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Sample GSM967817 Query DataSets for GSM967817
Status Public on Jun 09, 2015
Title SUM159neo_SNP6
Sample type genomic
Source name breast cancer cell line SUM159PT
Organism Homo sapiens
Characteristics cell line: SUM159PT
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_1
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 Jul 17, 2012
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]

Data table header descriptions
VALUE genotype

Data table
ID_REF VALUE Confidence
SNP_A-8575125 NoCall
SNP_A-8575115 NoCall
SNP_A-8575371 NoCall
SNP_A-8709646 NoCall
SNP_A-8497791 NoCall
SNP_A-1909444 BB 0
SNP_A-8358063 NoCall
SNP_A-8329892 NoCall
SNP_A-8408912 NoCall 999
SNP_A-8294056 NoCall
SNP_A-1886933 BB 0
SNP_A-2236359 NoCall
SNP_A-8515688 BB 0
SNP_A-2205441 AA 0
SNP_A-8524447 NoCall
SNP_A-8573955 NoCall 999
SNP_A-8530278 BB 0
SNP_A-8573668 BB 0
SNP_A-8573414 AB 0
SNP_A-8531044 AA 0

Total number of rows: 934147

Table truncated, full table size 18870 Kbytes.

Supplementary file Size Download File type/resource
GSM967817_34_SUM159neo_SNP6.CEL.gz 29.2 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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