|
| Status |
Public on Apr 15, 2009 |
| Title |
T47D genomic DNA |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
healthy female donors
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: reference (pooled genomic DNA)
gender: female
|
| Growth protocol |
Cell cultures were grown to 70-80% confluence in 175 cm2 flasks according to distributor's instructions (ATCC).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from untreated cells using the NucleoSpin Tissue kit with the protocol for cultured cells.
|
| Label |
Cy3
|
| Label protocol |
Six micrograms of digested and purified tumour and reference DNA was labelled with Cy5-dUTP and Cy3-dUTP, respectively, in a random priming reaction using BioPrime DNA Labelling System.
|
| |
|
| Channel 2 |
| Source name |
breast cancer cell line T47D
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: test
cell line: T47D breast cancer cell line
|
| Growth protocol |
Cell cultures were grown to 70-80% confluence in 175 cm2 flasks according to distributor's instructions (ATCC).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from untreated cells using the NucleoSpin Tissue kit with the protocol for cultured cells.
|
| Label |
Cy5
|
| Label protocol |
Six micrograms of digested and purified tumour and reference DNA was labelled with Cy5-dUTP and Cy3-dUTP, respectively, in a random priming reaction using BioPrime DNA Labelling System.
|
| |
|
| |
| Hybridization protocol |
Labelled tumor and reference samples were combined and hybridized onto the arrays according to manufacturer's (Agilent) instructions. After hybridization, arrays were washed according to manufacturer's instructions.
|
| Scan protocol |
Arrays were scanned using the G2565 scanner from Agilent Technologies. Signal intensities were quantified using the Feature Extraction software version 7.5.1 from Agilent.
|
| Description |
no additional information
|
| Data processing |
Agilent Feature Extraction Software (v 7.5.1) was used for spot quality filtering and normalization.
|
| |
|
| Submission date |
Mar 31, 2009 |
| Last update date |
Apr 01, 2009 |
| Contact name |
Henrik Edgren |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute for Molecular Medicine, University of Helsinki
|
| Street address |
Tukholmankatu 8
|
| City |
Helsinki |
| ZIP/Postal code |
00290 |
| Country |
Finland |
| |
|
| Platform ID |
GPL8355 |
| Series (1) |
| GSE15477 |
Data integration from two microarray platforms identifies genetic inactivation of RIC8A in a breast cancer cell line |
|
