna

value: F

value: control


title: PBMC Cells, Middle aged, Female, Covid stim, 58 (2)

description: M14_Cov stim_58_F

value: PBMC

value: Female

tag: treatment

value: Cov stim


title: PBMC Cells, Aged, Female, Covid stim, 71

description: A6_Cov stim_71_F


title: Brain, 15 Months, Rep10

description:
15M.N10
Brain_15M_N10
brain_RNA_gene_counts.tsv.gz

value: Brain

value: Male

value: 15 Months

value: Run 1


title: DMSO_303_MED_E_R1

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

value: liver progenitor cells

value: DMSO

value: dimethylsulfoxide

tag: dose

tag: batch nr_heparg

tag: plate

value: Plate 2 index E

tag: well

tag: dose group

value: GACTTCATT

value: GACCTTGCT

tag: technical control

tag: chemical type


title: Brain, 15 Months, Rep9

description:
15M.N9
Brain_15M_N9
brain_RNA_gene_counts.tsv.gz

tag: strain

tag: Sex

tag: age


title: PBMC Cells, Aged, Female, Unstim, 71

value: Unstim


title: DMSO_330_MED_E_R1

tag: tissue

tag: cell line

value: MED

value: E

tag: index

value: GTTTATACT

tag: group

value: DMSO E

tag: replicate

value: T

value: F

value: control

tag: cas-nr


title: Brain, 15 Months, Rep8

description:
15M.N8
Brain_15M_N8
brain_RNA_gene_counts.tsv.gz

value: Brain

value: Male

value: 15 Months

tag: library batch

value: Run 1


title: PBMC Cells, Middle aged, Female, Covid stim, 57

description: M12_Cov stim_57_F

tag: cell type

value: PBMC

value: Female

tag: treatment

value: Cov stim


title: PBMC Cells, Aged, Male, Covid stim, 73 (1)

description: A4_Cov stim_73_M


title: Brain, 15 Months, Rep7

description:
15M.N7
Brain_15M_N7
brain_RNA_gene_counts.tsv.gz


title: DMSO_326_MED_E_R3

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

value: liver progenitor cells

tag: chemical short_form

value: DMSO

tag: chemical long_name

value: dimethylsulfoxide

tag: dose

tag: batch nr_heparg

tag: plate

value: Plate 2 index E

value: GAACTGTAT

value: AATTCGGAA

tag: solvent control

tag: reference rna


title: PBMC Cells, Middle aged, Male, Covid stim, 63

description: M10_Cov stim_63_M

tag: Sex

tag: age


title: DMSO_326_MED_E_R2

tag: tissue

tag: cell line

tag: well

tag: dose group

value: MED

value: E

value: GGGTTGTTA

value: AAGGTGTTT

value: DMSO E

value: T

value: F

tag: technical control

tag: chemical type


title: Brain, 15 Months, Rep6

description:
15M.N6
Brain_15M_N6
brain_RNA_gene_counts.tsv.gz

value: Brain

tag: strain

value: Male

value: 15 Months

tag: library batch

value: Run 1


title: PBMC Cells, Middle aged, Female, Covid stim, 58 (1)

description: M8_Cov stim_58_F

tag: cell type

value: PBMC

value: Female

tag: treatment

value: Cov stim


title: DMSO_326_MED_E_R1

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

value: liver progenitor cells

tag: chemical short_form

value: DMSO

tag: chemical long_name

value: dimethylsulfoxide

tag: dose

value: Plate 2 index E

tag: index

value: AAGACTCTT

value: GATGGTTGT

tag: group

tag: replicate

value: control

tag: cas-nr


title: PBMC Cells, Middle aged, Female, Unstim, 58 (1)

tag: Sex

tag: age

value: Unstim


title: Brain, 15 Months, Rep5

description:
15M.N5
Brain_15M_N5
brain_RNA_gene_counts.tsv.gz

tag: tissue

value: Brain


title: Brain_R_R_H_NA

tag: cell line

value: Brain reference RNA

tag: batch nr_heparg

tag: plate

value: Plate 1 index H

tag: well

tag: dose group

value: R

value: H

value: ATCGCGACT

value: TGTAACGGC

tag: solvent control

value: F

tag: reference rna

value: T

value: reference


title: PBMC Cells, Young, Male, Cov stim, 27

description: Y4_Cov stim_27_M

tag: cell type

value: PBMC

value: Male

tag: treatment

value: Cov stim


title: PBMC Cells, Middle aged, Female, Unstim, 58 (2)

value: Female


title: Brain, 15 Months, Rep4

description:
15M.N4
Brain_15M_N4
brain_RNA_gene_counts.tsv.gz

tag: strain

value: 15 Months

tag: library batch

value: Run 1


title: Brain_R_R_E_NA

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

value: liver progenitor cells

tag: chemical short_form

tag: chemical long_name

tag: dose

value: Plate 2 index E

value: E

tag: index

value: AAGACTCTT

value: AAGGTGTTT

tag: group

tag: technical control

tag: chemical type


title: PBMC Cells, Young, Male, Cov stim, 33

description: Y2_Cov stim_33_M

tag: Sex

tag: age


title: PBMC Cells, Young, Male, Unstim, 33

value: Unstim


title: Brain, 15 Months, Rep3

description:
15M.N3
Brain_15M_N3
brain_RNA_gene_counts.tsv.gz

tag: tissue

value: Brain


title: mitomycinC_C4 R3

description:
count_table.tsv
S_MMC_330_C4_SP0250_P01_H09

data_processing:
Base calling was performed by bcl2fastq v 2.20.422
Quality trimming was performed using fastp v0.23.2
Alignment was performed using STAR v2.7.10b
Gene counts were performed with qCount in the QuasR R package v1.38.0
Normalization was performed with DESeq2 v1.38.0
Assembly: Biospyder Human Human_S1500+Surrogate2.0 Gene Set
Supplementary files format and content: count_table.tsv is a genes by samples count matrix of raw counts from the TempO-Seq data alignments.
Library strategy: TempO-Seq

treatment_protocol: At day 7, cells were exposed in triplicate to 4 concentrations of test chemical and refreshed with test chemical in HepaRGTM Induction Medium 640 (ADD640C, Biopredic International, Saint-Grégoire, France) daily for 72 hours (i.e., 3-day repeat exposures; 0 h, 24 h, 48 h). Cells were exposed to mitomycin C (0.17, 0.5, 1.5, 4.5 µM), 4-nitroquinoline-N-oxide (0.9, 2.7, 8, 12 µM), aflatoxin B1 (0.025, 0.1, 0.5, 1.5 µM), colchicine (0.1, 0.3, 1, 3 µM), cyclophosphamide (78, 233, 700, 2100 µM), eugenol (60, 170, 500, 1000 µM) and 2-chloroethyltrimethylammoniumchloride (370, 1100, 3300 and 10000 µM). After 72 h exposure, cells were used to generate cell lysates for gene expression analysis (n = 3 per treatment group per assay for TempO-Seq®).

tag: cell line

value: MMC

value: mitomycinC

tag: batch nr_heparg

tag: well

tag: dose group

tag: replicate

value: F

value: test

tag: cas-nr


title: PBMC Cells, Middle aged, Male, Unstim, 55

tag: cell type

value: PBMC

value: Male

tag: treatment


title: Brain, 15 Months, Rep2

description:
15M.N2
Brain_15M_N2
brain_RNA_gene_counts.tsv.gz

tag: strain

value: 15 Months

tag: library batch


title: PBMC Cells, Aged, Female, Cov stim, 73

description: A2_Cov stim_73_F

value: Female

value: Cov stim


title: PBMC Cells, Aged, Male, Unstim, 73 (1)


title: PBMC Cells, Middle aged, Male, Cov stim, 55

description: M6_Cov stim_55_M


title: PBMC Cells, Aged, Female, Unstim, 73


title: Brain, 15 Months, Rep1

description:
15M.N1
Brain_15M_N1
brain_RNA_gene_counts.tsv.gz

value: Run 1


title: PBMC Cells, Middle aged, Male, Cov stim, 52

description: M4_Cov stim_52_M


title: mitomycinC_C2 R3

description:
count_table.tsv
S_MMC_330_C2_SP0250_P01_F09

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

value: liver progenitor cells

tag: chemical short_form

tag: chemical long_name

tag: dose

tag: solvent control

tag: reference rna


title: Brain, 9 Months, Rep10

description:
9M.N10
Brain_9M_N10
brain_RNA_gene_counts.tsv.gz

tag: Sex

tag: age

value: 9 Months

value: Run 2


title: PBMC Cells, Middle aged, Male, Unstim, 63

value: Unstim


title: PBMC cells, Middle aged, Female, Cov stim, 57

description: M2_Cov stim_57_F


title: PBMC Cells, Middle aged, Male, Unstim, 52


title: PBMC cells, Middle aged, Female, Unstim, 57


title: Brain, 9 Months, Rep9

description:
9M.N9
Brain_9M_N9
brain_RNA_gene_counts.tsv.gz

tag: tissue

value: Brain


title: Sel-eIF3 DMSO rep 2

city: Rehovot

first: Benjamin

last: Weiss

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute of Science

data_processing:
Trimming with cutadapt (CTGTAGGCACCATCAAT -m 16) and QC with TRIMMOMATIC (MINLEN:16 TRAILING:15 SLIDINGWINDOW:5:15).
Successive mapping to rRNAs, tRNAs with bowtie and lncRNAs (hg38) with HISAT2. Final mapping to transcriptome hg38, MANE Ensemble DB v108  with HISAT2.
Counts with FeatureCounts
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts values for each sample
Library strategy: TCP-seq

source_name: HEK 293T

growth_protocol: Humidified incubator at 37 degrees supplemented with 5% CO2

extract_protocol:
Selective TCP-seq protocol. Cells were crosslinked with 0.15% HCHO and lysed. Follow lysis, cell extract was digested with Rnase 1 and submitted to ultracentrifugation fractionation. Further, IP against eIF3 was performed. RNA was extracted by hot acid phenol extraction and library was prepared.
Ingolia et al, 2012
TCP-seq / 48S Footprinting

