{"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-15609"],"description":["Primary human hepatocytes from 3 different donors as 3D spheroids treated with AZD1979 (5 concentrations) and vehicle for 7 h.  Data for Figure 4 in connected publication."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - RNA was then isolated from cell lysate following the manufacturer’s instructions using the Biomek i7 Hybrid robotic workstation (Beckman Coulter).","Sample Collection - Cells were processed by aspirating the cell culture medium and adding the lysis buffer mixture, containing Proteinase K, from the RNAdvance Cell kit (Beckman Coulter) directly to the wells of a 96-well plate while maintained on ice. The resulting cell lysates were mixed thoroughly by pipetting and incubated at room temperature for 30 minutes.","Library Construction - mRNA was selectively enriched and sequencing libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche) according to the manufacturer’s recommended procedure, utilizing a Tecan Fluent® liquid handler for all automation steps. The integrity and size distribution of the resulting libraries were assessed on a Fragment Analyzer (Agilent) using the SS NGS fragment kit (1–6000 bp).","Sequencing - Sequencing was carried out on the Illumina NovaSeq 6000 platform (Illumina) with libraries loaded at a concentration of 1.75 nM according to the manufacturer's guidelines."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - RNA-seq data were processed and subjected to quality control using an internal Nextflow pipeline (v23.10). Reference genomes utilized included the human genome (GRCh38, Gencode v43). Sequencing reads were trimmed with FastP (v0.23.4) and transcript-level quantification was performed using Salmon (v1.10.1) following mapping to a transcriptome index comprising both cDNA and ncRNA entries. Quality control included STAR alignment (v2.7.11a) for mapping assessment and additional QC metrics were generated using FastQC (v0.12.1), RNAseQC (v2.3.5), and Samtools (v1.18), with results summarized in MultiQC (v1.17)."],"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":"RNA-seq data of primary human hepatocytes spheroids treated with AZD1979","description":"Primary human hepatocytes from 3 different donors as 3D spheroids treated with AZD1979 (5 concentrations) and vehicle for 7 h.  Data for Figure 4 in connected publication.","dates":{"release":"2026-01-16T00:00:00Z","modification":"2026-05-31T01:35:22.346Z","creation":"2025-09-19T16:17:36.649Z"},"accession":"E-MTAB-15609","cross_references":{"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"],"doi":["10.1038/s43856-025-01306-7"]}}