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Sample GSM6825571 Query DataSets for GSM6825571
Status Public on Dec 14, 2022
Title Ovarian Clear Cell Carcinoma 21
Sample type genomic
 
Source name primary Ovarian Clear Cell Carcinoma
Organism Homo sapiens
Characteristics manual re-centering: no
Treatment protocol None
Growth protocol Not applicable
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from OCCC FFPE tissue sections using a QIAmp DNA FFPE Tissue kit (Qiagen)
Label biotin
Label protocol 80 ng of genomic DNA was subjected to SNP array OncoScan® FFPE (Thermo) according to manufacturer's instructions
 
Hybridization protocol According to manufacturer's instructions
Scan protocol The arrays were processed and loaded into the GeneChip® Scanner 3000 7G (Thermo Fisher Scientific/Affymetrix).
Description FFPE-derived genomic DNA was hybridyzed to OncoScan
Data processing The CEL files were generated by Affymetrix Gene Chip Command Console® software (v. 4.0). CEL files containing the raw data were processed via the Affymetrix OncoScan Console (Thermo). CN gains/amplifications were considered when the log R ratio (LRR) was > 0.1, and CN loss/deletions were considered when the LRR was < -0.1. The ASCAT algorithm was used to infer tumor ploidy, allele-specific copy numbers and segmentation. The ASCAT package for R used the following parameters: ascat.predictGermlineGenotypes(platform = "AffyOncoScan") and ascat.runAscat(gamma = 0.9).
Weighted Log2 ratios, Allellic Differences and B-allele frequencies are provided in the matrix tables. Three OSCHP files required manual re-centering.
 
Submission date Dec 13, 2022
Last update date Dec 14, 2022
Contact name Martin - Roffe
E-mail(s) MRoffe@cheo.on.ca
Organization name CHEO Research Institute
Street address 401 Smyth Rd
City Ottawa
State/province ON
ZIP/Postal code K1H 5B2
Country Canada
 
Platform ID GPL21558
Series (1)
GSE220891 Genomic landscapes of ovarian clear cell carcinoma from Latin countries reveal aberrations linked to survival and progression

Supplementary file Size Download File type/resource
GSM6825571_Occ21.OSCHP.gz 15.6 Mb (ftp)(http) OSCHP
GSM6825571_Occ21_A.CEL.gz 4.4 Mb (ftp)(http) CEL
GSM6825571_Occ21_C.CEL.gz 4.5 Mb (ftp)(http) CEL
Processed data provided as supplementary file

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