treatment_protocol: DMSO or 5 µM i14G1-12 for 1 hour at 37 C degrees

tag: cell line

value: HEK 293T

tag: genotype

value: WT

value: DMSO 1hr

tag: ip


title: mitomycinC_C1 R3

description:
count_table.tsv
S_MMC_330_C1_SP0250_P01_E09

value: MMC

value: mitomycinC

tag: batch nr_heparg

tag: well

tag: dose group

tag: group

tag: replicate

value: F

tag: technical control

tag: chemical type

value: test


title: PBMC Cells, Young, Male, Unstim, 27

tag: cell type

value: PBMC

value: Male

tag: treatment


title: mitomycinC_C4 R2

description:
count_table.tsv
S_MMC_328_C4_SP0250_P01_H05

tag: chemical short_form

tag: chemical long_name

tag: dose

tag: solvent control

tag: cas-nr


title: Sel-eIF3 DMSO  rep 1

tag: cell line


title: Brain, 9 Months, Rep8

description:
9M.N8
Brain_9M_N8
brain_RNA_gene_counts.tsv.gz

tag: tissue

tag: strain

tag: Sex

tag: age

tag: library batch

value: Run 1


title: Sel-eIF3 D12 rep 1

tag: genotype

tag: ip


title: Brain, 9 Months, Rep7

description:
9M.N7
Brain_9M_N7
brain_RNA_gene_counts.tsv.gz


title: mitomycinC_C2 R2

description:
count_table.tsv
S_MMC_328_C2_SP0250_P01_F05

value: liver tumor associated with chronic hepatitis C

tag: batch nr_heparg

tag: well

tag: dose group

tag: group

tag: replicate

tag: reference rna

tag: technical control


title: mitomycinC_C3 R2

description:
count_table.tsv
S_MMC_328_C3_SP0250_P01_G05

value: HepaRGTM

tag: cell type

tag: chemical short_form

tag: chemical long_name

tag: dose

tag: solvent control

tag: chemical type


title: Brain, 9 Months, Rep6

description:
9M.N6
Brain_9M_N6
brain_RNA_gene_counts.tsv.gz

tag: tissue

tag: strain

tag: Sex

tag: age


title: Sel-eIF2a D12 rep 2

extract_protocol:
Selective TCP-seq protocol. Cells were crosslinked with 0.15% HCHO and lysed. Follow lysis, cell extract was digested with Rnase 1 and submitted to ultracentrifugation fractionation. Further, IP against HA-eIF2a was performed. RNA was extracted by hot acid phenol extraction and library was prepared.
Ingolia et al, 2012
TCP-seq / 48S Footprinting

tag: cell line

tag: genotype

tag: treatment

tag: ip


title: Sel-eIF2a DMSO rep 1


title: mitomycinC_C3 R3

description:
count_table.tsv
S_MMC_330_C3_SP0250_P01_G09

value: liver progenitor cells

tag: batch nr_heparg

tag: well

tag: dose group

tag: group

tag: replicate

tag: cas-nr


title: Sel-eIF2a D12 rep 1


title: mitomycinC_C1 R2

description:
count_table.tsv
S_MMC_328_C1_SP0250_P01_E05

tag: cell type

tag: chemical short_form

tag: chemical long_name

tag: dose

tag: reference rna

tag: technical control


title: Brain, 9 Months, Rep5

description:
9M.N5
Brain_9M_N5
brain_RNA_gene_counts.tsv.gz

tag: tissue

tag: strain

tag: Sex

tag: age

value: 9 Months

tag: library batch


title: Sel-eIF3 D12 rep 2

tag: cell line

tag: genotype

tag: treatment

tag: ip


title: mitomycinC_C4 R1

description:
count_table.tsv
S_MMC_326_C4_SP0250_P01_D02

tag: batch nr_heparg

tag: well

tag: dose group

tag: group

tag: replicate

tag: solvent control

tag: chemical type


title: Brain, 9 Months, Rep4

description:
9M.N4
Brain_9M_N4
brain_RNA_gene_counts.tsv.gz


title: Sel-eIF4G1 DMSO rep 1

extract_protocol:
Selective TCP-seq protocol. Cells were crosslinked with 0.15% HCHO and lysed. Follow lysis, cell extract was digested with Rnase 1 and submitted to ultracentrifugation fractionation. Further, IP against eIF4G1 was performed. RNA was extracted by hot acid phenol extraction and library was prepared.
Ingolia et al, 2012
TCP-seq / 48S Footprinting


title: Sel-eIF4G1 DMSO rep 2


title: mitomycinC_C3 R1

description:
count_table.tsv
S_MMC_326_C3_SP0250_P01_C02

tag: cell type

tag: chemical short_form

tag: chemical long_name

tag: dose

tag: reference rna

tag: technical control

tag: cas-nr


title: Sel-eIF4G1 D12 rep 2

tag: cell line

tag: genotype


title: Sel-eIF4G1 D12 rep 3

tag: treatment

tag: ip


title: Brain, 9 Months, Rep3

description:
9M.N3
Brain_9M_N3
brain_RNA_gene_counts.tsv.gz

tag: tissue

tag: strain

tag: Sex

tag: age

tag: library batch


title: Brain, 9 Months, Rep2

description:
9M.N2
Brain_9M_N2
brain_RNA_gene_counts.tsv.gz


title: mitomycinC_C1 R1

description:
count_table.tsv
S_MMC_326_C1_SP0250_P01_A02

tag: batch nr_heparg

tag: well

tag: dose group

tag: group

tag: replicate

tag: solvent control

tag: chemical type


title: Sel-eIF4G1 D12 rep 1


title: Sel-eIF2a DMSO rep 2


title: Sel-eIF1HA DMSO rep 2

extract_protocol:
Selective TCP-seq protocol. Cells were crosslinked with 0.15% HCHO and lysed. Follow lysis, cell extract was digested with Rnase 1 and submitted to ultracentrifugation fractionation. Further, IP against HA was performed. RNA was extracted by hot acid phenol extraction and library was prepared.
Ingolia et al, 2012
TCP-seq / 48S Footprinting

value: HA


title: Sel-eIF1HA DMSO rep 3


title: Sel-eIF1HA DMSO rep 1


title: medium_MED R3

description:
count_table.tsv
S_MED_330_SP0250_P01_D09

tag: cell type

tag: chemical short_form

value: MED

tag: chemical long_name

value: medium

tag: dose

value: T

tag: reference rna

tag: technical control

value: control

tag: cas-nr


title: Sel-eIF4G1 DMSO rep 3

tag: cell line

value: HEK 293T

tag: genotype

value: WT

tag: treatment

value: DMSO 1hr

tag: ip


title: Sel-eIF1HA D12 rep 2


title: Brain, 2 Months, Rep10

description:
2M.N10
Brain_2M_N10
brain_RNA_gene_counts.tsv.gz

tag: tissue

value: Brain

tag: strain

tag: Sex

tag: age

value: 2 Months

tag: library batch

value: Run 2


title: Brain, 9 Months, Rep1

description:
9M.N1
Brain_9M_N1
brain_RNA_gene_counts.tsv.gz

value: Male


title: Sel-eIF1HA D12 rep 1


title: Sel-eIF1HA D12 rep 3


title: medium_MED R2

description:
count_table.tsv
S_MED_328_SP0250_P01_B09

tag: batch nr_heparg

tag: well

tag: dose group

tag: group

tag: replicate

tag: solvent control

value: F

tag: chemical type


title: shNRF2, 25 ug/mL CeO2 NP

city: Incheon

first: Jangyhun

last: Choi

state: Incheon

address: 5N521, 100 Inha-ro, Michuhol-gu

department: Department of biological sciences

country: South Korea

institute: Inha University

data_processing:
Raw sequencing reads were subjected to remove adapter sequences and low-quality reads using the Trimmomatic version 0.39 under the following parameters: ‘ILLUMINACLIP: TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36’.
The trimmed reads were aligned to the human genome reference GRCh38 (hg38) using HISAT2 version 2.2.1, employing the default parameters.
Reads with mapping quality score (MAPQ) > 30 were selected and converted to BAM format using SAMtools version 1.12 with the ‘-q 30 option’. PCR duplicates were then removed using the ‘rmdup’ function with the ‘-s’ option. The resulting BAM files were organized using the ‘sort’ function, applying the ‘-n’ option.
The resulting reads were assigned to transcripts and counted using htseq-count version 0.11.1 with the following parameters: ‘--strand=no --mode=intersection-nonempty -r name’.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files including raw count for each sample.

source_name: HaCaT

growth_protocol: Human HaCaT keratinocytes were maintained in DMEM (WelGene) supplemented with 10% FBS (WelGene) and 1% penicillin-streptomycin-glutamine solution (Hyclone) in humidified atmosphere with 5% CO2 at 37ºC.

extract_protocol:
Total RNA was prepared using an RNeasy mini plus kit (Qiagen) according to the manufacturer’s instructions.
Total RNAs were subjected to library preparation using the TruSeq RNA-seq kit (Illumina), and the resulting libraries were quantified using the Agilent Technologies 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: HaCaT cells were cultured until they reached 60% confluency, followed by exposure to 100 µM of H2O2 (Sigma) or 25 µg/mL of CeO2 NPs for a duration of 24 h. The CeO2 NPs were synthesized using a thermal method, as previously described (PMID: 33802993).

