|
| Status |
Public on Jun 09, 2015 |
| Title |
SUM159PN627_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_6
|
| 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 |
| E-mail(s) |
kornelia_polyak@dfci.harvard.edu
|
| 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] |
|
