biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsSaad Salman Khan LodhiIllumina HiSeq 2500Standard molecular biology equipment (per Lexogen SENSE mRNA-seq kit protocol)NanoDrop ND-1000 spectrophotometer; Agilent 2100 BioanalyzerCentrifuge (4 °C); ice/cold blockRNA-seq of coding RNAMus musculusMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16537Doxorubicin (DOX) is a widely used chemotherapeutic agent that can cause off-target gastrointestinal (GI) toxicity. This experiment profiles DOX-induced transcriptomic responses by RNA-seq in mouse colonoids (in vitro) across dose and time. Mouse colonoids were sampled at 24, 48 and 72 h after exposure to 0 (vehicle control), 0.1 or 10 µM DOX. The resulting RNA-seq data support analysis of GI toxicity mechanisms in an in vitro mouse intestinal model. A matched mouse colon (in vivo) RNA-seq dataset is deposited separately and will be cross-referenced via accession in the manuscript and/or the related accession field.biostudies-arrayexpressNucleic Acid Extraction - Total RNA was extracted using the miRNeasy Mini Kit (Qiagen) following the manufacturer’s instructions. RNA quantity/purity were assessed by NanoDrop and RNA integrity was assessed by Agilent 2100 Bioanalyzer; samples with RIN > 6 and sufficient yield were used for library preparation.Sequencing - Libraries were sequenced on an Illumina HiSeq 2500 platform using 100-bp paired-end reads (PE100), according to the manufacturer’s standard protocols.Library Construction - mRNA sequencing libraries were prepared from total RNA using the Lexogen SENSE mRNA-seq library preparation kit, following the manufacturer’s instructions, including sample indexing for multiplexing.Sample Collection - After exposure (24/48/72 h), Matrigel domes were dissolved on ice with cold PBS and colonoids were pelleted by centrifugation (200 × g, 5–10 min, 4 °C). Pellets were transferred to RNAlater (4 °C overnight) and stored at −80 °C until RNA extraction.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesSaad Salman Khan LodhifalseRNA-seq transcriptomics of doxorubicin (DOX) exposure in mouse colonoids (in vitro; 0, 0.1, 10 µM; 24, 48, 72 h), with raw paired-end FASTQ filesDoxorubicin (DOX) is a widely used chemotherapeutic agent that can cause off-target gastrointestinal (GI) toxicity. This experiment profiles DOX-induced transcriptomic responses by RNA-seq in mouse colonoids (in vitro) across dose and time. Mouse colonoids were sampled at 24, 48 and 72 h after exposure to 0 (vehicle control), 0.1 or 10 µM DOX. The resulting RNA-seq data support analysis of GI toxicity mechanisms in an in vitro mouse intestinal model. A matched mouse colon (in vivo) RNA-seq dataset is deposited separately and will be cross-referenced via accession in the manuscript and/or the related accession field.2026-02-28T00:00:00Z2026-02-28T02:02:24.175Z2026-01-16T18:00:57.928ZE-MTAB-16537ERP187664EFO_0002944EFO_0004170EFO_0005518EFO_0003738EFO_0004184