biostudies-arrayexpressEva WirthHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14973Thyroid hormones are important for many developmental processes. We evaluated the improvement of iPSC-derived hepatocyte-like cell maturation under hypoxic culture conditions, specialized cell culture media, and ±5 nM T3 during the final week of culture in two iPSC lines.biostudies-arrayexpressNucleic Acid Extraction - RNA from samples was extracted with Aurum™ Total RNA Mini Kit (Bio-Rad) according to manufacturer's instructions.Library Construction - Bulk RNA-seq libraries were generated using Poly(A) mRNA selection and prepared with the NEBNext Ultra II RNA Library Prep Kit for Illumina, following the manufacturer’s instructions.Sample Collection - On day 28 of differentiation, the cell culture medium was discarded, and cells were transferred and stored at -80 °C. On the day of RNA extraction, plates were thawed on ice, lysis buffer was added to the culture wells, and the surface was scraped to maximize lysate yield.Sequencing - Sequencing was performed using a paired-end configuration of 2x150 bp, generating approximately 25 million paired-end reads per sample on the Illumina platform.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Processing and analysis of RNA-seq data were performed using an established pipeline from BIH Core Unit Bioinformatics (1). Reads were mapped to GRCh38 (patch release 7) using the STAR aligner (v.2.7.10b; (2)) and counted using the featureCounts command (subreads v2.0.1; (3)) with GENCODE annotation (v25). 1. Pett P. SeA-SnaP: (Se)q (A)nalysis (Sna)kemake (P)ipeline. github.com/bihealth/seasnap-pipeline. Accessed April 26, 2024. 2. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15-21. 3. Liao Y, Smyth GK, and Shi W. The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Res. 2013;41(10):e108.UnknownTranscriptomicsGenomicsProteomicsIllumina HiSeq 3000RNA-seq of coding RNAHomo sapiensEva WirthfalseMaturation of iPSC-derived Hepatocyte-Like Cells with 5 nM T3Thyroid hormones are important for many developmental processes. We evaluated the improvement of iPSC-derived hepatocyte-like cell maturation under hypoxic culture conditions, specialized cell culture media, and ±5 nM T3 during the final week of culture in two iPSC lines.2025-07-31T00:00:00Z2025-03-26T10:08:57.446Z2025-03-26T10:08:57.446ZE-MTAB-14973ERP170844EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184