biostudies-arrayexpressAlma Sophia BarisaacHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16857To test the effect of LSm4 on RNA splicing and gene expression, we conducted RNA sequencing in U2OS cells treated with control or two LSm4-targeting siRNAs. In addition, we expressed either LSm4-WT or LSm4-del69-92 in U2OS cells treated with LSm4 siRNA #2.biostudies-arrayexpressSequencing - Sequencing was performed using Illumina NextSeq2000, using P3 XLEAP-SBS 300 cycles (Read1-150; Index1-8; Index2-8; Read2-150) (Illumina, cat no. 20100988) sequencing kit.Sample Collection - RNA was collected from 6-well plates using TRIzol reagent (Ambion) according to the manufacturer's protocol.Nucleic Acid Extraction - Total RNA was isolated using TRIzol reagent (Ambion) according to the manufacturer's instructions. In brief, chloroform was added and after vortexing, sample was centrifuged for 15 minutes at 12,000 x g, 4 degrees. Upper phase was collected, RNA was precipitated in -20 degrees using glyco blue and isopropanol, and the sample was then centrifuged for 15 minutes at 12,000 x g, 4 degrees. Then, samples were washed with ice-cold 70% ethanol and centrifuged for 5 minutes at 7,500 x g, 4 degrees. Pellet was dried and reconstituted in nuclease-free water on ice.Library Construction - RNA sequencing libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, cat no. E7760).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - For differential gene expression analysis, raw sequencing reads were aligned to GENCODE GRCh38 genome assembly using the splice-sensitive aligner HISAT2 (PMID: 25751142) and differential gene analysis was performed in R using the DESeq2 package (PMID: 25516281). Pathway enrichment analysis and gene ontology was conducted using ShinyGO (PMID: 31882993). To analyze alternative splicing events, HISAT2-aligned reads were subjected to alternative splicing events detection using rMATS package (PMID: 25480548).UnknownTranscriptomicsGenomicsProteomicsNextSeq 2000RNA-seq of coding RNAHomo sapiensAlma Sophia BarisaacfalseRNA-seq of U2OS cells treated with control or LSm4-targeting siRNAs, alone or with expression of either LSm4-WT or LSm4-del69-92To test the effect of LSm4 on RNA splicing and gene expression, we conducted RNA sequencing in U2OS cells treated with control or two LSm4-targeting siRNAs. In addition, we expressed either LSm4-WT or LSm4-del69-92 in U2OS cells treated with LSm4 siRNA #2.2026-04-15T00:00:00Z2026-04-17T01:01:35.282Z2026-04-02T12:47:15.914ZE-MTAB-16857ERP191730EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184