RNA-seq analysis of p62 knockout in murine oral carcinoma MOC2 cells

p62/SQSTM1 is an autophagy adaptor protein that regulates stress responses and contributes to tumor progression. To clarify its role in oral cancer, we generated p62 knockout clones of the murine oral carcinoma cell line MOC2 using CRISPR-Cas9. RNA-seq was performed on parental and p62-deficient cells to assess transcriptomic changes associated with p62 loss. The dataset includes raw FASTQ files and processed gene-level count matrices, providing a resource for the study of p62-dependent molecular pathways in cancer biology. Overall design: Bulk RNA-seq was performed on the murine oral carcinoma cell line MOC2 to compare transcriptomes of parental versus p62 knockout cells. Three biological replicates were generated per condition (n = 6 total). RNA was extracted using the RNeasy Mini Kit (Qiagen). Poly(A) RNA was isolated with the NEBNext Poly(A) mRNA Magnetic Isolation Module, and stranded libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Sequencing was performed on an Illumina NextSeq 2000 using NextSeq 1000/2000 P2 Reagents (100 Cycles, v3; cat. no. 20046811) to generate 2 × 50 bp paired-end reads. Libraries from both groups were prepared in parallel to minimize batch effects. Raw FASTQ files and processed gene-level count matrices are provided.