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Sample GSM487269 Query DataSets for GSM487269
Status Public on Apr 19, 2010
Title Integrative genomics of ovarian cancer IC321 [HuGene-1_0-st]
Sample type RNA
 
Source name Ovarian tumours at the time of diagnosis
Organism Homo sapiens
Characteristics histological subtype: mucinous
grade: 2
stage: -
age: 47
batch: 3
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 5.213142201
7892502 5.24616084
7892503 4.390903393
7892504 9.299826508
7892505 2.876646026
7892506 3.971460846
7892507 4.904056199
7892508 5.239123871
7892509 10.76628373
7892510 3.560940345
7892511 4.177512457
7892512 7.637678574
7892513 5.434299383
7892514 9.848708605
7892515 10.47567407
7892516 5.906108344
7892517 5.379996471
7892518 3.147253222
7892519 5.668374304
7892520 9.642584444

Total number of rows: 33252

Table truncated, full table size 645 Kbytes.




Supplementary file Size Download File type/resource
GSM487269.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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