snRNA-seq Analysis of Sox9f/f and Sox9HKO Mouse Liver Transcriptomes

Purpose: To identify the alterations of genes transcriptional profile of livers obtained from Sox9f/f mice and Sox9HKO mice treated with partial hepatectomy (PHx). Methods: Sox9HKO mice were generated by Sox9f/f mice injected with AAV-TBG-Cre via tail. Sox9f/f mice and Sox9HKO mice were treated with PHx to induce liver regeneration. Liver mRNA profiles of 12-week-old Sox9f/f and Sox9HKO mice treated with PHx were generated by deep sequencing, using 10 × library preparation, each cDNA molecule was tagged on the 3'end of a mRNA transcript with unique molecular identifiers (UMI) and cell labels indicating its cell of origin on cDNA synthesis. We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue < 0.05. Results: We identified the transcripts in the livers of Sox9f/f and Sox9HKO mice and identified the differential expression between Sox9f/f and Sox9HKO mouse hepatocytes, with a |log2FC| > 1 and P value < 0.05. Conclusion: Our study represents the first detailed analysis of liver transcriptomes of Sox9HKO mice during liver regeneration. snRNA-seq based transcriptome analysis would provide us with a better understanding of the complex biological functions of Sox9 in the hepatocyte during the process of hepatocyte proliferation in mice. Overall design: Examine the hepatocyte mRNA profiles of 12-week old Sox9f/f mice and Sox9HKO mice treated with PHx by snRNA-seq technolodgy