|
| Status |
Public on Feb 02, 2016 |
| Title |
FinHER_tumor_her2pos_3 |
| Sample type |
RNA |
| |
|
| Source name |
breast tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast tumor
Sex: female
batch: 1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA extraction was performed using ZYMO research pinpoint slide RNA isolation system II. Pinpoint solution was added ro the tissue on a glass slide. After air-dry, a thin blue film that embeds the tissue underneath is formed. This was then lifted from the slide and transferred to a tube. Following the treatment of the tissue with Proteinase K and RNA digestions and extraction buffers, the extracted RNA was washed and concentered using the Zymo-Spin TM IC Column
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 132 ng of cRNA were hybridized overnight at 45C on HG U219 96-array plate.
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner by Affymetrix.
|
| Data processing |
The data were analyzed with R-Bioconductor statistical suite. Data were normalized using the RMA function (affy package) and a batch effect correction was applied via the ComBat function of the sva package.
|
| |
|
| Submission date |
Jan 20, 2015 |
| Last update date |
Mar 01, 2023 |
| Contact name |
Christos Sotiriou |
| E-mail(s) |
christos.sotiriou@hubruxelles.be
|
| Phone |
+32 2 541 34 57
|
| Organization name |
Institut Jules Bordet – Université Libre de Bruxelles (ULB)
|
| Lab |
Breast Cancer Translational Research Laboratory J.C. Heuson (ULB 290)
|
| Street address |
Rue Meylemeersch 90
|
| City |
Brussels |
| ZIP/Postal code |
1070 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL13667 |
| Series (1) |
| GSE65095 |
FinHER trial : Patients with human epidermal growth factor receptor 2 (HER2)–positive breast cancer |
|
