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Sample GSM347577 Query DataSets for GSM347577
Status Public on Feb 17, 2009
Title 282_tumour_ovary
Sample type genomic
 
Source name Tumor, ovary
Organism Homo sapiens
Characteristics Primary tumour
Gender: F
Stage: IIIC
Histology: Undiff
Grade: 2
Treatment protocol DNA was extracted from whole tumor tissue for samples with ≥ 80% neoplastic cells. For samples with < 80% overall tumor cells, needle dissection of serial tumor sections was performed to enrich for the epithelial fraction prior to DNA extraction. Needle-dissected samples were stained with cresyl-violet to facilitate morphological distinction between tumor and stromal elements.
Growth protocol Fresh-frozen (LN2) tissue collected at surgery.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted using a DNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.
Label biotin
Label protocol The mapping array assays were performed according to the manufacturer’s protocol (Affymetrix, Santa Clara, CA).
 
Hybridization protocol DNA was XbaI restriction digested, adapter ligated, PCR amplified, fragmented, labelled and hybridized to a 50K SNP XbaI array according to the manufacturer's instructions.
Scan protocol Arrays were washed using an Affymetrix fluidics stations and scanned using the Gene Chip Scanner 3000.
Description Hybridized to Affymetrix GeneChip Mapping 100K Set Array (50K_Xba240_SNP).
Data processing CEL files and TXT files (generated by Affymetrix GTYPE using the DM algorithm) were processed by dChip and model-based expression performed using the PM/MM model. Copy number normalization, batch correction and smoothing steps were performed using GISTIC as described in Beroukhim et al., 2007 (PMID 18077431) and Etemadmoghadam et al., in press.
Copy number ratio was generated by normalizing each tumor sample to the mean of normal reference samples with similar baseline signal intensity profiles to minimize systematic noise resulting from undetermined experimental factors. We used the 5 closest references, measured by Euclidean distance between each normal and tumor signal profile. Additional normal (diploid) data (which supplement the 16 reference samples available from the current submission) were obtained from the Broad Institute, Boston (Beroukhim et al., 2007; GSE9635) and from the Affymetrix 100K HapMap Trio Dataset (available from https://www.affymetrix.com/support/technical/sample_data/hapmap_trio_data.affx).
 
Submission date Dec 03, 2008
Last update date Feb 17, 2009
Contact name Dariush Etemadmoghadam
E-mail(s) dariush.etemadmoghadam@petermac.org
Phone 61396561149
Organization name Peter MacCallum Cancer Centre
Street address St Andrew's Place
City East Melbourne
ZIP/Postal code 3002
Country Australia
 
Platform ID GPL2005
Series (1)
GSE13813 50K SNP Copy Number Analysis of Ovarian Carcinomas

Data table header descriptions
ID_REF
VALUE log2 tumor copy number ratio compared to the mean of normal (diploid) DNA references

Data table
ID_REF VALUE
SNP_A-1738457 -0.201402
SNP_A-1658232 -0.201402
SNP_A-1678466 -0.201402
SNP_A-1676440 -0.201402
SNP_A-1662392 -0.201402
SNP_A-1685736 -0.201402
SNP_A-1681384 -0.201402
SNP_A-1642581 -0.201402
SNP_A-1669029 -0.201402
SNP_A-1718237 -0.201402
SNP_A-1748467 -0.201402
SNP_A-1677302 -0.201402
SNP_A-1705537 -0.201402
SNP_A-1683756 -0.201402
SNP_A-1696782 -0.201402
SNP_A-1673422 -0.201402
SNP_A-1701279 -0.201402
SNP_A-1670878 -0.201402
SNP_A-1743511 -0.201402
SNP_A-1736635 -0.201402

Total number of rows: 57446

Table truncated, full table size 1301 Kbytes.




Supplementary file Size Download File type/resource
GSM347577.CEL.gz 14.2 Mb (ftp)(http) CEL
GSM347577.TXT.gz 524.2 Kb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file
Processed data are available on Series record

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