value: HaCaT

tag: cell type

value: Keratinocytes

value: NRF2 knockdown

value: 25 ug/mL CeO2 NPs


title: medium_MED R1

description:
count_table.tsv
S_MED_326_SP0250_P01_H01

value: liver tumor associated with chronic hepatitis C

tag: cell line

value: HepaRGTM

value: liver progenitor cells

tag: chemical short_form

tag: chemical long_name

tag: dose

tag: reference rna

tag: technical control

tag: cas-nr


title: Brain, 2 Months, Rep9

description:
2M.N9
Brain_2M_N9
brain_RNA_gene_counts.tsv.gz

tag: tissue

tag: strain

tag: Sex

tag: age


title: shNRF2, Untreated

tag: genotype

tag: treatment

value: Untreated


title: Brain, 2 Months, Rep8

description:
2M.N8
Brain_2M_N8
brain_RNA_gene_counts.tsv.gz

tag: library batch


title: Brain, 2 Months, Rep7

description:
2M.N7
Brain_2M_N7
brain_RNA_gene_counts.tsv.gz


title: eugenol_C4 R3

description:
count_table.tsv
S_EUG_330_C4_SP0250_P01_D12

value: EUG

value: eugenol

tag: batch nr_heparg

tag: well

tag: dose group

tag: group

tag: replicate

tag: solvent control

value: test


title: mitomycinC_C2 R1

description:
count_table.tsv
S_MMC_326_C2_SP0250_P01_B02

tag: cell line

tag: cell type

tag: chemical short_form

value: MMC

tag: chemical long_name

value: mitomycinC

tag: dose

tag: chemical type


title: shUTX, 100 uM H2O2

value: UTX knockdown


title: shNRF2, 100 uM H2O2


title: eugenol_C3 R3

description:
count_table.tsv
S_EUG_330_C3_SP0250_P01_C12

tag: tissue

tag: reference rna

tag: technical control

tag: cas-nr


title: shUTX, 25 ug/mL CeO2 NP

tag: genotype

tag: treatment


title: shMLL1, 25 ug/mL CeO2 NP

value: MLL1 knockdown


title: shMLL1, 100 uM H2O2


title: Brain, 2 Months, Rep6

description:
2M.N6
Brain_2M_N6
brain_RNA_gene_counts.tsv.gz

value: Brain

tag: strain

tag: Sex

value: Male

tag: age

value: 2 Months

tag: library batch

value: Run 2


title: eugenol_C2 R3

description:
count_table.tsv
S_EUG_330_C2_SP0250_P01_B12

tag: batch nr_heparg

tag: well

tag: dose group

tag: group

tag: replicate

tag: solvent control

value: F


title: shUTX, Untreated

tag: cell line

value: HaCaT

tag: cell type

value: Keratinocytes


title: shMLL1, Untreated


title: Brain, 2 Months, Rep5

description:
2M.N5
Brain_2M_N5
brain_RNA_gene_counts.tsv.gz

tag: tissue


title: eugenol_C1 R3

description:
count_table.tsv
S_EUG_330_C1_SP0250_P01_A12

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

tag: chemical short_form

tag: chemical long_name

tag: dose

tag: reference rna

tag: technical control

tag: chemical type


title: shControl, 25 ug/mL CeO2 NP

tag: genotype

value: WT

tag: treatment

value: 25 ug/mL CeO2 NPs


title: Brain, 2 Months, Rep4

description:
2M.N4
Brain_2M_N4
brain_RNA_gene_counts.tsv.gz

tag: strain

tag: Sex

tag: age

tag: library batch


title: shControl, 100 uM H2O2


title: eugenol_C4 R2

description:
count_table.tsv
S_EUG_328_C4_SP0250_P01_D08

value: liver progenitor cells

value: EUG

value: eugenol

tag: batch nr_heparg

tag: well

tag: dose group

tag: group

tag: replicate

tag: cas-nr


title: HaCaT, H3K27me3, 100 uM H2O2

data_processing:
Raw sequencing reads were processed using the Trimmomatic version 0.39 to remove adapter sequences and low-quality reads under the following parameters: ‘ILLUMINACLIP: TruSeq3-PE.fa:2:30:10, LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, and MINLEN:36’.
Bowtie2 was used to align trimmed reads with the human genome reference GRCh38 (hg38) on local mode (--local) with default parameters.
The resulting reads were subjected to three steps using SAMtools version 1.12. Initially, high-quality mapped reads (MAPQ > 30) were converted to BAM format using the ‘view -bh -q 30’ options. Subsequently, PCR duplicates were eliminated using the ‘rmdup’ function with its default parameters. Finally, the BAM files were organized and indexed using the ‘sort’ and ‘index’ functions, respectively.
The BAM files were converted to BED format using the bamToBed function from the Bedtools package version 2.30.0, employing the ‘-I’ option.
ChIP-seq coverage tracks (bigwig files) were created using the bamCoverage of deepTools package version 3.5.1, applying the parameters: ‘-bs 1 -e --normalizeUsing RPGC --effectiveGenomeSize 2700000000’,
Assembly: GRCh38/hg38
Supplementary files format and content: bigwig files

extract_protocol:
Cells were cross-linked with 1% formaldehyde (Sigma). Chromatins ranging from 200 and 700 base pairs were obtained following standard ChIP protocol. Chromatin (300 – 400 µg) was precleared with Protein A/G (Pierce) and incubated overnight with MLL1 (Bethyl, A300-086A), UTX (Abcam, ab36938), H3K4me3 (Abcam, ab8580), and H3K27me3 (Abcam, ab6002) antibodies. Immune complexes were reverse-crosslinked overnight. The resulting samples were treated with 10 µg of RNase A (Invitrogen) and 20 µg of Proteinase K (Invitrogen) and then ChIPed DNA was purified with phenol-chloroform solution (Sigma).
Libraries were prepared using the Illumina TruSeq ChIP Library Preparation Kit, and their quality, along with size distribution, was evaluated using a DNA 1000 chip on the Agilent Bioanalyzer 2100 system (Agilent Technologies).

treatment_protocol: HaCaT cells were cultured in 150 mm dishes until they reached 60% confluency, followed by exposure to 100 µM of H2O2 (Sigma) for a duration of 24 h.

tag: cell line

tag: cell type

tag: antibody

value: H3K27me3 (Abcam, ab6002)


title: shControl, Untreated

value: Untreated


title: eugenol_C3 R2

description:
count_table.tsv
S_EUG_328_C3_SP0250_P01_C08

tag: tissue

tag: chemical short_form

tag: chemical long_name

tag: dose

tag: solvent control

tag: reference rna

tag: technical control

value: test


title: HaCaT, H3K27me3, Untreated

tag: genotype

tag: treatment


title: Brain, 2 Months, Rep2

description:
2M.N2
Brain_2M_N2
brain_RNA_gene_counts.tsv.gz

value: Brain

tag: strain

tag: Sex

tag: age

tag: library batch


title: HaCaT, H3K4me2, 100 uMH2O2

value: H3K4me3 (Abcam, ab8580)


title: HaCaT, H3K4me3, Untreated


title: Brain, 2 Months, Rep1

description:
2M.N1
Brain_2M_N1
brain_RNA_gene_counts.tsv.gz

value: Male

value: 2 Months


title: HaCaT, UTX, 100 uM H2O2

value: UTX (Abcam, ab36938)


title: eugenol_C1 R2

description:
count_table.tsv
S_EUG_328_C1_SP0250_P01_A08

tag: batch nr_heparg

tag: well

tag: dose group

tag: group

tag: replicate

value: F

tag: chemical type

tag: cas-nr


title: HaCaT, MLL1, 100 uM H2O2

tag: cell line

value: HaCaT

tag: cell type

value: Keratinocytes

tag: antibody

value: MLL1 (Bethyl, A300-086A)


title: Liver, 30 Months, Rep12

description:
30M.N12
Liver_30M_N12
liver_RNA_gene_counts.tsv.gz

source_name: Liver

tag: tissue

value: Liver

value: 30 Months

value: Run 1


title: eugenol_C4 R1

description:
count_table.tsv
S_EUG_326_C4_SP0250_P01_H04

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

value: liver progenitor cells

tag: chemical short_form

value: EUG

tag: chemical long_name

tag: dose

tag: solvent control

tag: reference rna

tag: technical control


title: HaCaT, UTX, Untreated

tag: genotype

value: WT

tag: treatment

value: Untreated


title: Liver, 30 Months, Rep11

description:
30M.N11
Liver_30M_N11
liver_RNA_gene_counts.tsv.gz

tag: strain

tag: Sex

tag: age

tag: library batch


title: eugenol_C3 R1

description:
count_table.tsv
S_EUG_326_C3_SP0250_P01_G04

value: eugenol

tag: batch nr_heparg

tag: well

tag: dose group

tag: group

tag: replicate

tag: chemical type

value: test

tag: cas-nr


title: HaCaT, Input, Untreated

tag: cell line

tag: cell type

tag: antibody


title: WT, rep3

city: Shanghai

first: Guoyu

address: Xuhui District Yueyang Road 320

institute: PICB

data_processing:
raw sequencing reads were mapped to hg38/gencode v38 using hisat2
raw read counts were quantified using featureCounts
differential expression analysis were done by DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw counts for each sample

source_name: MDA-MB-231 PTX-resistant BCSC

extract_protocol:
Total RNA was extracted with TRIzol reagent (Invitrogen) and 1 μg was used for synthesis of first-strand cDNA with Maxima First Strand cDNA Synthesis Kit (Takara). 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prey Kit following manufacturer's protocols.

