biostudies-arrayexpressMuntadher Al ZaidiHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16661This study investigates transcriptomic changes in human coronary artery endothelial cells (HCAEC) following siRNA-mediated gene silencing. Cells were transfected with either scrambled control siRNA or siRNA targeting VKORC1 or VKORC1L1. Total RNA was extracted and subjected to bulk RNA sequencing to assess differential gene expression profiles associated with loss of VKORC1 or VKORC1L1 function. The dataset enables analysis of gene expression changes related to vitamin K metabolism and downstream signaling pathways in endothelial cells.biostudies-arrayexpressSample Collection - Human coronary artery endothelial cells (HCAEC) were cultured under standard conditions and harvested at 24h point following siRNA transfection. Cells were washed with PBS and collected directly into lysis reagent (Trizol)for RNA isolation.Sequencing - Pooled libraries were sequenced on an Illumina instrument using standard sequencing-by-synthesis chemistry to generate FASTQ files. Base calling and demultiplexing were performed with the manufacturer’s software and default settings.Nucleic Acid Extraction - Total RNA was extracted using TRIzol–chloroform phase separation followed by isopropanol precipitation and ethanol washes. RNA was resuspended in RNase-free water and assessed for concentration, purity, and integrity prior to library preparation.Library Construction - RNA-seq libraries were prepared from total RNA using poly(A) mRNA enrichment and strand-specific library preparation. mRNA was fragmented, reverse transcribed, end-repaired, adapter-ligated, PCR-amplified, and quality-checked before sequencing.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Raw FASTQ files were quality-checked and adapter-trimmed prior to alignment to the Homo sapiens reference genome (GRCh38) using a splice-aware aligner. Gene-level read counts were generated based on annotated gene models. Downstream analysis was performed in R using DESeq2. Count data were normalized using the median-of-ratios method to account for library size differences. Variance-stabilizing transformation (VST) was applied for visualization and downstream exploratory analyses. Differential gene expression was calculated using a negative binomial generalized linear model, and multiple testing correction was performed using the Benjamini–Hochberg method to control the false discovery rate.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNAHomo sapiensMuntadher Al ZaidifalseRNA-Seq of HCAEC treated with siRNA against scrambled or VKORC1 or VKORC1L1This study investigates transcriptomic changes in human coronary artery endothelial cells (HCAEC) following siRNA-mediated gene silencing. Cells were transfected with either scrambled control siRNA or siRNA targeting VKORC1 or VKORC1L1. Total RNA was extracted and subjected to bulk RNA sequencing to assess differential gene expression profiles associated with loss of VKORC1 or VKORC1L1 function. The dataset enables analysis of gene expression changes related to vitamin K metabolism and downstream signaling pathways in endothelial cells.2026-02-17T00:00:00Z2026-02-17T17:44:26.078Z2026-02-13T14:47:47.061ZE-MTAB-16661ERP189120EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184