Transcriptome profiling of USP40-silenced mouse podocytes

USP40 is a deubiquitinating enzyme implicated in podocyte cytoskeletal organization and cellular homeostasis. To investigate the transcriptional consequences of USP40 depletion, conditionally immortalized mouse podocytes were transfected with two independent USP40-targeting siRNAs (siRNA#1 and siRNA#2) or a non-targeting control siRNA. Three independent biological replicates were prepared for each condition. Total RNA was extracted 48 hours after transfection, followed by poly(A)+ RNA enrichment and strand-specific library preparation. Paired-end RNA sequencing (2 × 36 bp) was performed on an Illumina NextSeq 500 platform, generating two FASTQ files (R1 and R2) per sample. Sequence reads were aligned to the Mus musculus reference genome (GRCm39), and gene-level raw read counts were generated. Differential expression analysis was conducted using DESeq2, and genes with adjusted p-value < 0.1 and |log2 fold change| > 0.3 were considered differentially expressed. To ensure biological robustness, downstream analyses focused on genes commonly altered in both independent siRNA-mediated knockdowns. This dataset provides insight into USP40-dependent transcriptional reprogramming toward an injury-prone, cytoskeleton-remodeling state in podocytes.