RNA-seq analysis of Huh7 cells based on NME7 knockdown

Purpose: Analysis of the regulatory network involved in NME7 in liver cancer cells . Methods: mRNA profiles of Huh7-shNME7 and Huh7-shCtrl group were generated by deep sequencing, using Illumina Novaseq platform. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed. Clusterprofiler software was used to perform GO function enrichment analysis and KEGG pathway enrichment analysis of the differential gene sets. Results: We identified 873 differential genes, of which 420 were up-regulated and 453 were down-regulated. In GO enrichment analysis, the biological process is mainly in purine nucleoside triphosphate metabolic process and oxidative phosphorylation process. KEGG analysis shows that differential genes are enriched in thermogenesis and aminoacyl-tRNA biosynthesis . Conclusion: Based on RNA-seq analysis, the regulatory network involved in NME7 in liver cancer is depicted. mRNA profiles of Huh7-shNME7 and Huh7-shCtrl group