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Sample GSM1664570 Query DataSets for GSM1664570
Status Public on Jun 09, 2015
Title SUM159-ZR75_SNP6
Sample type genomic
Source name breast cancer cell line heterofusion SUM159PT-ZR75-1
Organism Homo sapiens
Characteristics cell line: heterofusion SUM159PT-ZR75-1
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from breast cancer cell lines and the fusion cell lines with a standard method using proteinase K digestion, phenol-chloroform extraction and ethanol precipitation. The DNA was subjected to genotyping.
Label Biotin
Label protocol Affymetrix standard procedure
Hybridization protocol Affymetrix standard procedure
Scan protocol Affymetrix standard procedure
Description SNP_array_18
Data processing Genotypes were derived from the CEL files using custom Reference Supported Genotyper software after calibration with 270 Hapmap samples and allowable genotyping distance of 1.5 standard deviations from the mean of the allele cluster.
CEL files were processed using custom RSG genotyper with 270 HapMap samples as reference. Further analysis was performed using scripts described in [Maruyama et al] primary data description: Genotype Call (SNP call): AA, AB, BB, and NoCall; 'Confidence' = Confidence call from RSG algorithm. Values left blank represent NA, not available.
Customized algorithm used to generate the data. We processed three SNP data (three CEL files: luminal parent, basal parent and their heterofusion) at the same time to generate ONE processed data (TableS4-SNP-updated_121114.xlsx).
Submission date Apr 22, 2015
Last update date Jun 10, 2015
Contact name Kornelia Polyak
Phone 617-632-2106
Organization name Dana-Farber Cancer Institute
Department Medical Oncology
Lab Polyak
Street address 450 Brookline Ave
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
Platform ID GPL6801
Series (2)
GSE38548 Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer
GSE39412 Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [SNP]

Supplementary file Size Download File type/resource
GSM1664570_6_SUM159_ZR75-1.CEL.gz 25.7 Mb (ftp)(http) CEL
Processed data are available on Series record

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