A numeric matrix containing filtered and normalized gene expression data from the Marthandan et al. (2016) study (GEO accession GSE63577).
Usage
data(counts_example)Details
Raw FASTQ files were downloaded using fasterq-dump (v2.11.0) and processed in a reproducible conda environment (Python v3.11.5).
Quality control was conducted using FastQC (v0.12.1) and summarised with MultiQC (v1.14). Pseudo-alignment to the RefSeq transcriptome (NCBI release 109)
was performed using kallisto (v0.44.0). Genes with low expression (mean count < 70 in all conditions) were filtered out. Count normalization factors were
calculated with edgeR::calcNormFactors, and log2-transformed values were obtained via limma::voom.
Intermediate time points for HFF and MRC5 cell lines were excluded, resulting in a final dataset with 45 high-quality samples across proliferative, quiescent, and senescent conditions.
For illustration and package size reduction, genes with variance in the bottom 10% across samples were removed, retaining the 90% most variable genes in the dataset.
References
Marthandan S, Priebe S, Baumgart M, Groth M et al. Similarities in Gene Expression Profiles during In Vitro Aging of Primary Human Embryonic Lung and Foreskin Fibroblasts. Biomed Res Int 2015;2015:731938. PMID: 26339636
Marthandan S, Baumgart M, Priebe S, Groth M et al. Conserved Senescence Associated Genes and Pathways in Primary Human Fibroblasts Detected by RNA-Seq. PLoS One 2016;11(5):e0154531. PMID: 27140416