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Sample GSM1324293 Query DataSets for GSM1324293
Status Public on Jul 01, 2014
Title G776
Sample type RNA
 
Source name ovarian cancer
Organism Homo sapiens
Characteristics block age: 4
diagnosis: clear cell carcinoma
percent tumor: 60-70
percent necrosis: 20-30
Extracted molecule total RNA
Extraction protocol RNA was extracted from paraffin scrolls using the RNeasy FFPE kit (Qiagen) with modification. In brief, 1 ml of xylene was first added to a 25 μm paraffin scroll, vortexed vigorously for 10 sec and centrifuged at full speed for 2 min. Supernatant was then removed and 1 ml of ethanol (100%) was added to the pellet, mixed by vortexing and centrifuged at full speed for 2 min. Supernatant was removed and the tube was incubated at room temperature from 10 min with lid opened. Subsequently, RNA was extracted using reagents provided in the RNeasy FFPE extraction kit according to the manufacturer’s instruction. Finally, purified RNA was eluted from the RNeasy MinElute spin column using 30 μl RNase-free water.
Label biotin
Label protocol WT-Ovation FFPE System V2 (NuGEN Inc; San Carlos, CA)
 
Hybridization protocol Affymetrix protocol
Scan protocol Affymetrix protocol
Data processing The data were RMA normalized using Bioconductor package 'oligo' version 1.24.2.
 
Submission date Feb 10, 2014
Last update date Jul 01, 2014
Contact name Svitlana Tyekucheva
E-mail(s) svitlana@jimmy.harvard.edu
Organization name Dana-Farber Cancer Institute
Street address 450 Brookline Ave
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platform ID GPL6244
Series (2)
GSE54807 RNA profiling from ovarian FFPE specimens
GSE54809 RNA profiling from ovarian and prostate FFPE specimens

Data table header descriptions
ID_REF
VALUE RMA normalized values

Data table
ID_REF VALUE
7892501 1.465962752
7892502 4.143964422
7892503 2.234438799
7892504 10.0422683
7892505 3.868501576
7892506 1.826017306
7892507 5.40221976
7892508 3.188601466
7892509 8.134405147
7892510 2.995509616
7892511 4.475754061
7892512 3.97932966
7892513 2.851345341
7892514 9.942671302
7892515 8.758701182
7892516 3.511278942
7892517 2.819899683
7892518 1.906354786
7892519 1.802603491
7892520 9.375999602

Total number of rows: 33297

Table truncated, full table size 646 Kbytes.




Supplementary file Size Download File type/resource
GSM1324293_15_Sample_15_ver_1.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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