{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Saad Salman Khan Lodhi"],"instrument_platform":["Illumina HiSeq 2500","Standard molecular biology equipment (per Lexogen SENSE mRNA-seq kit protocol)","NanoDrop ND-1000 spectrophotometer; Agilent 2100 Bioanalyzer","Centrifuge (4 °C); ice/cold block"],"study_type":["RNA-seq of coding RNA"],"organism":["Mus musculus"],"species":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16537"],"description":["Doxorubicin (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."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Saad Salman Khan Lodhi"],"additional_accession":[]},"is_claimable":false,"name":"RNA-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 files","description":"Doxorubicin (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.","dates":{"release":"2026-02-28T00:00:00Z","modification":"2026-02-28T02:02:24.175Z","creation":"2026-01-16T18:00:57.928Z"},"accession":"E-MTAB-16537","cross_references":{"ENA":["ERP187664"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003738","EFO_0004184"]}}