|
| Status |
Public on Jul 16, 2022 |
| Title |
Breast Cancer 204 |
| Sample type |
RNA |
| |
|
| Source name |
Breast tumor
|
| Organism |
Homo sapiens |
| Characteristics |
filename: A1764-078
plate_pos: G6
subject_id: 204
crna_conc_ng_per_ul: 871
ratio_260_280: 2.29
ratio_260_230: 2.59
conc_ug_per_ul: 0.871
final_vol_ul_1: 22
crna_yield_ug: 19.162
crna_used_ug: 4
vol_crna_used_ul: 4.59242250287026
final_vol_ul_2: 22.5
rnase_free_water_ul: 17.9075774971297
batch: Batch1
cdna_conc_ng_per_ul: NA
cdna_yield_ug: NA
cdna_used_ug: NA
vol_cdna_used_ul: NA
dataset: FinHER
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from FFPE tumor tissue according to the method described in Bohmann et al, Clinical Chemistry 2009
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA was prepared according to Affymetrix's standard protocols
|
| |
|
| Hybridization protocol |
Hybridization was done according to Affymetrix's standard protocols for 96 array plate. The GeneTitan Hybridization, Wash and Stain kit for 3' IVT arrays was used for preparing hybridization mixes
|
| Scan protocol |
96 array plates were scanned using Affymetriix's automated GeneTitan system according to the manufacturer's instructions
|
| Description |
Biotinylated cRNA was prepared according to Affymetrix's standard protocols
|
| Data processing |
The probe level intensities were background adjusted using the Robust multi-array analysis (RMA) method followed by quantile normalization as impletemented in the R/Bioconductor package affy. Probe level annotations were obtained from Affymetrix’s website. In particular, we used release 32 of the NetAffx annotation files.
|
| |
|
| Submission date |
Jun 16, 2013 |
| Last update date |
Jan 10, 2024 |
| 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) |
| GSE47994 |
Tumor-infiltrating lymphocytes, prognosis and trastuzumab benefit in early-stage breast cancer patients from the FinHER trial |
|
