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Sample GSM487265 Query DataSets for GSM487265
Status Public on Apr 19, 2010
Title Integrative genomics of ovarian cancer IC293 [HuGene-1_0-st]
Sample type RNA
 
Source name Ovarian tumours at the time of diagnosis
Organism Homo sapiens
Characteristics histological subtype: endometrioid
grade: 3
stage: 1
age: 59
batch: 2
Treatment protocol All tumours were fresh-frozen and OCT embedded. Lymphocytic DNA was extracted from stored blood samples.
Extracted molecule total RNA
Extraction protocol 10uM slices of tumour were hand-microdissected to obtain regions with >80% epithelial cells and reduce contamination from fibroblasts, blood vessels etc. Following this, for DNA extraction, slides containing sections were stained with Haematoxylin and Eosin and DNA was extracted using the Qiagen DNEasy kit. For RNA, identical slides were stained with Cresyl violet and total RNA was extracted using the Ambion mirVana kit according to manufacturer's instructions.
Label biotin
Label protocol According to Affymetrix protocol, Biotin labelled
 
Hybridization protocol According to Affymetrix protocol using recommended instrumentation
Scan protocol According to Affymetrix protocol and using GeneChip Operating Software
Description Gene Expression Data from Epithelial ovarian cancers
Data processing QC measures using Affymetrix Genotyping Conole and “affyPLM” package in the R open-source environment. Arrays were normalised using robust multichip average (rma) in the aroma.affymetrix package. All gene expression analyses were performed in the R environment using limma package.
 
Submission date Dec 17, 2009
Last update date Apr 19, 2010
Contact name Manasa Ramakrishna
E-mail(s) manasa.ramakrishna@petermac.org
Organization name Peter MacCallum Cancer Centre
Street address St Andrew's Pl
City Melbourne
State/province Victoria
ZIP/Postal code 3002
Country Australia
 
Platform ID GPL6244
Series (1)
GSE19539 Identification of Novel Oncogene Loci in Ovarian Cancer through Integrated Copy Number and Expression Analysis

Data table header descriptions
ID_REF
VALUE RMA Normalised logged (base2) expression values

Data table
ID_REF VALUE
7892501 3.054960303
7892502 4.609080532
7892503 4.695765445
7892504 9.010552691
7892505 3.477293216
7892506 3.290653942
7892507 4.450546772
7892508 4.42884267
7892509 9.430146496
7892510 3.936820507
7892511 4.661689388
7892512 7.948168827
7892513 4.007772591
7892514 9.225707433
7892515 10.09162876
7892516 4.115056672
7892517 4.72325847
7892518 3.259900691
7892519 6.042293944
7892520 9.74903087

Total number of rows: 33252

Table truncated, full table size 645 Kbytes.




Supplementary file Size Download File type/resource
GSM487265.CEL.gz 3.9 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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