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Sample GSM152905 Query DataSets for GSM152905
Status Public on Jan 16, 2007
Title Metastatic prostate tumor samples in liver from patient FB561 FB561_5BU95B
Sample type RNA
 
Source name FB561_5B, metastatic prostate tumor samples in liver from patient FB561
Organism Homo sapiens
Characteristics Tissue: prostate tumor metastases in liver
Treatment protocol Specimens were received directly from the operating room. Samples (>500 mg) were excised and snap frozen in liquid nitrogen within 30 min of excision and stored at -80°C until extraction of RNA. Metastatic tumor samples were obtained from a warm autopsy program and processed similarly to primary tumors. 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. Dissection of the frozen tissue block was performed with the guidance of a marked H & E slide to minimize the presence of host tissue in the metastatic samples. All samples used in the study contained >80% tumor. Metastatic tumor samples were minced and divided into two equal portions to be extracted with the sample protocol used for each set of primary tumors.
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-U95B array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
Description Gene expression data from metastatic 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 GPL92
Series (2)
GSE6605 Expression data from Metastatic Prostate Tumor
GSE6919 Expression Data from Normal and Prostate Tumor Tissues

Data table header descriptions
ID_REF 12553
VALUE MAS5-calculated Signal intensity

Data table
ID_REF VALUE
41880_at 83.7
41881_at 177.5
41882_at 72.6
41883_at 31.7
41884_at 56.8
41885_at 96.5
41886_r_at 275.8
41887_at 108.2
41888_at 77
41889_at 35.7
41890_at 49
41891_at 15.4
41892_at 298.2
41893_at 75.3
41894_r_at 85.2
41895_at 277.7
41896_at 4.4
41897_at 28.4
41898_at 231.6
41899_at 182.3

Total number of rows: 12553

Table truncated, full table size 178 Kbytes.




Supplementary file Size Download File type/resource
GSM152905.CEL.gz 2.6 Mb (ftp)(http) CEL

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