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Sample GSM152932 Query DataSets for GSM152932
Status Public on Jan 16, 2007
Title Tumor samples from patient No.35 PT35U95Av2
Sample type RNA
 
Source name PT35, tumor samples from patient No.35
Organism Homo sapiens
Characteristics Tissue:primary prostate tumor
Tumor stage: T2b
Gleason Grade: 5
Treatment protocol Fresh prostate tissues were recovered immediately after surgical removal. Tissues were dissected/trimmed to obtain pure tumor then snap frozen in liquid nitrogen within 30 mintues of excision and stored in -80C untill RNA extraction. An H&E stained frozen section of each sample was evaluated by a pathologist, to determine epithelial and stromal content and verify the presence of tumor in the sample. Only tumor tissues with less than 30% of tromal components were selected.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with Qiagen Rneasy kit according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U95Av2 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Description Gene expression data from primary prostate cancer
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 200.
 
Submission date Dec 22, 2006
Last update date Mar 16, 2009
Contact name Federico Alberto Monzon
E-mail(s) [email protected]
Organization name The Methodist Hospital
Department Pathology
Lab Molecular Diagnostics
Street address 6565 Fannin St, MS205
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL8300
Series (2)
GSE6606 Expression data from Primary Prostate Tumor
GSE6919 Expression Data from Normal and Prostate Tumor Tissues

Data table header descriptions
ID_REF 12625
VALUE MAS5-calculated Signal intensity

Data table
ID_REF VALUE
100_g_at 303.6
1000_at 452.7
1001_at 39.6
1002_f_at 8.9
1003_s_at 38.1
1004_at 20
1005_at 3038.9
1006_at 20.8
1007_s_at 1519
1008_f_at 1855.2
1009_at 1804.2
101_at 169.2
1010_at 16
1011_s_at 334.1
1012_at 22.8
1013_at 56.7
1014_at 237.8
1015_s_at 12.5
1016_s_at 3.3
1017_at 73.7

Total number of rows: 12625

Table truncated, full table size 178 Kbytes.




Supplementary file Size Download File type/resource
GSM152932.CEL.gz 2.5 Mb (ftp)(http) CEL

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