RNA-seq data from human umbilical vein endothelial cells (HUVECs)

This dataset contains bulk RNA-seq data generated from primary human umbilical vein endothelial cells (HUVECs) from Homo sapiens. Cells were allocated to three experimental groups: a control group (CK), a model group exposed to oxidised low-density lipoprotein (ox-LDL), and a treatment group (ox-LDLx). Each group contains three independent biological replicates, giving a total of nine RNA-seq libraries.<br>Total RNA was extracted from cultured HUVECs, and sequencing libraries were prepared with an approximate insert size of 380 bp. Libraries were sequenced on an Illumina NovaSeq platform in paired-end mode (2 × 150 bp), yielding around 15 Gb of clean data per sample after quality filtering. Reads were aligned to the human reference genome (GRCh38) and gene-level raw read counts were generated using standard tools. Gene-level expression values are provided as both raw counts and FPKM.<br>The following files are included in this figshare record:<br>1) HUVEC_RNAseq_counts_FPKM_with_annotation.xlsx- Gene-level expression matrix with functional annotation.- Rows correspond to genes. Columns include Ensembl gene identifiers, raw read counts and FPKM values for each of the nine samples (Control1–3, Model1–3, Treat1–3), together with gene name, description and external database identifiers (for example GO, KEGG and eggNOG, where available). Raw counts are suitable for downstream differential expression analyses, whereas FPKM values are provided for exploratory analyses and visualisation.<br>2) HUVEC_sample_metadata.tsv- Minimal sample-level metadata for the nine RNA-seq libraries.- Each row represents one sample. Columns include the sample identifier (matching the expression matrix), experimental group (Control, Model, Treatment), biological replicate number, cell type, species, treatment label (CK, ox-LDL, ox-LDLx), library identifier, approximate library insert size, sequencing platform and read type.<br>3) README_HUVEC_RNAseq.txt- A detailed description of the experimental design, sequencing and bioinformatic processing, together with guidance on file structure, typical usage and citation.<br>All experiments involving HUVECs were conducted under institutional ethics approval. The dataset does not contain any personally identifiable information and consists solely of aggregated gene expression measurements from cultured human endothelial cells.<br>Researchers can use the raw count columns for differential expression analysis with tools such as DESeq2 or edgeR, and the associated sample metadata to define the experimental design. The FPKM columns are useful for clustering, visualisation and exploratory transcriptomic profiling.<br>