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Series GSE81137 Query DataSets for GSE81137
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
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.
 
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).
 
Contributor(s) Vijayamma JM, Paul AM, Joshi S, Reshmi G, Gheit T, Tommasino M, Vinoda J, Sankaranarayanan R, Pillai MR
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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
Department Cancer Research Program
Lab CRP-9
Street address poojappura
City trivandrum
State/province KERALA
ZIP/Postal code 695014
Country India
 
Platforms (1)
GPL16384 [miRNA-3] Affymetrix Multispecies miRNA-3 Array
Samples (12)
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
Relations
BioProject PRJNA320715

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE81137_Full_RMA_Matrix.xls.gz 4.4 Mb (ftp)(http) XLS
GSE81137_RAW.tar 30.7 Mb (http)(custom) TAR (of CEL)
GSE81137_RMA_Normalized_data_human_miRNA.xlsx 1.2 Mb (ftp)(http) XLSX
Processed data included within Sample table
Processed data are available on Series record

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