|
| Status |
Public on Dec 31, 2016 |
| Title |
IJB_patient_2 |
| Sample type |
RNA |
| |
|
| Source name |
HER2 breast tumor sample
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: HER2 breast cancer tumor
treatment: trastuzumab
age: 42
tumor size: 13
nodes positive: 18
er status: 0
pgr status: 0
distant metastasis: 0
time to ddfs: 2621
intratumoral lymphocytic infiltration: 0
stromal lymphocytic infiltration: 3
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using TRIzol (Life Technologies, Carlsbad, California) following the manufacturer’s instructions. RNA concentration was measured using the NanoDrop 1000 (Thermo Scientific, Waltham, Massachusetts), and RNA integrity (RIN: RNA Integrity Number) was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, California).
|
| 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 |
After purification of the aRNA, 12.5 μg were fragmented and labeled prior to hybridization to the HG-U133_Plus_2 chips.
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner by Affymetrix.
|
| Description |
HER2 breast tumor patient treated with adjuvant trastuzumab
|
| Data processing |
The data were analyzed with R-Bioconductor statistical suite. Data were normalized using the fRMA function (affy and fRMA packages)
|
| |
|
| Submission date |
Jul 01, 2014 |
| Last update date |
Jun 13, 2018 |
| Contact name |
Sylvain Brohée |
| E-mail(s) |
sylvain.brohee@gmail.com
|
| Organization name |
Institut Jules Bordet
|
| Lab |
Functional Genomics Unit
|
| Street address |
Boulevard de Waterloo 127
|
| City |
Brussels |
| ZIP/Postal code |
1000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE58984 |
Gene profiling of HER2 breast cancer patients treated with adjuvant trastuzumab |
|
