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Sample GSM905021 Query DataSets for GSM905021
Status Public on Jun 10, 2012
Title Normal cortex of patient 1524
Sample type RNA
 
Source name Gene expression profiling of normal cortex of patient 1524
Organism Homo sapiens
Characteristics patient id: 1524
tissue: Normal cortex
gender: Male
age: 70
disease state: Clear-cell renal cell carcinoma
bap1 status: wild type
pbrm1 status: wild type
vhl status: wild type
Extracted molecule total RNA
Extraction protocol Tissues were homogenized with an RNase-free pestle alternating freeze/thaw cycles and subsequently passed through a QIAshredder column (Qiagen). RNA fraction was extracted using mirVana (Ambion) kit.
Label Biotin
Label protocol RNA was reverse-transcribed and biotin-labeled using Affymetrix one-cycle cDNA synthesis and IVT labeling kits (Affymetrix).
 
Hybridization protocol Arrays were washed and hybridized using Affymetrix Fluidics Station 450.
Scan protocol Arrays were scanned using Affymetrix GeneChip Scanner 3000 7G.
Data processing CEL files were pre-processed and normalized using the RMA algorithm through the Affy package of R/Bioconductor.
 
Submission date Mar 28, 2012
Last update date Jun 10, 2012
Contact name Samuel Peña-Llopis
E-mail(s) Samuel.Pena-Llopis@UTSouthwestern.edu, James.Brugarolas@UTSouthwestern.edu
Phone (01) 214-648-4099
Fax (01) 214-648-1960
Organization name UT Southwestern Medical Center
Department Internal Medicine - Oncology Division
Lab Brugarolas Lab
Street address 6000 Harry Hines Blvd., NB5.102
City Dallas
State/province TX
ZIP/Postal code 75390-9133
Country USA
 
Platform ID GPL570
Series (1)
GSE36895 Molecular Genetic Classification of clear-cell Renal Cell Carcinoma (ccRCC) based on the Gene Expression Profiling of Tumors and Tumorgrafts deficient for BAP1 or PBRM1

Data table header descriptions
ID_REF
VALUE Log2-transformed RMA signal.

Data table
ID_REF VALUE
1007_s_at 11.52508262
1053_at 7.614654099
117_at 6.464297804
121_at 10.80955141
1255_g_at 3.365012012
1294_at 8.135745318
1316_at 7.250303258
1320_at 6.039354204
1405_i_at 8.717573587
1431_at 4.806587876
1438_at 6.503445496
1487_at 8.889836745
1494_f_at 6.464978208
1552256_a_at 7.706703511
1552257_a_at 8.204604111
1552258_at 6.12399189
1552261_at 5.371656125
1552263_at 7.501749203
1552264_a_at 7.247072601
1552266_at 3.85422519

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM905021_1524N_Exp.CEL.gz 6.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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