biostudies-arrayexpressRobin XuHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16933Extrachromosomal DNA (ecDNA) is a major driver of oncogene amplification, intratumoural heterogeneity and rapid genetic change. We observe that ecDNA frequently undergoes segregation errors and is incorporated into micronuclei (MN) in ecDNA positive cancer cells. Different ecDNA species can coalesce into MN and lead to asymmetric inheritance. EcDNA in MN undergoes epigenetic changes and shows decreased oncogene transcription. Cells harbouring ecDNA-positive MN show prolonged cell cycle progression and an increased likelihood of cell death. Here we assess ecDNA oncogene transcription after hydroxyurea treatment. COLO 320DM cells were treated with 80 µM hydroxyurea or DMSO (vehicle control) for 3 days. RNA was extracted and subjected to mRNA library preparation and single-end sequencing.biostudies-arrayexpressLibrary Construction - RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina) at the Berlin Institute of Health (BIH) Genomics Technology Platform.Sequencing - Libraries were sequenced on the NovaSeq X Plus Platform (Illumina) in 100-nt single-end mode.Sample Collection - Cells were washed with 1x PBS, trypsinized (Gibco) and centrifuged at 300xg for 5 min and subjected for RNA extractionNucleic Acid Extraction - RNA was extracted using the RNeasy Mini Kit (Qiagen, 74104). Genomic DNA was removed by DNase treatment using the RNase-Free DNase Set (Qiagen,79254).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Reads were quality and adapter-trimmed using Trim Galore and aligned to the human reference assembly GRCh38 with an added EBV contig (NC_007605.1) using STAR (v2.7.11b) with parameters --twopassMode Basic --outSAMtype BAM SortedByCoordinate. Reads were counted per gene against GENCODE gene annotation (Release 47) using htseq(v2.0.5) htseq-count with parameters -r pos -s no.Data Transformation - Counts were normalized for library size and composition using sizefactors from DEseq(v1.38.3). Counts were z-score normalized for visualization using the scale function in R-base (v4.2.2). Geneset enrichment analysis (GSEA) was performed using Clusterprofiler (v4.6.2).MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq XRNA-seq of coding RNAHomo sapiensRobin XufalseRNAseq of the ecDNA-positive colon cancer cell line COLO 320DM with and without hydroxyurea treatmentExtrachromosomal DNA (ecDNA) is a major driver of oncogene amplification, intratumoural heterogeneity and rapid genetic change. We observe that ecDNA frequently undergoes segregation errors and is incorporated into micronuclei (MN) in ecDNA positive cancer cells. Different ecDNA species can coalesce into MN and lead to asymmetric inheritance. EcDNA in MN undergoes epigenetic changes and shows decreased oncogene transcription. Cells harbouring ecDNA-positive MN show prolonged cell cycle progression and an increased likelihood of cell death. Here we assess ecDNA oncogene transcription after hydroxyurea treatment. COLO 320DM cells were treated with 80 µM hydroxyurea or DMSO (vehicle control) for 3 days. RNA was extracted and subjected to mRNA library preparation and single-end sequencing.2026-07-02T00:00:00Z2026-07-02T14:19:15.855Z2026-04-20T13:24:06.394ZE-MTAB-16933ERP192364EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184