GSE115616
Transcriptome analysis of control and BRG1-depleted 22RV-1 cells with or without PTEN ablation
We conduct transcriptome comparison of control and BRG1-depleted 22RV-1 cells with or without PTEN ablation to gain genomic insights on the biological processes that BRG1 is involved in depend on PTEN deletion.  Through unsupervised cluster analysis of differentially expressed genes (DEGs), we found the expressions of 5489 genes were significantly altered in PTEN/BRG1 double knockdown cells, whereas they remained consistent or opposite pattern in control, BRG1-KD and PTEN-KD cells. Differential principal component analysis (PCA) suggested ablation of BRG1 in PTEN-depleted cells forced the cells undergoing a distinct transcriptome as compared to the others. In keeping with these findings, KEGG-DEGs relationship network indicated BRG1 loss in PTEN-deficient cells significantly altered the process related to “Prostate cancer”, “Cell cycle”, “Cell motility” and etc. Overall design: 22RV-1 cells  were infected with control and BRG1-KD letivirus. After puromycin selection, the two types of cells were infected with control and PTEN-KD letivirus individually.  Total RNA was extracted using TRIzol followed by RNeasy Mini kit (Qiagen) cleanup.