{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["John Hellgren"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15601"],"description":["HepG2 treated with 40 compounds (3 concentrations, 0.1xCmax, Cmax and 10xCmax) and vehicle for 7 h. Compounds have different degree of drug-induced liver injury concern.   Data for Figure 2 in connected publication."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Reverse transcription (RT) primers containing unique molecular identifiers (UMIs) were dispensed into cell lysates using the Echo 665 instrument. An RT mix containing a Template Switching Oligo (TSO) was subsequently added to each well, and the reaction was incubated at 42°C for 2 hours. After incubation, material from individual wells was pooled and purified using the DNA Clean & Concentrator-100 kit (Zymo Research). The pooled sample was treated with Exonuclease I (ExoI) and further purified, then pre-amplified using DRUG-seq PCR primers. The resulting cDNA was tagmented using loaded Tn5 transposase (Diagenode) and indexed during the final PCR amplification. Final libraries underwent cleaning and size selection with SPRIselect beads. Library quality and concentration were assessed using Qubit (Thermo Fisher Scientific) and Fragment Analyzer (Agilent).","Nucleic Acid Extraction - With the DRUG-seq protocol, there is no requirement for nucleic acid extraction","Sequencing - Sequencing was conducted on the Illumina NovaSeq 6000 platform with a loading concentration of 1.85 nM and a custom primer utilized for Read 1.","Sample Collection - Following treatment, compound-containing media were aspirated and the cells were washed with phosphate-buffered saline (PBS). The cells were then lysed at room temperature for 15 minutes."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - DRUG-seq data were processed using an internal Snakemake pipeline (v5.14.0). Sequencing reads were trimmed for adapter sequences with cutadapt (v2.10), then aligned to the human genome using STARsolo (STAR v2.7.3a) for demultiplexing, with subsequent generation of a UMI count matrix. Quality control metrics were obtained with FastQC (v0.11.8), Qualimap (v2.2.2d), and RSeQC (v4.0.0), and QC results were summarized using MultiQC (v1.7)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_title":["Apoptotic signatures allow early and rapid screening of drug-induced liver injury to accelerate drug discovery"],"pubmed_authors":["John Hellgren","Bhavik Chouhan","Hellgren, J., Chouhan, B., Uatay, A., Elgendy, R., Lindgren, J., Toki, N., Bonetti, A., Chaudhari, A., Pryde, K., Andersson, P., Kalm, M., Karlsson, F., Sagemark, J., Williams, D., Tan, J., John, B., Gallon, J."],"additional_accession":[]},"is_claimable":false,"name":"DRUG-seq data of HepG2 treated with compounds","description":"HepG2 treated with 40 compounds (3 concentrations, 0.1xCmax, Cmax and 10xCmax) and vehicle for 7 h. Compounds have different degree of drug-induced liver injury concern.   Data for Figure 2 in connected publication.","dates":{"release":"2026-01-16T00:00:00Z","modification":"2026-05-27T16:10:21.739Z","creation":"2025-09-17T21:48:03.869Z"},"accession":"E-MTAB-15601","cross_references":{"ENA":["ERP180259"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"],"doi":["10.1038/s43856-025-01306-7"]}}