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Series GSE46699 Query DataSets for GSE46699
Status Public on Jan 10, 2014
Title Smoking and Obesity Related Molecular Alterations in Clear Cell Renal Cell Carcinoma
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Both cigarette smoking and obesity have been implicated in increased risk of clear cell renal cell carcinoma (ccRCC); however, there are limited data regarding the molecular mechanisms that underlie these associations. We used a multi-stage design to identify and validate specific molecular targets that are associated with smoking or obesity-related ccRCC.
 
Overall design The data deposited herein are comprised of two batches of samples that were processed at two different time periods (please see Supplementary Data in Eckel-Passow et al. Carcinogenesis first published online December 28, 2013; doi:10.1093/carcin/bgt485).  The first batch of samples consisted of 12 obese subjects and 13 non-obese subjects; all of whom were self-reported never-smokers.  Each of the 12 obese subjects had  microarray data available on both the patient-matched tumor and adjacent-normal tissues.  All of the 13 non-obese subjects had microarray data available on the tumor tissue; however, only 9 of these 13 also had microarray data available on the patient-matched adjacent-normal tissue.  The second batch of samples consisted of 16 self-reported smokers and 19 self-reported never smokers; all of whom were non-obese.   This second batch of samples also contained 7 subjects who were obese and self-reported smokers.  All subjects in the second batch had microarray data available on both the patient-matched tumor and adjacent-normal tissues.  Lastly, two of the 13 patients in batch 1 were replicated in batch 2; both were non-obese and a non-smoker. 
These two technical replicates (two tumor samples and two normal samples) were included during normalization but removed prior to analysis. The cel files are
Par007U133Plus2.0.CEL
Par008U133Plus2.0.CEL
Par041U133Plus2.0.CEL
Par042U133Plus2.0.CEL
The metadata "duplicate" column can also be used to exclude these samples.
 
Contributor(s) Serie DJ, Eckel-Passow JE
Citation(s) 24479813, 24374825
Submission date May 07, 2013
Last update date Mar 25, 2019
Contact name Daniel Serie
E-mail(s) serie.daniel@mayo.edu
Phone 9049536451
Organization name Mayo Clinic
Street address 4500 San Pablo Rd
City Jacksonville
State/province Florida
ZIP/Postal code 32224
Country USA
 
Platforms (1)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Samples (130)
GSM1134764 patient 1 normal tissue no smoking no obese Par059HG-U133_Plus_2.cel
GSM1134765 patient 1 tumor tissue no smoking no obese Par060HG-U133_Plus_2.cel
GSM1134766 patient 14 normal tissue yes smoking no obese Par061HG-U133_Plus_2.cel
Relations
BioProject PRJNA201858

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
GSE46699_RAW.tar 642.8 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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