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Status |
Public on Aug 01, 2018 |
Title |
microRNA expression profiling in HPV-16/HIV associated Cervical Cancer |
Platform organism |
synthetic construct |
Sample organism |
Homo sapiens |
Experiment type |
Non-coding RNA profiling by array
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Summary |
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.
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Overall design |
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).
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Contributor(s) |
Vijayamma JM, Paul AM, Joshi S, Reshmi G, Gheit T, Tommasino M, Vinoda J, Sankaranarayanan R, Pillai MR |
Citation missing |
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Submission date |
May 05, 2016 |
Last update date |
Aug 02, 2018 |
Contact name |
Radhakrishna Madhavan Pillai |
Organization name |
Rajiv Gandhi Centre for Biotechnology
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Department |
Cancer Research Program
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Lab |
CRP-9
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Street address |
poojappura
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City |
trivandrum |
State/province |
KERALA |
ZIP/Postal code |
695014 |
Country |
India |
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Platforms (1) |
GPL16384 |
[miRNA-3] Affymetrix Multispecies miRNA-3 Array |
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Samples (12)
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GSM2143420 |
HPV 16 Negative and HIV positive cases Sample1 |
GSM2143421 |
HPV 16 Negative and HIV positive cases Sample2 |
GSM2143422 |
HPV 16 Negative and HIV positive cases Sample3 |
GSM2143423 |
HPV 16 positive and HIV positive cases Sample1 |
GSM2143424 |
HPV 16 positive and HIV positive cases Sample2 |
GSM2143425 |
HPV 16 positive and HIV positive cases Sample3 |
GSM2143426 |
HPV 16 positive and HIV negative cases Sample1 |
GSM2143427 |
HPV 16 positive and HIV negative cases Sample2 |
GSM2143428 |
HPV 16 positive and HIV negative cases Sample3 |
GSM2143429 |
Healthy Population Control sample 1 (HIV and HPV Negative cases) |
GSM2143430 |
Healthy Population Control sample 2 (HIV and HPV Negative cases) |
GSM2143431 |
Healthy Population Control sample 3 (HIV and HPV Negative cases) |
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Relations |
BioProject |
PRJNA320715 |