value: MDA-MB-231 PTX-resistant BCSC

value: Breast cancer stem cells


title: Liver, 30 Months, Rep10

description:
30M.N10
Liver_30M_N10
liver_RNA_gene_counts.tsv.gz

tag: tissue

value: Male

value: Run 2


title: eugenol_C2 R1

description:
count_table.tsv
S_EUG_326_C2_SP0250_P01_F04

tag: chemical short_form

tag: chemical long_name

tag: dose

tag: solvent control

value: F

tag: reference rna

tag: technical control


title: WT, rep2

tag: genotype


title: eugenol_C2 R2

description:
count_table.tsv
S_EUG_328_C2_SP0250_P01_B08

tag: batch nr_heparg

tag: well


title: WT, rep1


title: Brain, 2 Months, Rep3

description:
2M.N3
Brain_2M_N3
brain_RNA_gene_counts.tsv.gz

value: Brain

tag: strain

tag: Sex

tag: age

value: 2 Months

tag: library batch


title: Liver, 30 Months, Rep9

description:
30M.N9
Liver_30M_N9
liver_RNA_gene_counts.tsv.gz

value: Liver

value: 30 Months


title: LINC00115 KD, rep2

tag: cell line

value: LINC00115 knockdown


title: eugenol_C1 R1

description:
count_table.tsv
S_EUG_326_C1_SP0250_P01_E04

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

tag: cell type

tag: dose group

tag: group

tag: replicate

tag: chemical type

tag: cas-nr


title: LINC00115 KD, rep3


title: LINC00115 KD, rep1


title: non-BCSC, rep3

source_name: MDA-MB-231 PTX-resistant cells

extract_protocol:
By utilizing RNA as a template and random oligonucleotides as primers, the initial strand of cDNA was synthesized. Subsequently, RNaseH was utilized to degrade the RNA strand.
Within the DNA polymerase I system, dNTP with dUTP served as the raw material for the synthesis of the second strand of cDNA. The resultant double-stranded cDNA was purified, followed by double-end repair and introduction of an "A" base at the3' end to facilitate connection with the sequencing adapter. Alongside this process, USER enzyme was added to degrade the second strand of cDNA containing U.
lncRNA-seq

value: MDA-MB-231 PTX-resistant cells


title: Liver, 30 Months, Rep8

description:
30M.N8
Liver_30M_N8
liver_RNA_gene_counts.tsv.gz

tag: tissue

value: Run 1


title: dimethylsulfoxide_DMSO R3

description:
count_table.tsv
S_DMSO_330_SP0250_P01_C09

value: liver progenitor cells

tag: chemical short_form

value: DMSO

tag: chemical long_name

value: dimethylsulfoxide

tag: dose

tag: solvent control

value: T

tag: reference rna

value: control


title: Liver, 30 Months, Rep7

description:
30M.N7
Liver_30M_N7
liver_RNA_gene_counts.tsv.gz

tag: strain

value: Male


title: dimethylsulfoxide_DMSO R2

description:
count_table.tsv
S_DMSO_328_SP0250_P01_A09

tag: batch nr_heparg

tag: well

tag: technical control


title: non-BCSC, rep1

tag: cell line

value: Breast cancer stem cells


title: dimethylsulfoxide_DMSO R1

description:
count_table.tsv
S_DMSO_326_SP0250_P01_G01

tag: cell type

value: F


title: paclitaxel (PTX)-resistant MDA-MB-231 BCSC, rep3


title: Liver, 30 Months, Rep5

description:
30M.N5
Liver_30M_N5
liver_RNA_gene_counts.tsv.gz

tag: Sex

tag: age

tag: library batch


title: Liver, 30 Months, Rep6

description:
30M.N6
Liver_30M_N6
liver_RNA_gene_counts.tsv.gz


title: paclitaxel (PTX)-resistant MDA-MB-231 BCSC, rep2


title: HaCaT, MLL1, Untreated

value: HaCaT

value: Keratinocytes

tag: genotype

value: WT

tag: antibody

value: MLL1 (Bethyl, A300-086A)

tag: treatment

value: Untreated


title: paclitaxel (PTX)-resistant MDA-MB-231 BCSC, rep1


title: Liver, 30 Months, Rep4

description:
30M.N4
Liver_30M_N4
liver_RNA_gene_counts.tsv.gz

tag: tissue

value: Liver

value: 30 Months


title: MSC_1981_3

city: La Jolla

first: Robert

middle: E

last: Morey

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

description:
DESeq2_normalized_counts.csv
rawCounts_hgnc.csv

data_processing:
Reads were mapped to GRCh38.p10 (GENCODE release 26) using STAR (v. 2.7.3a) and annotated using featureCounts (subread v.1.6.3, GENCODE release 26 primary assembly annotation). The STAR parameters used were: --runMode alignReads --outSAMmode Full --outSAMattributes Standard --genomeLoad LoadAndKeep --clip3pAdapterSeq AGATCGGAAGAGC --clip3pAdapterMMp 1. The featureCounts parameters were: -s 2 -p -t exon -T 13 -g gene_id.
ENSEMBL genes without at least three samples with 10 or more reads were removed from analysis.
Normalization and differential expression analysis were performed using the R (v. 4.2.1) package DESeq2 (v. 1.36.0)89. BiomaRt (v. 2.42.1) was used to convert Ensembl gene ID’s to HUGO gene names90, and gene set enrichment analysis was done using the R(v. 4.2.1) package FGSEA (v. 1.22.0).
Assembly: GRCh38.p10
Supplementary files format and content: comma separated values text file contains raw counts for each sample
Supplementary files format and content: comma separated values text file contains DESeq2 normalized counts for each sample

growth_protocol: Derivation of the TSC line from primed hPSC was performed under a protocol approved by the UCSD Institutional Review Board and Embryonic Stem Cell Research Oversight Committee (ESCRO Protocol number: 171648).  Previously established and characterized primed-iPSCs, which preeclampsia (PE) with severe features showed placental pathologic findings of MVM, and control (non-PE) cases show absence of maternal hypertensive disease or fetal growth restriction, with no evidence of MVM or other placental disc lesions, were used in the study. pTSC was derived using the previously published protocol. In brief, primed-iPSC were cultured on Geltrex- (ThermoFisher) coated plates (using 1:200 diluted Geltrex) in StemFlex (ThermoFisher) or mTeSR Plus (Stem Cell Technologies). The cells were differentiated to trophectoderm (TE)-like cells using the first step of a previously established protocol. In brief, hPSCs were dissociated using TrypLE Express (ThermoFisher) and plated for 1.0 x105 cells/well of the 6 well plate coated with Geltrex (ThermoFisher) in the presence of 5μM Y-27632 (Selleck Chemicals). The next day, media was changed to first-step differentiation media: DMEM/F12 (ThermoFisher), with 1x ITS (Millipore-Sigma), 64μg/ml L-ascorbic acid (Millipore-Sigma), 543μg/ml NaHCO3 (Fisher Scientific), 2% BSA (Gemini), 10 ng/mL BMP4 (ThermoFisher), and 2μM IWP2 (Selleck Chemicals). Media was changed every day for 4 days. Conversion into TE-like cells was confirmed based on surface EGFR expression of over 90% by flow cytometry. Subsequently, cells were replated on collagen IV (Millipore Sigma, 5 μg/mL) in iCTB media: Advanced DMEM/F12 (ThermoFisher), 1X N2 (ThermoFisher), 1X B27 (ThermoFisher), 1X Glutmax (ThermoFisher), 150 μM 1-thioglycerol (Millipore Sigma), 0.05% BSA (Gemini), 1% knockout serum replacement (KSR; ThermoFisher), 2 μM CHIR99021 (Millipore Sigma), 0.5 μM A83-01 (Tocris), 1 μM SB431542 (Millipore Sigma), 5 μM Y27632 (Selleck Chemicals), 130 μg/mL VPA sodium salt (Millipore Sigma), 100 ng/mL recombinant human FGF2 (BioPioneer), 50 ng/mL recombinant human EGF (R&D Systems), 50 ng/mL recombinant human HGF (Stem Cell Technologies), and 20 ng/mL Noggin (R&D System). Cells were passaged for 5 times to derive primed-PSC derived TSC (pTSC). Cell purity were checked for surface expression of CTB marker (EGFR) and EVT marker (HLA-G) to ensured that the cells over 90% EGFR+, and less then 20% HLA-G+ cells. Naïve-iPSC was derived using previously published protocol84,85. In brief, primed-iPSC were seeded on a MEF feeder layer in mTeSR Plus under 5% O2 and 5% CO2. Two days later, media was switched to 5i/L/A, then after 7 to 10 days, cells were passaged using TrypLE Express on a MEF feeder layer under 5% O2 and 5% CO2. Cells were passaged for 6-8 times to establish naïve iPSC. Subsequently, cells were single cell dissociated using TryPLE Express, and  0.5-1.0x106 cells/well were seeded in one well of a 6-well plate coated with 5μg/mL Collagen IV initially in hTSC media for 5 passages, then transitioned to iCTB media for an additional 3-4 passages to derive nTSC.

extract_protocol:
Total RNA was isolated using mirVana RNA Isolation Kit (Ambion). RNA concentration was measured using Qubit RNA BR assay kit (ThermoFisher). RNA integrity was checked using RNA 6000 Nano chip read by a 2100 bioanalyzer (Agilent). All samples had a RIN above 8.0.
Total RNA was isolated using mirVana RNA Isolation Kit (Ambion). RNA concentration was measured using Qubit RNA BR assay kit (ThermoFisher). RNA integrity was checked using RNA 6000 Nano chip read by a 2100 bioanalyzer (Agilent). All samples had a RIN above 8.0.

treatment_protocol: Differentiation of TSCs into EVT were followed by modified Okae protocol. Prior to differentiation, TSCs were tested for the purity to ensure the starting cells are over 90% EGFR+, and less then 20% HLA-G+ cells. TSC were dissociated using TrypLE Express, and seeded for 2.0x105 cells per well of 6 well plate on 20 μg/ml fibronectin coated plate in 2 mL EVT basal media [DMEM/F12 no HEPES (ThermoFisher) supplemented with 0.1 mM 2-mercaptoethanol (ThermoFisher), 0.3% BSA, 1% ITS-X (ThermoFisher), 7.5 mM A83-01 (Tocris), 2.5 mM Y27632(Selleck Chemicals)] supplemented with 4% KSR (ThermoFisher), 100 ng/mL NRG1 (Abcam), and 2% Matrigel (Corning). On day 3, the media were replaced with EVT basal medium supplemented with 4% KSR, and 0.5% Matrigel. On day 5, cells were collected for the flow cytometric analysis, RNA-seq, and WGBS.

