|
| Status |
Public on Dec 30, 2011 |
| Title |
20% breast cancer cell line HCC38 genomic DNA, 80% paired B lymphoblastoid cell line HCC38-BL genomic DNA |
| Sample type |
genomic |
| |
|
| Source name |
Triple-negative breast cancer cell line HCC38, paired B lymphoblastoid cell line HCC38-BL
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Triple negative invasive ductal carcinoma
cell line: 20% HCC38
cell line: 80% HCC38-BL
|
| Growth protocol |
Cell lines were grown according to standard conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.
|
| Label |
Biotin
|
| Label protocol |
As per manufacturer (Affymetrix)
|
| |
|
| Hybridization protocol |
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
|
| Scan protocol |
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
|
| Description |
Hybridized to 250K_Nsp
|
| Data processing |
CEL files and TXT files (generated by Affymetrix GTYPE using the DM algorithm) were processed by dChip and model-based expression performed using the PM/MM model. Normalization was performed using the reference normalization algorithm developed at St Jude and described in Mullighan et al Nature 2007;446:758. The data matrix contains the normalized expression values produced by that algorithm.
|
| |
|
| Submission date |
Dec 28, 2011 |
| Last update date |
Dec 30, 2011 |
| Contact name |
Qiyuan Li |
| E-mail(s) |
qiyuan_li@dfci.harvard.edu
|
| Organization name |
Dana Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Street address |
44 Binney Street
|
| City |
Boston |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL3718 |
| Series (1) |
| GSE34754 |
Affymetrix SNP array data of mixtures of tumor and normal DNA |
|
