|
| Status |
Public on Oct 20, 2012 |
| Title |
BT474_20%tumor |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
BT474 20% tumor diluted with normal DNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BT474
cell type: breast cancer cells
percent tumor cells: 20%
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Buffart et al., J Pathol. 2007 Jan;211(1):45-51 (PMID 17117405).
|
| Label |
Cy5
|
| Label protocol |
DNA labeling protocol according to Enzo Life Sciences.
|
| |
|
| Channel 2 |
| Source name |
Reference DNA
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: pool of 19 healthy individuals
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Buffart et al., J Pathol. 2007 Jan;211(1):45-51 (PMID 17117405).
|
| Label |
Cy3
|
| Label protocol |
DNA labeling protocol according to Enzo Life Sciences.
|
| |
|
| |
| Hybridization protocol |
Standard Agilent protocol.
|
| Scan protocol |
Standard Agilent protocol.
|
| Description |
BT474.20
The tumor cell line BT474 has a dual copy number gain (6 copies in a background of 4 copies) of 46Mb. This corresponds to a single copy number gain in a diploid sample.
|
| Data processing |
Median normalization in R/Bioconductor.
Raw data files:
Test: Cy5 sample in the 'US22502676_252252210461_S01_CGH_107_Sep09_1_2.txt' file.
Reference: Cy3 sample in the 'US22502676_252252210461_S01_CGH_107_Sep09_1_1.txt' file.
|
| |
|
| Submission date |
Mar 27, 2012 |
| Last update date |
Oct 20, 2012 |
| Contact name |
Daoud Sie |
| E-mail(s) |
[email protected]
|
| Phone |
+31 20 4442428
|
| Organization name |
Vrije Universiteit Medical Center
|
| Department |
Pathology
|
| Lab |
Microarray Core Facility
|
| Street address |
De Boelelaan 1117
|
| City |
Amsterdam |
| ZIP/Postal code |
1081 HV |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL8687 |
| Series (2) |
| GSE36856 |
Ten percent of aberrant cells is sufficient for detection of DNA copy number alterations (part 1) |
| GSE36993 |
Ten percent of aberrant cells is sufficient for detection of DNA copy number alterations |
|
