|
Status |
Public on Jan 29, 2013 |
Title |
Tumor sample 182 (SNP) |
Sample type |
genomic |
|
|
Source name |
Genomic DNA isolated from breast of subject 182
|
Organism |
Homo sapiens |
Characteristics |
gender: female age: 44 tissue: breast (tumor) tumor grade: 2 race: African-American diagnosis: invasive ductal carcinoma subtype: luminal A estrogen receptor: positive progesterone receptor: positive her2: negative
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Genomic DNA was isolated with phenol extraction according to the standard protocol (Sambrook, J., Fritsch, E. F. & Maniatis, T. Molecular cloning; a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1989).
|
Label |
biotin
|
Label protocol |
Samples were end labeled using terminal deoxynucleotidyl transferase according to the Affymetrix protocol.
|
|
|
Hybridization protocol |
Samples were hybridized for 16-18 hr and washed and stained on the GeneChip fluidics station 450 using the appropriate fluidics protocol.
|
Scan protocol |
The arrays were inserted into the Affymetrix autoloader carousel and scanned using the GeneChip Scanner 3000 7G.
|
Description |
182
|
Data processing |
Genotyping Console 3.02 was used for data processing and GeneChip quality control. Data quality control and data analysis was performed using Partek GS 6.4. SNP calls were made using Birdseed V-2. The following criteria were applied for quality control parameters: Contrast QC>0.4, QC call rate >86%, SNP call rate >97% and MAPD<0.4. Copy number calls of SNP 6.0 data were determined using a Hidden Markov Model and a minimum criterion of 50 markers was used to identify significant CNAs.
The CNA data are available as supplementary files of the GSE26232 record.
|
|
|
Submission date |
Sep 30, 2011 |
Last update date |
Jan 29, 2013 |
Contact name |
Theresa V Strong |
E-mail(s) |
tvstrong@uab.edu
|
Phone |
205-975-9878
|
Fax |
205-934-9511
|
Organization name |
University of Alabama at Birmingham
|
Department |
Medicine
|
Lab |
Strong
|
Street address |
1530 3rd Avenue South
|
City |
Birmingham |
State/province |
AL |
ZIP/Postal code |
35294 |
Country |
USA |
|
|
Platform ID |
GPL6801 |
Series (2) |
GSE26232 |
Genomic profiles vary with race and subtype in young African American and European American breast cancer (SNP) |
GSE26233 |
Genomic profiles vary with race and subtype in young African American and European American breast cancer |
|