|
| Status |
Public on Feb 17, 2010 |
| Title |
Renal_Cell_Carcinoma_C11 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Renal Clear Cell Carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
identifier: C11
tissue: kidney
histology: Clear Cell
disease state: Clear Cell Carcinoma
biosourcetype: Frozen Sample
|
| Biomaterial provider |
BioSource Provider: University of North Carolina
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen RCCs were obtained through University of North Carolina - Chapel Hill's Tissue Procurement Facility
RNA was extracted with a Qiagen RNeasy kit.
RNA quality was determined using an Agilent LabChip Bioanalyzer. H&E was performed on tumor tissue samples to confirm clear cell or normal histopathology
|
| Label |
Cy5
|
| Label protocol |
Tumor sample RNA and reference RNA was labelled using the Agilent Two-Color Microarray-Based Gene Expression Analysis v 5.2 protocol by UNC Lineberger Comprehensive Cancer Center Genomics Core.
|
| |
|
| Channel 2 |
| Source name |
Perou lab reference RNA
|
| Organism |
Homo sapiens |
| Characteristics |
biosourcetype: Cancer cell lines
cell line: various cancer cell lines (reference)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen RCCs were obtained through University of North Carolina - Chapel Hill's Tissue Procurement Facility
RNA was extracted with a Qiagen RNeasy kit.
RNA quality was determined using an Agilent LabChip Bioanalyzer. H&E was performed on tumor tissue samples to confirm clear cell or normal histopathology
|
| Label |
Cy3
|
| Label protocol |
Tumor sample RNA and reference RNA was labelled using the Agilent Two-Color Microarray-Based Gene Expression Analysis v 5.2 protocol by UNC Lineberger Comprehensive Cancer Center Genomics Core.
|
| |
|
| |
| Hybridization protocol |
Tumor sample RNA and reference RNA were hybridized on Agilent Whole Human Genome 4x44k arrays by UNC Lineberger Comprehensive Cancer Center Genomics Core
|
| Scan protocol |
Agilent gene chips were scanned on an Agilent model C scanner by UNC Lineberger Comprehensive Cancer Center Genomics Core
|
| Description |
Gene expression data from Human RCC sample
|
| Data processing |
Data was retrieved from the UNC Microarray Database as LOWESS normalized, log2 of processed Red/Green signal (median), filter for 70% good data (Exclude if spot is not found in either channel, spot or spot background is a non-uniform outlier, spot or spot background is a non-uniform outlier for the population, spot is not a positive and significant signal in either channel, or Ch1 and 2 lowess normalized net (median) <10). Missing data was imputed with KNN (k=10) in SAM. Data from three RNA preparation types was merged using Distance Weighted Discriminant. Each array was standard normalized (subtract the mean of the array and divide by the standard deviation).
|
| |
|
| Submission date |
Jun 05, 2009 |
| Last update date |
Oct 21, 2011 |
| Contact name |
Kimryn Rathmell |
| E-mail(s) |
kimryn.rathmell@vanderbilt.edu
|
| Organization name |
Vanderbilt
|
| Department |
Medicine
|
| Lab |
Rathmell
|
| Street address |
2220 Pierce Ave
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
| GSE16449 |
Molecular Stratification of Clear Cell Renal Cell Carcinoma Reveals Distinct Subtypes and Survival Patterns |
|
| Relations |
| Reanalyzed by |
GSE33093 |
