|
| Status |
Public on Jan 29, 2013 |
| Title |
Tumor sample 116, rep2 (SNP) |
| Sample type |
genomic |
| |
|
| Source name |
Genomic DNA isolated from breast of subject 116
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
age: 43
tissue: breast (tumor)
tumor grade: 3
race: African-American
diagnosis: invasive ductal carcinoma with focal mucinous features
subtype: luminal B
estrogen receptor: positive
progesterone receptor: negative
her2: positive
|
| 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 |
bioitin
|
| 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 |
116_Repeat
|
| 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 |
|
