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Sample GSM997662 Query DataSets for GSM997662
Status Public on Sep 11, 2014
Title Tumor epthelial component - sample 780
Sample type RNA
 
Source name Microdissected ovarian tumor epthelial component
Organism Homo sapiens
Characteristics tissue: Microdissected ovarian tumor epthelial component
Extracted molecule total RNA
Extraction protocol Cancer specimens were obtained from the primary tumors of previously untreated ovarian cancer patients at the Brigham and Women’s Hospital (Boston, MA). Normal human ovarian surface epithelium (HOSE) specimens were obtained from the normal ovaries of patients at the time of surgery for benign indications. All specimens were collected under protocols approved by the institutional review boards of the institution.
Frozen sections were affixed onto FRAME slides (Leica, Wetzlar, Germany), fixed in 70% alcohol and stained by 1% methyl green. Air-dried tissue sections were then taken for microdissection using a MD LMD laser microdissecting microscope (Leica). Different types of tissues were dissected and harvested. Total RNA was isolated using the RNeasy Micro kit (Qiagen).
Label Biotin
Label protocol RNA samples were amplified and labeled using the two-cycle amplification protocol (Affymetrix).
 
Hybridization protocol For each sample, 15 microgram of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array.
Scan protocol GeneChip Scanner 3000 (Affymetrix) was used for array scanning and data collection.
Description Gene expression data from microdissected ovarian tumor epthelial component
Data processing Microarray data analysis software, GeneSpring V.11.0.2 (Agilent Technologies Inc.) was used to perform the primary data analysis. RMA summerization algorithm was used and baseline transformation to median of all samples were performed.
 
Submission date Sep 04, 2012
Last update date Sep 11, 2014
Contact name Tsz-Lun Yeung
Organization name University of Texas MD Anderson Cancer Center
Department Gynecologic Oncology and Reproductive Medicine
Street address 1515 Holcombe Blvd. Unit 1362
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL570
Series (1)
GSE40595 A cancer associated fibroblasts (CAFs) specific gene signature in high grade serous ovarian cancer

Data table header descriptions
ID_REF
VALUE Normalized intensity values are displayed in the log base 2 values

Data table
ID_REF VALUE
AFFX-BioB-5_at -2.617144
AFFX-BioB-M_at -2.627141
AFFX-BioB-3_at -2.6550884
AFFX-BioC-5_at -2.548008
AFFX-BioC-3_at -2.7092142
AFFX-BioDn-5_at -2.495863
AFFX-BioDn-3_at -2.5973158
AFFX-CreX-5_at -2.4984722
AFFX-CreX-3_at -2.2739105
AFFX-DapX-5_at 0.10406923
AFFX-DapX-M_at 0
AFFX-DapX-3_at 0.13892698
AFFX-LysX-5_at -0.025219679
AFFX-LysX-M_at 0.11740923
AFFX-LysX-3_at 0.013121367
AFFX-PheX-5_at -0.03883338
AFFX-PheX-M_at 0.25907612
AFFX-PheX-3_at -0.11076689
AFFX-ThrX-5_at 0.17700696
AFFX-ThrX-M_at 0.2721603

Total number of rows: 54675

Table truncated, full table size 1174 Kbytes.




Supplementary file Size Download File type/resource
GSM997662_780T.CEL.gz 5.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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