{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Alexandra Gatzios"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15891"],"description":["92 human skin-derived precursor (hSKP) cell lines, isolated from unique donors, were genotyped for the following SNPs that have been linked to metabolic dysfunction-associated steatotic liver disease (MASLD) onset and progression: PNPLA3 rs738409 C>G, TM6SF2 rs58542926 C>T, GCKR rs1260326 C>T and MBOAT7 rs641738 C>T. Based on carriage of these SNPs, the polygenic risk score for hepatic fat content (PRS-HFC) was calculated for each cell line and used for classification in either a low, intermediate or high risk category. From the low and high risk category, five cell lines were selected and differentiated to hepatic progenitor-like cells (hSKP-HPCs) before exposing the cells for 24 hours to either vehicle-matched control medium or a mixture of MASH-related triggers including sodium oleate, "],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Bulk RNA Barcoding and sequencing (BRB-seq) as published by Alpern et al 2019 (doi 10.1186/s13059-019-1671-x).","Library Construction - The sequencing libraries were built by tagmentation using 50 ng of ds cDNA with the Illumina Nextera XT Kit (Cat no. FC-131-1024) following the manufacturer’s recommendations.","Sample Collection - Samples were lysed directly in the cell culture vessels (Falcon 6-well Clear Flat Bottom Polystyrene) using Buffer RLT (QIAwave RNA Mini Kit, Cat no. 74534), supplemented with beta mercaptoethanol, and QIAshredder cell-lysate homogenizers (Cat no. 79656).","Nucleic Acid Extraction - Total RNA was extracted from adherent cells using the QIAwave RNA Mini Kit (Cat no. 74534) according to the manufacturer's protocols."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - The first read contains 16 bases that must have a quality score higher than 10. The first 6 bp correspond to a unique sample-specific barcode and the following 10 bp to a unique molecular identifier (UMI). The second reads were aligned to the homo sapiens reference transcriptome from the UCSC website (release hg38) using BWA version 0.7.4.4 with the parameter “-l 24”.","Data Transformation - Raw count matrices were generated and normalized with the DESeq2 package in R."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Alexandra Gatzios"],"additional_accession":[]},"is_claimable":false,"name":"BRBseq of human skin-derived precursor hepatic progenitor-like cells with varying polygenic risk score for hepatic fat content exposed in vitro to vehicle-matched control medium or triggers related to MASH","description":"92 human skin-derived precursor (hSKP) cell lines, isolated from unique donors, were genotyped for the following SNPs that have been linked to metabolic dysfunction-associated steatotic liver disease (MASLD) onset and progression: PNPLA3 rs738409 C>G, TM6SF2 rs58542926 C>T, GCKR rs1260326 C>T and MBOAT7 rs641738 C>T. Based on carriage of these SNPs, the polygenic risk score for hepatic fat content (PRS-HFC) was calculated for each cell line and used for classification in either a low, intermediate or high risk category. From the low and high risk category, five cell lines were selected and differentiated to hepatic progenitor-like cells (hSKP-HPCs) before exposing the cells for 24 hours to either vehicle-matched control medium or a mixture of MASH-related triggers including sodium oleate, ","dates":{"release":"2026-07-20T00:00:00Z","modification":"2026-07-20T13:09:22.803Z","creation":"2026-07-20T13:09:06.708Z"},"accession":"E-MTAB-15891","cross_references":{"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}