|
| Status |
Public on Nov 05, 2011 |
| Title |
K17 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
mRNA from Renal Clear Cell Carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
organism part: Kidney
histology: Clear Cell
biosource type: Frozen Sample
biosource provider: University of North Carolina
|
| Growth protocol |
Frozen RCCs were obtained through University of North Carolina - Chapel Hill's Tissue Procurement Facility
|
| Extracted molecule |
total RNA |
| Extraction protocol |
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 |
biosource type: Cancer cell lines
|
| Growth protocol |
Frozen RCCs were obtained through University of North Carolina - Chapel Hill's Tissue Procurement Facility
|
| Extracted molecule |
total RNA |
| Extraction protocol |
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. Each array was standard normalized (subtract the mean of the array and divide by the standard deviation). See GSE3538 et al. sample data were re-downloaded from the Stanford Microarray Database (http://smd.stanford.edu/) with Entrez ID annotation as log2 normalized ratios (median). Raw data from remaining studies utilized Affymetrix arrays and were retrieved from GEO (http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/geo/). For the See GSE22541 et al. dataset, metastatic tumors were excluded. Raw data files were imported into Partek Genomics Suite software, version 6.5 (Partek Inc., St. Louis, MO) using RMA normalization. Each Affymetrix array type was imported separately and data was subsequently merged into one file containing only the overlapping probes. Entrez IDs common to all datasets were identified using MergeMaid in R, and the Affymetrix data was merged with the Agilent datasets. This combined dataset was imported into Partek, and batch effect from each source removed. All reanalyzed data is linked to GSEnnnnn as GSEnnnnn_reanalysis.txt.
|
| |
|
| Submission date |
Oct 21, 2011 |
| Last update date |
Nov 05, 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 |
GPL4133 |
| Series (1) |
| GSE33093 |
Meta-analysis of Clear Cell Renal Cell Carcinoma Gene Expression Defines a Variant Subgroup and Identifies Gender Influences on Tumor Biology |
|