tag: progenitor type

value: primary

value: MSC

tag: disease state

value: preeclamptic

tag: fetal sex

value: Female


title: cyclophosphamide_C4 R3

description:
count_table.tsv
S_CPP_330_C4_SP0250_P01_H12

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

value: liver progenitor cells

tag: chemical short_form

value: CPP

tag: chemical long_name

value: cyclophosphamide

tag: dose

tag: dose group

tag: group

tag: replicate

tag: solvent control

tag: reference rna

tag: chemical type

value: test

tag: cas-nr


title: MSC_1981_1

tag: cell line

tag: cell type


title: Liver, 30 Months, Rep3

description:
30M.N3
Liver_30M_N3
liver_RNA_gene_counts.tsv.gz

tag: strain

tag: Sex

value: Male

tag: age

tag: library batch

value: Run 1


title: iPSC11_1981_Prime_iPSC_3

tag: progenitor type

value: prime

value: iPSC

tag: disease state

tag: fetal sex


title: iPSC11_1981_Prime_iPSC_2


title: Liver, 30 Months, Rep2

description:
30M.N2
Liver_30M_N2
liver_RNA_gene_counts.tsv.gz

tag: tissue


title: non-BCSC, rep2

value: MDA-MB-231 PTX-resistant cells

value: Breast cancer stem cells


title: iPSC11_1981_Prime_iPSC_1


title: iPSC11_1981_Prime_hTSC_3

value: hTSC


title: cyclophosphamide_C1 R3

description:
count_table.tsv
S_CPP_330_C1_SP0250_P01_E12

tag: chemical short_form

tag: chemical long_name

tag: dose

tag: batch nr_heparg

tag: well

tag: dose group

value: F

tag: technical control


title: Liver, 30 Months, Rep1

description:
30M.N1
Liver_30M_N1
liver_RNA_gene_counts.tsv.gz

value: Liver

value: 30 Months

value: Run 2


title: iPSC11_1981_Prime_hTSC_2

tag: cell line

value: preeclamptic

value: Female


title: iPSC11_1981_Prime_hTSC_1

tag: cell type


title: iPSC11_1981_Prime_EVT_3

value: EVT


title: Liver, 24 Months, Rep10

description:
24M.N10
Liver_24M_N10
liver_RNA_gene_counts.tsv.gz

tag: strain

value: 24 Months


title: Liver, 24 Months, Rep9

description:
24M.N9
Liver_24M_N9
liver_RNA_gene_counts.tsv.gz

tag: Sex


title: cyclophosphamide_C3 R3

description:
count_table.tsv
S_CPP_330_C3_SP0250_P01_G12

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

value: liver progenitor cells

value: CPP

value: cyclophosphamide

tag: group

tag: replicate

tag: solvent control

tag: reference rna

tag: chemical type

tag: cas-nr


title: iPSC11_1981_Prime_EVT_2

tag: progenitor type

value: prime

tag: disease state

tag: fetal sex


title: iPSC11_1981_Naive_iPSC_3

value: naive

value: iPSC


title: cyclophosphamide_C2 R2

description:
count_table.tsv
S_CPP_328_C2_SP0250_P01_F08

tag: tissue

tag: chemical short_form

tag: chemical long_name

tag: dose

tag: batch nr_heparg

value: test


title: cyclophosphamide_C1 R2

description:
count_table.tsv
S_CPP_328_C1_SP0250_P01_E08

tag: cell line

tag: cell type

tag: well

tag: dose group

value: F

tag: technical control


title: cyclophosphamide_C2 R3

description:
count_table.tsv
S_CPP_330_C2_SP0250_P01_F12

tag: group

tag: replicate

tag: solvent control


title: iPSC11_1981_Naive_iPSC_1


title: cyclophosphamide_C3 R2

description:
count_table.tsv
S_CPP_328_C3_SP0250_P01_G08

tag: reference rna

tag: chemical type

tag: cas-nr


title: MSC_1981_2

tag: progenitor type

value: primary

value: MSC

tag: disease state

tag: fetal sex


title: iPSC11_1981_Naive_hTSC_3

value: hTSC


title: iPSC11_1981_Naive_hTSC_2

value: preeclamptic


title: iPSC11_1981_Naive_iPSC_2

value: Female


title: Liver, 24 Months, Rep6

description:
24M.N6
Liver_24M_N6
liver_RNA_gene_counts.tsv.gz

tag: tissue

value: Liver

tag: strain

tag: Sex

value: Male

tag: age

tag: library batch

value: Run 2


title: cyclophosphamide_C4 R1

description:
count_table.tsv
S_CPP_326_C4_SP0250_P01_D05

value: liver tumor associated with chronic hepatitis C

tag: cell line

value: HepaRGTM

tag: cell type

tag: chemical short_form

tag: chemical long_name

tag: dose

tag: batch nr_heparg

tag: well


title: iPSC11_1981_Naive_hTSC_1


title: cyclophosphamide_C4 R2

description:
count_table.tsv
S_CPP_328_C4_SP0250_P01_H08

value: liver progenitor cells

value: CPP

tag: dose group

tag: group

tag: replicate

tag: solvent control

tag: reference rna

tag: technical control

tag: chemical type


title: iPSC11_1981_Naive_EVT_3

tag: progenitor type

value: EVT

tag: disease state

tag: fetal sex


title: iPSC11_1981_Naive_EVT_2

value: naive

tag: cell line


title: cyclophosphamide_C3 R1

description:
count_table.tsv
S_CPP_326_C3_SP0250_P01_C05

tag: tissue

tag: cell type

value: cyclophosphamide

tag: cas-nr


title: cyclophosphamide_C2 R1

description:
count_table.tsv
S_CPP_326_C2_SP0250_P01_B05

tag: chemical short_form

tag: chemical long_name

tag: dose

value: test


title: Liver, 24 Months, Rep4

description:
24M.N4
Liver_24M_N4
liver_RNA_gene_counts.tsv.gz

tag: strain

tag: Sex

tag: age

value: 24 Months

tag: library batch


title: MSC_1947_3

description:
DESeq2_normalized_counts.csv
rawCounts_hgnc.csv

value: primary

value: control


title: iPSC11_1981_Naive_EVT_1


title: MSC_1947_2

value: MSC


title: cyclophosphamide_C1 R1

description:
count_table.tsv
S_CPP_326_C1_SP0250_P01_A05

tag: batch nr_heparg

tag: well

tag: dose group

tag: group

tag: replicate

tag: solvent control

value: F

tag: reference rna


title: Liver, 24 Months, Rep8

description:
24M.N8
Liver_24M_N8
liver_RNA_gene_counts.tsv.gz

tag: tissue


title: Liver, 24 Months, Rep7

description:
24M.N7
Liver_24M_N7
liver_RNA_gene_counts.tsv.gz


title: Liver, 24 Months, Rep3

description:
24M.N3
Liver_24M_N3
liver_RNA_gene_counts.tsv.gz


title: MSC_1947_1

tag: progenitor type

tag: cell line

tag: cell type

tag: disease state

tag: fetal sex

value: Female


title: Liver, 24 Months, Rep2

description:
24M.N2
Liver_24M_N2
liver_RNA_gene_counts.tsv.gz

value: Liver

tag: strain


title: iPSC8_1947_Prime_iPSC_3

value: prime

value: iPSC


title: iPSC11_1981_Prime_EVT_1

value: preeclamptic


title: Liver, 24 Months, Rep5

description:
24M.N5
Liver_24M_N5
liver_RNA_gene_counts.tsv.gz

tag: Sex

value: Male

value: Run 2


title: colchicine_C4 R3

description:
count_table.tsv
S_COL_330_C4_SP0250_P01_D11

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

value: liver progenitor cells

tag: chemical short_form

value: COL

tag: chemical long_name

value: colchicine

tag: dose

tag: technical control

tag: chemical type

tag: cas-nr


title: iPSC8_1947_Prime_hTSC_2

value: hTSC


title: iPSC8_1947_Prime_hTSC_1


title: colchicine_C2 R3

description:
count_table.tsv
S_COL_330_C2_SP0250_P01_B11

tag: batch nr_heparg

tag: well

tag: dose group

tag: group

tag: replicate

value: test


title: Liver, 15 Months, Rep9

description:
15M.N9
Liver_15M_N9
liver_RNA_gene_counts.tsv.gz

tag: tissue

tag: age

value: 15 Months

tag: library batch

value: Run 1


title: Liver, 24 Months, Rep1

description:
24M.N1
Liver_24M_N1
liver_RNA_gene_counts.tsv.gz

value: 24 Months


title: iPSC8_1947_Prime_hTSC_3

tag: progenitor type

tag: cell line

tag: cell type

tag: disease state

value: control

tag: fetal sex

value: Female


title: colchicine_C3 R3

description:
count_table.tsv
S_COL_330_C3_SP0250_P01_C11

tag: chemical short_form

tag: chemical long_name

tag: dose

tag: solvent control

value: F

tag: reference rna


title: Liver, 15 Months, Rep10

description:
15M.N10
Liver_15M_N10
liver_RNA_gene_counts.tsv.gz

value: Liver

tag: strain

tag: Sex


title: iPSC8_1947_Prime_EVT_1

value: prime

value: EVT


title: iPSC8_1947_Prime_iPSC_1

value: iPSC


title: iPSC8_1947_Prime_EVT_3


title: colchicine_C1 R3

description:
count_table.tsv
S_COL_330_C1_SP0250_P01_A11

value: liver tumor associated with chronic hepatitis C

tag: batch nr_heparg

tag: well

tag: dose group

tag: group

tag: technical control

tag: chemical type

tag: cas-nr


title: iPSC8_1947_Prime_EVT_2

tag: progenitor type

tag: cell line

tag: cell type


title: Liver, 15 Months, Rep7

description:
15M.N7
Liver_15M_N7
liver_RNA_gene_counts.tsv.gz

tag: tissue

value: Male

tag: age

tag: library batch


title: colchicine_C3 R2

description:
count_table.tsv
S_COL_328_C3_SP0250_P01_C07

value: HepaRGTM

value: liver progenitor cells

tag: chemical short_form

tag: chemical long_name

tag: dose

tag: replicate

tag: solvent control


title: iPSC8_1947_Naive_hTSC_3

value: naive

tag: disease state

tag: fetal sex


title: iPSC8_1947_Naive_iPSC_2


title: iPSC8_1947_Prime_iPSC_2


title: Liver, 15 Months, Rep6

description:
15M.N6
Liver_15M_N6
liver_RNA_gene_counts.tsv.gz

tag: strain

tag: Sex


title: colchicine_C2 R2

description:
count_table.tsv
S_COL_328_C2_SP0250_P01_B07

value: COL

value: colchicine

tag: batch nr_heparg

tag: well

tag: dose group

tag: group

tag: reference rna

tag: technical control

