{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Frédéric Santer"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15987"],"description":["CDK12/13 are transcriptional cyclin-dependent kinases shown to phosphorylate the C-terminal domain of RNA polymerase II. Here, we investigated the changes on the transcriptome level after inhibition of CDK12/13 by the specific inhibitor SR-4835 in a panel of ovarian cancer cell lines: SK-OV-3, A2780, A2780 cis, Caov-3, Caov-3 cis. All cell lines were treated for 24h with 90 nM SR-4835 prior RNA extraction and paired-end RNA sequencing. Differential gene expression, Ingenuity pathway analysis and genes with alternative exon usage was determined."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - total RNA was extracted by the TriReagent-method and RNA quality was assessed using Bionanalyzer 2100.","Sample Collection - Ovarian cancer cell lines were seeded at 70% confluency in 6-wells in full growth medium. On the next day, cells were treated with 90 nM SR-4835 or vehicle (DMSO) for 24 hours.","Sequencing - The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount","Library Construction - Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Data analysis was performed in R (version 4.1.3). Read alignment (GENCODE release 39, GRCh38.p13) and counting were performed using the R subread package (version 2.8.2)."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Frédéric Santer"],"additional_accession":[]},"is_claimable":false,"name":"Transcriptomic changes after CDK12/13 inhibition by SR-4835 in ovarian cancer cell lines","description":"CDK12/13 are transcriptional cyclin-dependent kinases shown to phosphorylate the C-terminal domain of RNA polymerase II. Here, we investigated the changes on the transcriptome level after inhibition of CDK12/13 by the specific inhibitor SR-4835 in a panel of ovarian cancer cell lines: SK-OV-3, A2780, A2780 cis, Caov-3, Caov-3 cis. All cell lines were treated for 24h with 90 nM SR-4835 prior RNA extraction and paired-end RNA sequencing. Differential gene expression, Ingenuity pathway analysis and genes with alternative exon usage was determined.","dates":{"release":"2025-10-28T00:00:00Z","modification":"2026-05-27T16:08:20.975Z","creation":"2025-11-06T11:52:51.487Z"},"accession":"E-MTAB-15987","cross_references":{"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}