Comment[ArrayExpressAccession]	E-GEOD-44914
MAGE-TAB Version	1.1						
Public Release Date	2014-03-01
Investigation Title	HIV gp120 modulates the vaginal transcriptome						
Comment[Submitted Name]	HIV gp120 modulates the vaginal transcriptome
Experiment Description	During sexual transmission of HIV-1 from male to female partners, the vagina is the initial site of contact with HIV infected semen. The mechanism of HIV traversing the CD4 negative multi-layered stratified squamous epithelial barrier of the vagina to infect sub-epithelial susceptible immune cells, is hitherto unknown. HIV gp120 binds to several host proteins on vaginal epithelial cells. To gain an insight into the physiologic changes that may occur in vaginal epithelial cells in response to interactions with HIV gp120, and obtain an understanding of the molecular mechanisms by which HIV breaches the vaginal epithelium, a global snap shot of gene expression profiles in the vaginal epithelial cell line Vk2/E6E7, treated with HIV gp120 was determined. The vaginal epithelial cell line Vk2/E6E7 was treated with HIV gp120 (83nM) for 24 hr, and Agilent one colour, microarrays were performed. Agilent one-color experiment,Organism: Human ,Agilent-Custom Whole Genome Human 8x60k designed by Genotypic Technology Pvt. Ltd. (AMADID: 027114), Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)						
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl					
Person Last Name	Bandivdekar	Bandivdekar	Modi	Fanibunda			
Person First Name	Atmaram	Atmaram	Deepak	Sashaina			
Person Mid Initials		H	N	E			
Person Email	atmarambandivdekar@gmail.com						
Person Affiliation	National Institute for Research in Reproductive Health, Indian Council of Medical Research						
Person Phone	91-22-24192021						
Person Address	Division of Biochemistry, National Institute for Research in Reproductive Health, Indian Council of Medical Research, Jehangir Merwanji Street, Mumbai, Maharashtra, India						
Person Roles	submitter						
Protocol Name	P-GSE44914-1	P-GSE44914-5	P-GSE44914-6	P-GSE44914-2	P-GSE44914-3	P-GSE44914-4	P-GSE44914-7
Protocol Description	Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX V 11. ID_REF =  VALUE = Log base 2	The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40M-0C and converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40M-0C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.	The labeled cRNA samples were hybridized on to a Genotypic designed Custom Whole Genome Human 8x60k (AMADID No: 027114). 600ng of cy3 labeled samples were fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in AgilentM-bM-^@M-^Ys Surehyb Chambers at 65M-: C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)	Vk2/E6E7 cells were grown in six well plates (BD Falcon, US) to 100% confluence for the experiments. Confluent monolayers were treated with HIV gp120 (83nM) for a time course of 24 hr. Untreated cells served as a control.	The human vaginal epithelial cell line Vk2/E6E7 was employed in the study. Briefly, cells were grown in keratinocyte serum free medium (K-SFM) supplemented with 0.1 ng/ml EGF, 50 M-5g/ml bovine pituitary extract (Invitrogen, Carlsbad, CA) and 0.4 mM CaCl2 (Sigma, St. Louis, MO), at 37M-0C and 5% CO2. Cells were split 1:3 at 60% confluence, for passaging the cells.	TRIzol Method following the manufacturer's recommendations	Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1)
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Comment[SecondaryAccession]	GSE44914						
Comment[GEOReleaseDate]	2014-03-01						
Comment[ArrayExpressSubmissionDate]	2013-03-06						
Comment[GEOLastUpdateDate]	2014-03-01						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-44914.sdrf.txt