Chromosome 20 RNA-seq Analysis: TDP-43 Knockout vs Wild-Type Rescue

We analyzed RNA-seq data from TDP-43 knockout (KO) and wild-type rescue (WT) HeLa cells, focusing on chromosome 20 genes. Using a standard bioinformatics pipeline (FastQC, fastp, Salmon, DESeq2), we identified 14 differentially expressed genes (DEGs) on chr20 (adjusted p < 0.05, |log ₂ FC| ≥ 1). Of these, 12 were upregulated and 2 were downregulated in KO cells. The upregulated genes included transcription factors ( FOXS1 , MAFB ), signaling molecules ( SIRPA , PLCB1 ), and ion channel KCNG1 . The downregulated genes were TSHZ2 (a transcriptional repressor) and ENSG00000289720 . Gene Ontology enrichment analysis revealed significant terms related to interleukin-12 response, monocyte extravasation, and negative regulation of transcription. These results show that TDP-43 loss disrupts gene regulatory and immune-related networks even within a single chromosome.