GSE173575
RNA-seq analysis of HT8 cells based on PPDPF knockdown
Purpose: Analysis of the regulatory network involved in PPDPF in colon cancer cells. Methods: mRNA profiles of HT8-cas1 and HT8 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 3233 differential genes, of which 1877 were up-regulated and 1356 were down-regulated. In GO enrichment analysis,the biological process is mainly in the cell ions homeostasis and the molecular function is mainly in viral life cycle,response to virus,neutrophil activation, and the transmembrane signaling receptor activity. KEGG analysis shows that differential genes are enriched in Epstein-Barr virus infection ,Glutathione metabolism and Proteasome pathways. Conclusion: Based on RNA-seq analysis, the regulatory network involved in PPDPF in colon cancer . Overall design: mRNA profiles of HT8-cas1 and HT8 group