Comment[ArrayExpressAccession]	E-GEOD-46857
MAGE-TAB Version	1.1						
Public Release Date	2013-10-10
Investigation Title	Gene expression profiling of cervical cancer tissues at progressive FIGO defined stages						
Comment[Submitted Name]	Gene expression profiling of cervical cancer tissues at progressive FIGO defined stages
Experiment Description	This is a study indented to investigate the alterations in the molecular profile of cervix uteri, as it progresses thorough various FIGO stages of carcinoma, by means of global gene expression profiling, in a cohort of Indian patients. In addition expresion profiles of early and advanced stage cervical cancer were compared to identify biomarkers and therapeutic targets for the advanced stages. Cervical cancer and non-malignant cervical tissues are obtained from consenting patients following hospital ethics committee approved protocols. The samples are profiled against universal Human reference RNA from Stratagene on 19K EST microarrays from Microarray Center, University Health Network, Toronto, Canada. Biological replicates: Normal = 4; Cervical cancer Stage I = 8; Cervical cancer Stage II = 9; Cervical cancer Stage III = 8. One replicate per array.						
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	Mulherkar	Mulherkar	Thomas	Kumar-Sinha	Mahantshetty	Shrivastava	
Person First Name	Rita	Rita	Asha	Chandan	Umesh	Shyam	
Person Mid Initials						K	
Person Email	rmulherkar@gmail.com						
Person Affiliation	Advanced Centre for Treatment, Research and Education in Cancer (ACTREC)						
Person Phone	91 22 27405044						
Person Fax	91 22 27405085						
Person Address	Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Kharghar, Navi Mumbai, Maharashtra, India						
Person Roles	submitter						
Protocol Name	P-GSE46857-1	P-GSE46857-4	P-GSE46857-5	P-GSE46857-2	P-GSE46857-7	P-GSE46857-3	P-GSE46857-6
Protocol Description	Data was analyzed using Agilent Genespring GX11.5 software. The raw intensity data was normalized by log2 transformation and Lowess normalization. Baseline correction was done to median of all samples. ID_REF =  VALUE = Normalized log2 ratio (Cy5/Cy3) representing test/reference.	For generation of fluorescently labeled cDNA, post-labeling method was utilized. In the first step, the RNA is converted into cDNA in the presence of aminoallyl-dUTP and other dNTPs. The addition of Cy3 and Cy5 N- hydroxysuccinimidyl esters (NHS esters) to the prepared cDNA in the second step leads to chemical coupling (esterification reaction) at the aminoallyl-dUTP site.	Hybridization was done in 2X Hyb buffer containing 50% formamide, 10X SSC and 0.2% SDS (adapted from Quackenbush protocol) in a 42 degrees Centigrade waterbath overnight in a Hyb chamber, with the probe under a coverslip, as described by Pat Brown Lab http://cmgm.stanford.edu/pbrown/protocols/index.html	Snap frozen in Liquid nitrogen	RNA isolation was done using the RNeasy RNA extraction kit (Qiagen) as per manufacturer’s instructions. RNA obtained was quantitated using Nanodrop and quality checked using formaldehyde-agarose gel electrophoresis.	RNA isolation was done using TriZol reagent (Life Technologies) as per standard protocol followed by clean up using RNeasy extraction kit (Qiagen). RNA obtained was quantitated using Nanodrop and quality checked using formaldehyde-agarose gel electrophoresis.	Scanned in Axon 4200A Professional according to the manufacturer's instructions. Gridding and alignment was done using GenePix Version 5.0 and the files were saved as GPR files.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	nucleic acid extraction protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	CANCER STAGE						
Experimental Factor Type	cancer stage						
Comment[SecondaryAccession]	GSE46857						
Comment[GEOReleaseDate]	2013-10-10						
Comment[ArrayExpressSubmissionDate]	2013-05-13						
Comment[GEOLastUpdateDate]	2013-10-10						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-46857.sdrf.txt