tag: chemical type


title: iPSC8_1947_Naive_hTSC_2

description:
DESeq2_normalized_counts.csv
rawCounts_hgnc.csv

tag: progenitor type

tag: cell line

tag: cell type

value: hTSC


title: iPSC8_1947_Naive_hTSC_1


title: colchicine_C1 R2

description:
count_table.tsv
S_COL_328_C1_SP0250_P01_A07

tag: tissue

tag: chemical short_form

tag: chemical long_name

tag: dose

value: test

tag: cas-nr


title: Liver, 15 Months, Rep5

description:
15M.N5
Liver_15M_N5
liver_RNA_gene_counts.tsv.gz

tag: strain

tag: age

value: 15 Months

tag: library batch

value: Run 1


title: iPSC8_1947_Naive_EVT_2

tag: disease state

value: control

tag: fetal sex

value: Female


title: colchicine_C4 R1

description:
count_table.tsv
S_COL_326_C4_SP0250_P01_H03

tag: batch nr_heparg

tag: well

tag: dose group

tag: group

tag: replicate

tag: solvent control

value: F


title: iPSC8_1947_Naive_EVT_3

tag: progenitor type

tag: cell line

tag: cell type


title: colchicine_C4 R2

description:
count_table.tsv
S_COL_328_C4_SP0250_P01_D07

tag: tissue

tag: chemical short_form

tag: chemical long_name

tag: reference rna

tag: technical control

tag: chemical type


title: colchicine_C3 R1

description:
count_table.tsv
S_COL_326_C3_SP0250_P01_G03

tag: dose

tag: cas-nr


title: Liver, 15 Months, Rep8

description:
15M.N8
Liver_15M_N8
liver_RNA_gene_counts.tsv.gz

value: Liver

tag: strain

tag: Sex

tag: age

tag: library batch


title: MSC_1938_3

value: primary

value: MSC

tag: disease state

tag: fetal sex


title: iPSC8_1947_Naive_iPSC_3

tag: progenitor type

value: iPSC


title: colchicine_C2 R1

description:
count_table.tsv
S_COL_326_C2_SP0250_P01_F03

value: liver tumor associated with chronic hepatitis C

tag: cell line

tag: batch nr_heparg

tag: well

tag: dose group

tag: group

tag: replicate

tag: solvent control


title: MSC_1938_2

tag: cell type

value: Male


title: Liver, 15 Months, Rep2

description:
15M.N2
Liver_15M_N2
liver_RNA_gene_counts.tsv.gz

tag: tissue


title: Liver, 15 Months, Rep3

description:
15M.N3
Liver_15M_N3
liver_RNA_gene_counts.tsv.gz


title: iPSC8_1947_Naive_iPSC_1


title: iPSC3_1938_Prime_iPSC_3

value: prime


title: MSC_1938_1


title: iPSC3_1938_Prime_iPSC_2


title: Liver, 15 Months, Rep1

description:
15M.N1
Liver_15M_N1
liver_RNA_gene_counts.tsv.gz


title: iPSC3_1938_Prime_iPSC_1


title: Liver, 9 Months, Rep10

description:
9M.N10
Liver_9M_N10
liver_RNA_gene_counts.tsv.gz

value: 9 Months

value: Run 2


title: aflatoxinB1_C4 R3

description:
count_table.tsv
S_AFB1_330_C4_SP0250_P01_H10

value: HepaRGTM

value: liver progenitor cells

tag: chemical short_form

tag: chemical long_name

tag: dose

tag: reference rna

tag: technical control

tag: chemical type

tag: cas-nr


title: iPSC3_1938_Prime_hTSC_3

tag: progenitor type

value: hTSC

tag: disease state

tag: fetal sex


title: iPSC3_1938_Prime_hTSC_2

tag: cell line


title: iPSC3_1938_Prime_hTSC_1


title: iPSC8_1947_Naive_EVT_1

value: naive

value: EVT


title: Liver, 15 Months, Rep4

description:
15M.N4
Liver_15M_N4
liver_RNA_gene_counts.tsv.gz

tag: strain

tag: Sex

tag: age

value: 15 Months

tag: library batch

value: Run 1


title: Liver, 9 Months, Rep9

description:
9M.N9
Liver_9M_N9
liver_RNA_gene_counts.tsv.gz


title: aflatoxinB1_C3 R3

description:
count_table.tsv
S_AFB1_330_C3_SP0250_P01_G10

tag: cell type

tag: batch nr_heparg

tag: well

tag: dose group

tag: group

tag: replicate

tag: solvent control

value: F

value: test


title: iPSC3_1938_Prime_EVT_3

value: control


title: iPSC3_1938_Prime_EVT_2


title: iPSC3_AN1_Naive_iPSC_3

value: Female


title: aflatoxinB1_C2 R3

description:
count_table.tsv
S_AFB1_330_C2_SP0250_P01_F10

tag: tissue

tag: chemical short_form

tag: chemical long_name

tag: dose

tag: reference rna

tag: technical control

tag: chemical type


title: Liver, 9 Months, Rep7

description:
9M.N7
Liver_9M_N7
liver_RNA_gene_counts.tsv.gz

value: Liver

tag: strain

tag: Sex


title: aflatoxinB1_C1 R3

description:
count_table.tsv
S_AFB1_330_C1_SP0250_P01_E10

value: liver tumor associated with chronic hepatitis C

tag: cell line

tag: cas-nr


title: colchicine_C1 R1

description:
count_table.tsv
S_COL_326_C1_SP0250_P01_E03

tag: cell type

value: COL

value: colchicine

tag: batch nr_heparg


title: iPSC3_AN1_Naive_iPSC_2

description:
DESeq2_normalized_counts.csv
rawCounts_hgnc.csv

tag: progenitor type

value: iPSC

tag: disease state


title: iPSC3_AN1_Naive_hTSC_3


title: iPSC3_1938_Prime_EVT_1

value: prime

tag: fetal sex

value: Male


title: aflatoxinB1_C3 R2

description:
count_table.tsv
S_AFB1_328_C3_SP0250_P01_G06

value: HepaRGTM

value: liver progenitor cells

tag: well

tag: dose group

tag: group

tag: replicate

tag: solvent control


title: aflatoxinB1_C4 R2

description:
count_table.tsv
S_AFB1_328_C4_SP0250_P01_H06

tag: tissue

tag: chemical short_form

tag: chemical long_name

tag: dose

tag: reference rna


title: Liver, 9 Months, Rep6

description:
9M.N6
Liver_9M_N6
liver_RNA_gene_counts.tsv.gz

tag: strain

tag: Sex

tag: age

value: 9 Months

tag: library batch


title: iPSC3_AN1_Naive_hTSC_2

tag: progenitor type

value: naive

tag: cell line

tag: cell type

value: hTSC


title: Liver, 9 Months, Rep5

description:
9M.N5
Liver_9M_N5
liver_RNA_gene_counts.tsv.gz

value: Run 2


title: iPSC3_AN1_Naive_hTSC_1

tag: disease state


title: iPSC3_AN1_Naive_iPSC_1


title: aflatoxinB1_C2 R2

description:
count_table.tsv
S_AFB1_328_C2_SP0250_P01_F06

tag: batch nr_heparg

tag: well

tag: dose group

value: F

tag: technical control

tag: chemical type

tag: cas-nr


title: iPSC3_AN1_Naive_EVT_2

value: EVT


title: aflatoxinB1_C1 R2

description:
count_table.tsv
S_AFB1_328_C1_SP0250_P01_E06

tag: tissue

tag: chemical short_form

tag: chemical long_name

tag: group

tag: replicate

tag: solvent control

value: test


title: iPSC3_AN1_Naive_EVT_1

value: control

tag: Sex

value: Female


title: iPSC3_AN1_Naive_EVT_3

tag: progenitor type


title: Liver, 9 Months, Rep4

description:
9M.N4
Liver_9M_N4
liver_RNA_gene_counts.tsv.gz

value: Liver

tag: strain

tag: age

tag: library batch

value: Run 1


title: Liver, 9 Months, Rep8

description:
9M.N8
Liver_9M_N8
liver_RNA_gene_counts.tsv.gz


title: aflatoxinB1_C4 R1

description:
count_table.tsv
S_AFB1_326_C4_SP0250_P01_D03

value: liver tumor associated with chronic hepatitis C

tag: cell line

tag: cell type

tag: dose

tag: batch nr_heparg

tag: reference rna


title: MSC_1933_2

value: primary

value: MSC

tag: disease state

value: preeclamptic

tag: fetal sex


title: MSC_1933_1

value: Male


title: MSC_1933_3


title: aflatoxinB1_C3 R1

description:
count_table.tsv
S_AFB1_326_C3_SP0250_P01_C03

tag: tissue

value: HepaRGTM

value: liver progenitor cells

tag: chemical short_form

tag: well

tag: dose group

tag: technical control

tag: chemical type

tag: cas-nr


title: Liver, 9 Months, Rep2

description:
9M.N2
Liver_9M_N2
liver_RNA_gene_counts.tsv.gz

tag: strain

tag: Sex

value: 9 Months


title: Liver, 9 Months, Rep1

description:
9M.N1
Liver_9M_N1
liver_RNA_gene_counts.tsv.gz

tag: age

tag: library batch


title: aflatoxinB1_C2 R1

description:
count_table.tsv
S_AFB1_326_C2_SP0250_P01_B03

tag: cell line

tag: cell type

tag: chemical long_name

tag: group

tag: replicate

tag: solvent control


title: iPSC5_1933_Prime_iPSC_2

tag: progenitor type

value: prime

value: iPSC

tag: disease state

tag: fetal sex


title: iPSC5_1933_Prime_iPSC_3


title: Liver, 2 Months, Rep10

description:
2M.N10
Liver_2M_N10
liver_RNA_gene_counts.tsv.gz

tag: tissue

value: 2 Months

value: Run 2


title: iPSC5_1933_Prime_iPSC_1


title: Liver, 2 Months, Rep9

description:
2M.N9
Liver_2M_N9
liver_RNA_gene_counts.tsv.gz


title: iPSC5_1933_Prime_hTSC_3

value: hTSC


title: 4nitroquinolineNoxide_C4 R3

description:
count_table.tsv
S_4NNO_330_C4_SP0250_P01_D10

tag: chemical short_form

tag: dose

tag: batch nr_heparg

tag: well

tag: dose group

value: F

tag: reference rna

tag: technical control

value: test


title: 4nitroquinolineNoxide_C3 R3

description:
count_table.tsv
S_4NNO_330_C3_SP0250_P01_C10

tag: cell line

tag: chemical type

tag: cas-nr


title: aflatoxinB1_C1 R1

description:
count_table.tsv
S_AFB1_326_C1_SP0250_P01_A03

tag: cell type

tag: chemical long_name

tag: group


title: iPSC5_1933_Prime_EVT_2

description:
DESeq2_normalized_counts.csv
rawCounts_hgnc.csv

tag: progenitor type

value: EVT


title: iPSC5_1933_Prime_hTSC_1

tag: disease state


title: iPSC5_1933_Prime_EVT_3

tag: fetal sex


title: iPSC5_1933_Prime_hTSC_2


title: NativePrrx103

city: shanghai

first: hongshang

last: chu

address: 800 Dongchuan RD. Minhang District, Shanghai, China

