NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM153055 Query DataSets for GSM153055
Status Public on Jan 16, 2007
Title Tumor samples from patient No.35 PT35U95C
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-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) [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 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 40.4
AFFX-MurIL10_at 43.2
AFFX-MurIL4_at 11.2
AFFX-MurFAS_at 134
AFFX-BioB-5_at 1759.5
AFFX-BioB-M_at 3198.5
AFFX-BioB-3_at 1855.7
AFFX-BioC-5_at 5294.2
AFFX-BioC-3_at 4242.4
AFFX-BioDn-5_at 3899.1
AFFX-BioDn-3_at 24414.6
AFFX-CreX-5_at 43115.4
AFFX-CreX-3_at 66388.6
AFFX-BioB-5_st 369.8
AFFX-BioB-M_st 176.5
AFFX-BioB-3_st 92.2
AFFX-BioC-5_st 24.5
AFFX-BioC-3_st 39.2
AFFX-BioDn-5_st 269.8
AFFX-BioDn-3_st 460.6

Total number of rows: 12646

Table truncated, full table size 181 Kbytes.




Supplementary file Size Download File type/resource
GSM153055.CEL.gz 2.5 Mb (ftp)(http) CEL

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap