RNA-seq of CD146-positive vs CD146-negative cells isolated from human meniscus

This study aims to characterize the transcriptomic differences between CD146-positive and CD146-negative cells isolated from human meniscus tissues. Meniscus tissue samples were collected from total knee arthroplasty (TKA) patients lacking significant joint space narrowing. CD146-positive and CD146-negative cells were isolated from each patient's meniscus tissue, yielding a total of 6 samples (3 CD146-positive and 3 CD146-negative). Total RNA was extracted using Trizol reagent, and cDNA libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina following poly(A) mRNA selection. Libraries were sequenced on the DNBSEQ-T7 platform with 150 bp paired-end reads. Raw sequencing reads were quality-filtered and aligned to the human reference genome GRCh38 (Ensembl104) using HISAT2. Gene-level counts were obtained with HTSeq-count, and differentially expressed genes between CD146-positive and CD146-negative cells were identified using DESeq2 with thresholds of |fold change| > 2 and FDR < 0.05. Functional enrichment analyses including Gene Ontology (GO) and KEGG pathway analysis were performed to interpret the biological significance of the differentially expressed genes.