institute: Shanghai Jiao Tong University

data_processing:
DNBs were transformed to single end 50 bases reads and sequencing on BGISEQ-500 platform (BGI-Shenzhen, China).
We used SOAPnuke (v1.5.2) to filter reads and generate FASTQ format
Then aligned clean reads to the reference mouse genome using the Bowtie2 (v2.2.5) with default parameters
calculated gene expression level with RSEM (v1.2.12)
Assembly: mm9
Supplementary files format and content: In GO analysis and pathway analysis, DEGs were classified according to official classification with the GO or KEGG annotation results and phyper (a function of R) was performed in GO and pathway functional enrichment.

source_name: chondrocyte

extract_protocol:
flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Sex

value: male

value: chondrocyte

tag: strain

tag: treatment

value: Native Prrx


title: Liver, 9 Months, Rep3

description:
9M.N3
Liver_9M_N3
liver_RNA_gene_counts.tsv.gz

tag: tissue

value: Liver

tag: age

tag: library batch

value: Run 1


title: Liver, 2 Months, Rep7

description:
2M.N7
Liver_2M_N7
liver_RNA_gene_counts.tsv.gz

value: Male


title: Liver, 2 Months, Rep6

description:
2M.N6
Liver_2M_N6
liver_RNA_gene_counts.tsv.gz


title: NativePrrx102


title: iPSC5_1933_Prime_EVT_1

value: preeclamptic


title: iPSC5_1933_Naive_iPSC_3

value: naive


title: 4nitroquinolineNoxide_C1 R3

description:
count_table.tsv
S_4NNO_330_C1_SP0250_P01_A10

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

value: liver progenitor cells

tag: chemical short_form

tag: dose

tag: batch nr_heparg

tag: well

tag: dose group

tag: replicate

tag: solvent control

tag: reference rna


title: NativePrrx101

tag: cell type


title: iPSC5_1933_Naive_iPSC_2

tag: progenitor type

tag: cell line

value: iPSC

tag: disease state


title: 4nitroquinolineNoxide_C4 R2

description:
count_table.tsv
S_4NNO_328_C4_SP0250_P01_D06

tag: chemical long_name

tag: group

tag: technical control

tag: chemical type

tag: cas-nr


title: Liver, 2 Months, Rep5

description:
2M.N5
Liver_2M_N5
liver_RNA_gene_counts.tsv.gz

tag: tissue

tag: strain

tag: Sex

tag: age

value: 2 Months

tag: library batch

value: Run 2


title: Liver, 2 Months, Rep4

description:
2M.N4
Liver_2M_N4
liver_RNA_gene_counts.tsv.gz


title: 4nitroquinolineNoxide_C3 R2

description:
count_table.tsv
S_4NNO_328_C3_SP0250_P01_C06

tag: chemical short_form

tag: dose

tag: batch nr_heparg

tag: well

tag: dose group

tag: replicate

value: F


title: iPSC5_1933_Naive_iPSC_1

tag: progenitor type

tag: cell line

tag: cell type

tag: disease state

tag: fetal sex


title: InjectPrrx102

tag: treatment

value: Inject Prrx


title: Liver, 2 Months, Rep8

description:
2M.N8
Liver_2M_N8
liver_RNA_gene_counts.tsv.gz

tag: tissue


title: 4nitroquinolineNoxide_C2 R2

description:
count_table.tsv
S_4NNO_328_C2_SP0250_P01_B06

tag: chemical long_name

tag: group

tag: solvent control

tag: reference rna

tag: technical control

tag: chemical type

value: test

tag: cas-nr


title: InjectPrrx101

tag: Sex

value: male

tag: strain


title: iPSC5_1933_Naive_hTSC_2

value: hTSC


title: iPSC5_1933_Naive_hTSC_1


title: Liver, 2 Months, Rep3

description:
2M.N3
Liver_2M_N3
liver_RNA_gene_counts.tsv.gz

tag: age

tag: library batch


title: iPSC5_1933_Naive_EVT_3

tag: progenitor type

tag: cell line

value: EVT


title: Liver, 2 Months, Rep2

description:
2M.N2
Liver_2M_N2
liver_RNA_gene_counts.tsv.gz

value: Liver


title: 4nitroquinolineNoxide_C2 R3

description:
count_table.tsv
S_4NNO_330_C2_SP0250_P01_B10

tag: cell type

tag: chemical short_form

tag: dose

tag: batch nr_heparg

tag: well

tag: dose group

tag: replicate


title: 4nitroquinolineNoxide_C1 R2

description:
count_table.tsv
S_4NNO_328_C1_SP0250_P01_A06

tag: tissue

tag: chemical long_name

tag: group

tag: solvent control

tag: reference rna


title: Liver, 2 Months, Rep1

description:
2M.N1
Liver_2M_N1
liver_RNA_gene_counts.tsv.gz

tag: strain

tag: Sex


title: 4nitroquinolineNoxide_C3 R1

description:
count_table.tsv
S_4NNO_326_C3_SP0250_P01_G02

tag: technical control

tag: chemical type

tag: cas-nr


title: Colon, 30 Months, Rep12

description:
30M.N12
Colon_30M_N12
colon_RNA_gene_counts.tsv.gz

source_name: Colon

value: Colon

tag: age

value: 30 Months

tag: library batch

value: Run 3


title: 4nitroquinolineNoxide_C4 R1

description:
count_table.tsv
S_4NNO_326_C4_SP0250_P01_H02

tag: cell line

tag: cell type

tag: chemical short_form

tag: dose


title: SAEC, NVP728, biological replicate 2, RNAseq

city: Hangzhou

first: Sida

last: Shao

address: 18 Shilongshan Rd, Xihu District

institute: Westlake University

data_processing:
bcl2fastq software used for basecalling. Quantification of transcript abundance was obtained from sequenced reads using Salmon v.0.7.2. Abundance measurements in transcripts per million (TPM) units were calculated at the gene-level.
Assembly: GRCh38 release 25 (GENCODE)
Supplementary files format and content: tsv files include measure of abundance in TPM (transcripts per million) units

source_name: lung

growth_protocol: Small airway epithelial cells(SAECs) were maintained in Small Airway Epithelial Cell Growth Medium from LONZA. For the experiments comparing effects of treatment, SAECs were maintained in minimal media as described in manuscript.

extract_protocol:
After 4-day treatment with compounds, cells were washed once with PBS and then trypsinized with 500 µL of TrypLE Express dissociation reagent (Gibco) and neutralized with the addition of 1 mL of growth medium. After pelleting cells with centrifugation (300g) for 3 minutes in 1.5 mL microfuge tubes, total RNA was isolated using a RNeasy kit (Qiagen).
Three biological replicates were submitted for library preparation at BGI.

treatment_protocol: SAECs were treated with DMSO or indicated growth factors and small molecules for 4 days.

value: lung

value: SAEC

tag: treatment

value: NVP728, 2 µM


title: SAEC, Saxagliptin, biological replicate 3, RNAseq

tag: tissue

value: Saxagliptin, 1 µM


title: SAEC, NVP728, biological replicate 3, RNAseq


title: iPSC5_1933_Naive_EVT_2

description:
DESeq2_normalized_counts.csv
rawCounts_hgnc.csv

tag: progenitor type

value: naive

tag: disease state

value: preeclamptic

tag: fetal sex

value: Male


title: Colon, 30 Months, Rep10

description:
30M.N10
Colon_30M_N10
colon_RNA_gene_counts.tsv.gz


title: 4nitroquinolineNoxide_C2 R1

description:
count_table.tsv
S_4NNO_326_C2_SP0250_P01_F02

extract_protocol:
Cell lysates were used directly for TempO-Seq library building
TempO-Seq® gene expression analysis was conducted on exposed and control HepaRGTM cell lysates. Libraries were prepared in a 96-well plate format using the TempO-Seq® Human Whole Transcriptome Panel reagent kit (BioSpyder Technologies, Carlsbad, CA, USA), following the manufacturer’s protocol. Human Brain Total RNA and qPCR Human Reference Total RNA (Takara Bio, CA, USA) were included as positive assay controls and a no-lysate control (1X TempO-Seq® R Lysis Buffer only) was included as a negative assay control (two replicates per control). In brief, 2 µl cell lysates were hybridized with the targeted detector oligo (DO) probe mix in 1X TempO-Seq® R Lysis Buffer for 10 min at 70oC followed by a temperature gradient with a ramp rate of 0.5oC/min to 45oC over a 50 min period, followed by a nuclease digestion at 37oC for 90 min to remove excess, unbound, or incorrectly bound DOs enzymatically. Ligation of the DO pairs bound to adjacent target sequences was then completed with a 60 min incubation at 37oC, immediately followed with a 15 min enzyme denaturation at 80oC to generate a pool of amplification templates. All amplification templates (i.e., 10 µl of ligated DOs) were transferred to its corresponding well of the 96-well PCR Pre-Mix and Primers plate. Amplification proceeded with a CFX96 Real-Time PCR Detection System (Bio-Rad, Mississauga, ON, Canada) to attach a unique sequence tag and the sequencing adaptors to each sample using the following PCR program settings: 37oC for 10 min, 95oC for 2 min; 6 cycles of 95oC for 30 sec, 54oC for 30 sec, 72oC for 120 sec; 16 cycles of 95oC for 30 sec; 72oC for 2 min; 72oC for 1 min. The TempO-Seq® libraries were pooled (5 µl of all 96 samples) and purified using the Macherey-Nagel NucleoSpin® Gel and PCR Clean-Up kit (Clontech Laboratories Inc., Bethlehem, PA, USA), according to the manufacturer’s instructions for PCR cleanup with three modifications outlined in the TempO-Seq® Assay User Guide. The pooled, purified TempO-Seq® libraries were sequenced using a NextSeq® 2000 High Output flow cell (v2 kit, 75 cycles) on an Illumina NextSeq® 2000 Sequencing platform (Illumina, San Diego, CA, USA).

