GSE169344
RNA-seq analysis of BT549 cells based on SIK2 knockdown
Purpose: Analysis of the regulatory network involved in SIK2 in breast cancer cells activated by the Wnt/ß-catenin pathway. Methods: mRNA profiles of BT549-shSIK2 and BT549-Scrambled group that Wnt3a treated for 2 hours 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 1709 differential genes, of which 1147 were up-regulated and 562 were down-regulated. In GO enrichment analysis, the biological process is mainly in the cell ions homeostasis, the cell components are mainly enriched on the cell surface, and the molecular function is mainly in the transmembrane signaling receptor activity. KEGG analysis shows that differential genes are enriched in Axon guidance and Nicotinate and nicotinamide metabolism pathways. Conclusion: Based on RNA-seq analysis, the regulatory network involved in SIK2 in breast cancer response to Wnt signaling is depicted. Overall design: mRNA profiles of BT549-shSIK2 and BT549-Scrambled group that Wnt3a treated for 2 hours