biostudies-arrayexpressSimon HenrietHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15864The goal of the experiment is to reveal splicing changes associated with the expression of U2AF2 splicing factors genes. U2AF2 constructs were transfected into HEK293-T cells and RNA was extracted for polyA transcriptome sequencing 3 days post transfection.biostudies-arrayexpressLibrary Construction - Barcoded sequencing libraries were prepared from poly-A+ RNA with the NEBNext Ultra II RNA Library Prep kit (NEB)Nucleic Acid Extraction - RNA was extracted with Trizol, and mRNA was enriched with Dynabeads mRNA Purification kit (Ambion)Sequencing - Pooled libraries were sequenced 150bp PE on a 1.5B NovaSeqXPlus flow cell at the Norwegian Sequencing Centre (Oslo, Norway)Sample Collection - Cells were harvested 3days post-transfection and washed with PBSOrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - We used Salmon v1.10.3 to quantify gene expression, and we conducted Differential Gene Expression (DGE) analysis with R packages tximport v1.32.0 and DeSeq2 v1.44.0. We determined AS events with two-pass STAR genome-aligned bam files using the rMATS turbo software v4.3.0 with --novelSS function enabled to allow the detection of novel splice sites. The AS events detected were filtered using a significance threshold of FDR ≤ 0.05.Sequence Alignment - Basic trimming of raw reads was performed with FastP v0.24.0 to remove adapter sequences and keep Q20 reads. The data was mapped with STAR v2.5.2b to H. sapiens GRCh38.p14 primary genome assembly using the latest gene annotation file retrieved from GENCODE. The mapping results were used to run an additional STAR two-pass mapping for further analysis of AS events.UnknownTranscriptomicsGenomicsProteomicsMolecular Biology laboratoryIllumina NovaSeq XMammalian cell culture laboratoryRNA-seq of coding RNAHomo sapiensSimon HenrietfalseRNA-seq of human HEK293-T cells expressing U2AF2 paralogues of Fritillaria borealisThe goal of the experiment is to reveal splicing changes associated with the expression of U2AF2 splicing factors genes. U2AF2 constructs were transfected into HEK293-T cells and RNA was extracted for polyA transcriptome sequencing 3 days post transfection.2026-06-11T00:00:00Z2026-06-11T07:14:51.73Z2025-10-24T16:35:16.772ZE-MTAB-15864ERP182999EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184