|
| Status |
Public on Jan 30, 2015 |
| Title |
Breast cancer cell line untreated gene expression SKBR3 |
| Sample type |
RNA |
| |
|
| Source name |
HER2 positive breast cancer cell line, untreated
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
cell line: SKBR3
|
| Growth protocol |
All cells were grown according to protocol provided by manufacturer.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from all cell lines using the Rneasy kit by Qiagen, and isolated according to the protocol provided by Qiagen.
|
| Label |
biotin
|
| Label protocol |
3μg of total RNA per sample was prepared according to the manufacturer's protocols (Affymetrix).
|
| |
|
| Hybridization protocol |
15 µg of fragmented cRNA was used for hybridization. The arrays were stained with phycoerythrin-streptavidin and the signal intensity was amplified by treatment with a biotin-conjugated anti-streptavidin antibody, followed by a second staining using phycoerythrin-streptavidin.
|
| Scan protocol |
The arrays were scanned using the GeneChip Scanner 3000 (Affymetrix).
|
| Data processing |
Data were pre-processed using the R language and the RMA method implementation in Bioconductor package ‘affy’. ‘Alternative CDF files’ (version 14) mapping Affymetrix probes directly to Ensembl gene ids were used in pre-processing, resulting in one expression value per Ensembl gene id. Ensembl gene positions are based on Ensembl database version 63 (hg19).
|
| |
|
| Submission date |
Jun 20, 2014 |
| Last update date |
Jan 30, 2015 |
| Contact name |
Sandra Jernström |
| E-mail(s) |
[email protected]
|
| Organization name |
OUS The Norwegian Radium hospital
|
| Department |
Genetics
|
| Street address |
Ullernchausséen 70
|
| City |
Oslo |
| ZIP/Postal code |
0310 |
| Country |
Norway |
| |
|
| Platform ID |
GPL18850 |
| Series (2) |
| GSE58700 |
Drug screening and genomic analyses of HER2 positive breast cancer cell lines reveal predictors for treatment response [Expression profiling] |
| GSE58887 |
Drug screening and genomic analyses of HER2 positive breast cancer cell lines reveal predictors for treatment response |
|
