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Sample GSM487254 Query DataSets for GSM487254
Status Public on Apr 19, 2010
Title Integrative genomics of ovarian cancer IC026 [HuGene-1_0-st]
Sample type RNA
 
Source name Ovarian tumours at the time of diagnosis
Organism Homo sapiens
Characteristics histological subtype: serous
grade: 2
stage: 3
age: 51
batch: 8
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 3.554029031
7892502 4.845098823
7892503 5.942235906
7892504 9.351868787
7892505 3.289267792
7892506 4.011049428
7892507 5.13252546
7892508 4.222223279
7892509 9.690333416
7892510 3.920585106
7892511 4.335490674
7892512 7.959497207
7892513 3.944927648
7892514 9.418920624
7892515 10.33121684
7892516 6.133548793
7892517 5.661763531
7892518 2.826228622
7892519 6.632275827
7892520 9.714427277

Total number of rows: 33252

Table truncated, full table size 645 Kbytes.




Supplementary file Size Download File type/resource
GSM487254.CEL.gz 4.0 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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