biostudies-arrayexpressJurjun VeldeHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14664Deep RNA sequencing was performed to investigate the impact of CLKs inhibitor, T-025, on RNA splicing in triple-negative breast cancer cell lines. A total of 30 million MDA-MB-231 cells were seeded in a 6-well plate. The following day, cells were treated with 1 µM T-025 or 0.1% DMSO as negative control for 24 hours. Samples from 3 biological replicates were used. Total RNA was isolated using the RNeasy plus mini kit (Qiagen). Stranded PolyA-selected libraries were prepared using the DNBseq platform, and 100 M 150-bp paired-end reads were sequenced on a DNBSEQ-G400 sequencer by BGI Europe. The differentially expressed genes (DEGs) and alternative splicing events (ASEs) were analyzed to unravel the transcriptomic changes in TNBC cells upon T-025 treatment.biostudies-arrayexpressSample Collection - A total of 30 million MDA-MB-231 cells were seeded in a 6-well plate. The following day, cells were treated with 1 µM T-025 or 0.1% DMSO for 24 hours.Nucleic Acid Extraction - Total RNA was isolated using the RNeasy plus mini kit (Qiagen). Samples from 3 biological replicates were used. RNA quality and quantity were measured on an Agilent-4200 Bioanalyzer.Library Construction - Stranded PolyA-selected libraries were prepared using the DNBseq platform.Sequencing - 100 M 150-bp paired-end reads were sequenced on a DNBSEQ-G400 sequencer by BGI Europe.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Count data were normalized, and log2 fold change and adjusted p-value were calculated using the DESeq2 package (version 1.44.0). Differentially expressed genes (DEGs) were selected with a threshold of log2 fold change greater than 1 or less than -1 and an adjusted p-value less than 0.01 and used for GO enrichment analysis using the DAVID Gene Functional Classification Tool[22]. Alternative splicing events were analyzed using rMATS package (version 4.2.0). The significantly changed alternative splicing events (ASEs) were determined by average read counts in two samples (greater than 10), the absolute value of the difference for percentage spliced‐in value (|ΔPSI|) (greater than 0.1) and statistical significance of the change (FDR < 0.01). For GO enrichment analysis, we selected the ASEs with |ΔPSI| > 0.4 and FDR < 0.01.Sequence Alignment - Reads were aligned against the human GRCH38 reference genome (gencode version 45) using the STAR aligner (version 2.7.11b). Gene expression quantification was performed concurrently during mapping with the STAR --quantMode option set to GeneCounts.UnknownTranscriptomicsGenomicsProteomicsDNBSEQ-G400RNA-seq of coding RNAHomo sapiensBob WaterSylvia DévédecJurjun VeldeNasi LiufalseRNA-seq of human breast cancer cell line MDA-MB-231 treated with T025 against untreated controlsDeep RNA sequencing was performed to investigate the impact of CLKs inhibitor, T-025, on RNA splicing in triple-negative breast cancer cell lines. A total of 30 million MDA-MB-231 cells were seeded in a 6-well plate. The following day, cells were treated with 1 µM T-025 or 0.1% DMSO as negative control for 24 hours. Samples from 3 biological replicates were used. Total RNA was isolated using the RNeasy plus mini kit (Qiagen). Stranded PolyA-selected libraries were prepared using the DNBseq platform, and 100 M 150-bp paired-end reads were sequenced on a DNBSEQ-G400 sequencer by BGI Europe. The differentially expressed genes (DEGs) and alternative splicing events (ASEs) were analyzed to unravel the transcriptomic changes in TNBC cells upon T-025 treatment.2026-01-01T00:00:00Z2026-01-01T02:02:08.451Z2025-04-15T15:54:36.897ZE-MTAB-14664ERP171667EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184