Metabolic reprogramming of Kaposi’s sarcoma associated herpes virus infected B-cells in hypoxia
The differences in expression of host encoded genes in terms of fold change between BJAB-CoCl2 and BJAB cells were determined by CLC bio software. BJAB cells were grown under normoxic or CoCl2 induced hypoxic condition for 48 hours followed by RNA isolation through standard phenol chloroform extraction. The RNA samples were prepared for sequencing using Illumina RNA sequencing sample prep kit as described in materials and methods section. The indexed ready to run samples were run on Illumina platform at the University of Washington (Core services). The reads alignments with human genome, fold change differences and statistical significance in the terms of p-value were calculated by CLC bio software (Qiagen Inc., Hilden, Germany). (A) Data was analyzed for Fold change expression of VGEFA, a positively regulated target of HIF1α. Graph represents fold change expression of VGEFA in BJAB-CoCl2 cells compared to BJAB cells (RNA sequencing). (B) Difference in VEGFA gene expression was confirmed by real time PCR in RNA sample used for sequencing. Graph represents fold change expression of VGEFA in BJAB-CoCl2 cells compared to BJAB cells (Real Time PCR data). (C) Volcano plot for differential gene expression between BJAB-CoCl2/BJAB. Fold change differences and FDR-p value for each gene were feeded to R-software to generate volcano plot. (D) Top 10 up-regulated genes and top 10 down-regulated genes in BJAB-CoCl2 cells compared to BJAB cells. Asterisk (*) denotes FDR-p-value <0.05.