|
| Status |
Public on Jan 23, 2015 |
| Title |
BA TNBC, TUM024 |
| Sample type |
RNA |
| |
|
| Source name |
Breast tumor sample from IHC defined Triple Negative subgroup
|
| Organism |
Homo sapiens |
| Characteristics |
sample_group: TNBC
array_batch: B6
hybridation batch: H4
|
| Growth protocol |
Tumor samples were obtained from patients treated at the hospital of Institut Curie (Biological Resource Center, Paris, France). Healthy samples were obtained from mammary plastic surgery. Cell lines were grown from the American Type Culture Collection (ATCC),
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and purified from frozen tumor samples using the RNeasy Mini Kit (Qiagen) followed by the RNA clean up kit (Macherey Nagel), according to manufacturers’ instructions.
|
| Label |
biotin
|
| Label protocol |
Following RNA quality and quantity control, 2 µg of total RNA were amplified and labeled according to the Affymetrix one cycle synthesis target preparation protocol to hybridize Affymetrix U133 plus 2.0 chips, as described by the company.
|
| |
|
| Hybridization protocol |
standard Affymetrix protocol
|
| Scan protocol |
standard Affymetrix protocol
|
| Description |
Breast tumor sample from IHC defined Triple Negative subgroup
|
| Data processing |
Data were analyzed using standard AffyCDF or Brainarray HGU133Plus2_Hs_ENTREZG version 13 custom chipset definition file. Data were normalized using GC-RMA. Batch and hybridization effects were corrected using a linear model in which they were treated as fixed effects. Samples with technical replicates were subsequently averaged.
|
| |
|
| Submission date |
Jan 22, 2015 |
| Last update date |
Jun 18, 2015 |
| Contact name |
Thierry Dubois |
| E-mail(s) |
thierry.dubois@curie.fr
|
| Organization name |
Institut Curie
|
| Department |
Recherche Center
|
| Lab |
Breast Cancer Biology Group
|
| Street address |
26 rue d’Ulm
|
| City |
PARIS |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platform ID |
GPL14877 |
| Series (2) |
| GSE65212 |
Expression profiling of breast cancer samples from Institut Curie (Maire cohort) -- BrainArray CDF |
| GSE65216 |
Expression profiling of breast cancer samples from Institut Curie (Maire cohort) |
|
| Relations |
| Reanalysis of |
GSM1589004 |
| Reanalyzed by |
GSM1715200 |