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

value: liver progenitor cells

tag: chemical long_name

tag: batch nr_heparg

tag: well

tag: dose group

tag: group

tag: replicate

tag: solvent control

value: F

tag: reference rna


title: InjectPrrx103

tag: Sex

value: male

value: chondrocyte

tag: strain

value: Inject Prrx


title: iPSC5_1933_Naive_EVT_1

tag: cell line

tag: cell type

value: EVT


title: Colon, 30 Months, Rep11

description:
30M.N11
Colon_30M_N11
colon_RNA_gene_counts.tsv.gz

extract_protocol:
RNA was extracted from tissue samples of liver, colon and left brain hemisphere with the phenol-chloroform extraction method using for each tissue 1ml Qiazol Lysis Reagent (Qiagen, Hilden, Germany).
RNA was reverse transcripted into Illumina shotgun sequencing libraries at Competence Centre for Genomic Analysis (CCGA, Kiel Germany) with TruSeq RNA stranded kit (Illumina, San Diego, CA) with polyA enrichment according to the manufacturer’s instructions and sequenced for 2x75 cycles (2x100 for colon) in paired end mode with ~13 samples per lane on a HiSeq4000 machine. Demultiplexing was done with zero mismatches allowed in the barcodes.

value: Colon

tag: age

value: 30 Months

tag: library batch


title: SAEC, Saxagliptin, biological replicate 2, RNAseq

tag: tissue

value: lung

tag: treatment


title: 4nitroquinolineNoxide_C1 R1

description:
count_table.tsv
S_4NNO_326_C1_SP0250_P01_E02

tag: chemical short_form

tag: dose

tag: technical control

tag: chemical type

value: test

tag: cas-nr


title: MSC_1932_3

tag: progenitor type

value: primary

value: MSC

tag: disease state

tag: fetal sex

value: Female


title: Colon, 30 Months, Rep9

description:
30M.N9
Colon_30M_N9
colon_RNA_gene_counts.tsv.gz

value: Run 3


title: SAEC, Saxagliptin, biological replicate 1, RNAseq

value: SAEC

value: Saxagliptin, 1 µM


title: 2chloroethyltrimethylammoniumchloride _C4 R3

description:
count_table.tsv
S_2CTAC_330_C4_SP0250_P01_H11

value: liver tumor associated with chronic hepatitis C

value: HepaRGTM

tag: chemical long_name

tag: batch nr_heparg

tag: well

tag: dose group

tag: group

tag: replicate

tag: solvent control

tag: reference rna


title: iPSC5_1933_Naive_hTSC_3

value: naive

tag: cell line

tag: cell type

value: hTSC

value: preeclamptic

value: Male


title: Colon, 30 Months, Rep8

description:
30M.N8
Colon_30M_N8
colon_RNA_gene_counts.tsv.gz

tag: tissue

tag: strain

tag: Sex

tag: age

tag: library batch


title: 2chloroethyltrimethylammoniumchloride _C3 R3

description:
count_table.tsv
S_2CTAC_330_C3_SP0250_P01_G11

value: liver progenitor cells

tag: chemical short_form

tag: dose

value: F

tag: technical control

tag: chemical type

tag: cas-nr


title: Colon, 30 Months, Rep7

description:
30M.N7
Colon_30M_N7
colon_RNA_gene_counts.tsv.gz

value: Colon

value: 30 Months


title: SAEC, NVP728, biological replicate 1, RNAseq

value: lung

tag: treatment

value: NVP728, 2 µM


title: MSC_1932_2

tag: progenitor type

value: primary

value: MSC

tag: disease state

tag: fetal sex


title: MSC_1932_1

value: Female


title: SAEC, Sitagliptin, biological replicate 3, RNAseq

value: SAEC

value: Sitagliptin, 1 µM


title: 2chloroethyltrimethylammoniumchloride _C2 R3

description:
count_table.tsv
S_2CTAC_330_C2_SP0250_P01_F11

value: liver tumor associated with chronic hepatitis C

tag: chemical long_name

tag: batch nr_heparg

tag: well

tag: dose group

tag: group

tag: replicate

tag: solvent control

tag: reference rna

value: test


title: 2chloroethyltrimethylammoniumchloride _C1 R3

description:
count_table.tsv
S_2CTAC_330_C1_SP0250_P01_E11

tag: tissue

tag: cell line

value: HepaRGTM

tag: cell type

tag: chemical short_form


title: iPSC2_1932_Prime_iPSC_2

value: prime

value: iPSC


title: iPSC2_1932_Prime_iPSC_3

value: preeclamptic


title: SAEC, Sitagliptin, biological replicate 2, RNAseq


title: Colon, 30 Months, Rep5

description:
30M.N5
Colon_30M_N5
colon_RNA_gene_counts.tsv.gz

tag: strain

tag: Sex

value: Male

tag: age

tag: library batch

value: Run 3


title: SAEC, TGFb, biological replicate 3, RNAseq

tag: treatment

value: TGFb, 10 ng/mL


title: iPSC2_1932_Prime_iPSC_1

tag: progenitor type

tag: disease state

tag: fetal sex


title: 2chloroethyltrimethylammoniumchloride _C4 R2

description:
count_table.tsv
S_2CTAC_328_C4_SP0250_P01_H07

value: liver progenitor cells

tag: chemical long_name

tag: dose

tag: batch nr_heparg

tag: well

tag: dose group

value: F

tag: technical control

tag: chemical type

tag: cas-nr


title: Colon, 30 Months, Rep4

description:
30M.N4
Colon_30M_N4
colon_RNA_gene_counts.tsv.gz

tag: tissue

value: Colon

value: 30 Months


title: SAEC, Sitagliptin, biological replicate 1, RNAseq

value: lung

tag: cell type


title: SAEC, TGFb, biological replicate 2, RNAseq


title: iPSC2_1932_Prime_hTSC_3

tag: cell line

value: hTSC

value: Female


title: 2chloroethyltrimethylammoniumchloride _C3 R2

description:
count_table.tsv
S_2CTAC_328_C3_SP0250_P01_G07

tag: chemical short_form

tag: group

tag: replicate

tag: solvent control

tag: reference rna


title: Colon, 30 Months, Rep3

description:
30M.N3
Colon_30M_N3
colon_RNA_gene_counts.tsv.gz

tag: strain

tag: Sex

tag: age

tag: library batch


title: SAEC, TGFb, biological replicate 1, RNAseq

value: SAEC

tag: treatment


title: Colon, 30 Months, Rep2

description:
30M.N2
Colon_30M_N2
colon_RNA_gene_counts.tsv.gz


title: 2chloroethyltrimethylammoniumchloride _C2 R2

description:
count_table.tsv
S_2CTAC_328_C2_SP0250_P01_F07

value: liver tumor associated with chronic hepatitis C

tag: chemical long_name

tag: dose

tag: batch nr_heparg

tag: well

tag: dose group


title: Colon, 30 Months, Rep1

description:
30M.N1
Colon_30M_N1
colon_RNA_gene_counts.tsv.gz

tag: tissue


title: 2chloroethyltrimethylammoniumchloride _C1 R2

description:
count_table.tsv
S_2CTAC_328_C1_SP0250_P01_E07

tag: cell line

tag: cell type

tag: technical control

tag: chemical type

value: test

tag: cas-nr


title: iPSC2_1932_Prime_hTSC_1

description:
DESeq2_normalized_counts.csv
rawCounts_hgnc.csv

tag: progenitor type

tag: disease state

tag: fetal sex


title: Colon, 30 Months, Rep6

description:
30M.N6
Colon_30M_N6
colon_RNA_gene_counts.tsv.gz

tag: strain

tag: Sex

tag: age


title: Colon, 24 Months, Rep10

description:
24M.N10
Colon_24M_N10
colon_RNA_gene_counts.tsv.gz

value: 24 Months

tag: library batch


title: SAEC, IGF1, biological replicate 2, RNAseq

tag: treatment

value: IGF1, 5 ng/mL


title: 2chloroethyltrimethylammoniumchloride _C4 R1

description:
count_table.tsv
S_2CTAC_326_C4_SP0250_P01_D04

value: HepaRGTM

tag: chemical short_form

tag: chemical long_name

tag: dose

tag: batch nr_heparg

tag: group

tag: replicate

tag: solvent control

tag: reference rna


title: 2chloroethyltrimethylammoniumchloride _C3 R1

description:
count_table.tsv
S_2CTAC_326_C3_SP0250_P01_C04

tag: tissue

tag: cell line

tag: cell type

tag: well

tag: dose group

tag: technical control

tag: chemical type

tag: cas-nr


title: SAEC, IGF1, biological replicate 1, RNAseq

tag: treatment


title: Colon, 24 Months, Rep9

description:
24M.N9
Colon_24M_N9
colon_RNA_gene_counts.tsv.gz

tag: strain

tag: Sex

tag: age

tag: library batch


title: SAEC, DMSO, biological replicate 3, RNAseq

value: DMSO


title: Colon, 24 Months, Rep8

description:
24M.N8
Colon_24M_N8
colon_RNA_gene_counts.tsv.gz

value: Male


title: SAEC, DMSO, biological replicate 2, RNAseq


title: iPSC2_1932_Prime_EVT_1

tag: progenitor type

value: prime

value: EVT

tag: disease state

value: preeclamptic

tag: fetal sex