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Sample GSM153242 Query DataSets for GSM153242
Status Public on Jan 16, 2007
Title Normal prostate tissue adjacent to tumor from patient No.38 PN38U95C
Sample type RNA
 
Source name PN38, normal prostate tissue adjacent to tumor from patient No.38
Organism Homo sapiens
Characteristics Tissue:normal prostate tissue adjacent to tumor
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 minutes of excision and stored in -80C until 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. For prostate tissues adjacent to tumor, samples free of cancer cells, high-grade prostatic neoplasia, or any obvious neoplastic alterations, containing at least 60% glandular cells 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 normal prostate tissue adjacent to tumor
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)
GSE6608 Expression data from Normal Prostate Tissue Adjacent to 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
48609_r_at 36.7
48610_at 1583.5
48612_at 2417.5
48613_at 217.9
48615_at 555.6
48617_at 554.1
48619_at 428.8
48620_at 187.4
48622_at 25
48624_at 47.3
48626_at 239.1
48628_at 91.6
48629_s_at 156
48630_r_at 275.6
48631_at 328.4
48633_at 12.2
48634_at 121.1
48640_g_at 38.1
48643_r_at 16.5
48645_at 41.5

Total number of rows: 12646

Table truncated, full table size 182 Kbytes.




Supplementary file Size Download File type/resource
GSM153242.CEL.gz 2.5 Mb (ftp)(http) CEL

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