microRNA expression profiling in HPV-16/HIV associated Cervical Cancer

Identifying the differentially expressed miRNAs in Cervical cancer patients infected with only one virus i.e. either HIV or HPV-16 and patients infected with both viruses HIV and HPV-16 with respect to their controls which is the healthy population not infected by either HIV or any HPV The miRNA array was performed using the affymetrix GeneChip® miRNA 3.0 Array (Affymetrix, Santa Clara, California, United States). The chip was processed using a commercial Affymetrix array service (GeneTech Biotechnology Limited Company, Shanghai, China). The affymetrix GeneChip® miRNA 3.0 Array contains 2,999 probe sets unique to human, mouse and rat pre-miRNA hairpin sequences, 2,216 human snoRNA and scaRNA probe sets and covers 153 organisms (19,724 probe sets). Raw data sets were extracted from all Cel files (raw intensity file) after scanning of slides. These raw data sets were separately analyzed using Expression Console and GeneSpring GX12.5 software followed by differential miRNA expression, fold change & cluster analysis. We selected 3 samples each from the following categories (HIV+& HPV16+ ; HIV+only ; HPV-16+only and healthy population control which are not infected with either HPV or HIV) for the microRNA array. The HPV status of these samples was confirmed using HPV type-specific E7 PCR bead-based multiplex genotyping (TS-MPG).We isolated the total RNA from these 12 samples and performed the miRNA array (Affymetrix platform) to identify the differentially expressed miRNAs in cervical cancer patients infected with only one virus i.e. either HIV or HPV-16 and patients infected with both viruses HIV and HPV-16 with respect to their controls (healthy population).