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Sample GSM153080 Query DataSets for GSM153080
Status Public on Jan 16, 2007
Title Tumor samples from patient No.63 PT63U95C
Sample type RNA
 
Source name PT63, tumor samples from patient No.63
Organism Homo sapiens
Characteristics Tissue: primary prostate tumor
Tumor stage: T2b
Gleason Grade: 7
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-U95C 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 Jan 16, 2007
Contact name Federico Alberto Monzon
E-mail(s) famonzon@tmhs.org
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 GPL93
Series (2)
GSE6606 Expression data from Primary Prostate Tumor
GSE6919 Expression Data from Normal and Prostate Tumor Tissues

Data table header descriptions
ID_REF 12646
VALUE MAS5-calculated Signal intensity

Data table
ID_REF VALUE
AFFX-MurIL2_at 65.5
AFFX-MurIL10_at 40.4
AFFX-MurIL4_at 12.2
AFFX-MurFAS_at 29.1
AFFX-BioB-5_at 4175.7
AFFX-BioB-M_at 6781.6
AFFX-BioB-3_at 2721.3
AFFX-BioC-5_at 4850.1
AFFX-BioC-3_at 3260.8
AFFX-BioDn-5_at 3258.1
AFFX-BioDn-3_at 20438.9
AFFX-CreX-5_at 46003.2
AFFX-CreX-3_at 66923.3
AFFX-BioB-5_st 277.7
AFFX-BioB-M_st 171.9
AFFX-BioB-3_st 82.9
AFFX-BioC-5_st 72.3
AFFX-BioC-3_st 10
AFFX-BioDn-5_st 387.4
AFFX-BioDn-3_st 348.7

Total number of rows: 12646

Table truncated, full table size 182 Kbytes.




Supplementary file Size Download File type/resource
GSM153080.CEL.gz 2.5 Mb (ftp)(http) CEL

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