|
| Status |
Public on May 26, 2013 |
| Title |
Normal breast, P8_25_1_05 |
| Sample type |
RNA |
| |
|
| Source name |
Breast tissue, normal
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: normal breast
age: NA
er_status: NA
size: NA
grade: NA
lymph node status: NA
relapse free survival time_days: NA
relapse free survival event: NA
overall survival time_days: NA
overall survival event: NA
|
| Treatment protocol |
Tissues were stored at -70°C/-80°C prior to RNA isolation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were homogenised, on ice, in 1 ml TriReagent (Sigma; Poole, UK) and total RNA was subsequently isolated according to the manufacturer's instructions. RNA quantity and purity were assessed at 260 nm and 280 nm using a Nanodrop (ND-1000; Labtech. International); an Agilent Bioanalyser (Agilent 2100; Agilent Technologies) was used to assess RNA qualitatively after isolation and, subsequently, following biotin-labelling and after fragmentation.
|
| Label |
biotin
|
| Label protocol |
100 ng of each specimen was amplified and labelled using the Affymetrix GeneChip Eukaryotic 2 Cycle Labelling Assays for Expression Analysis, (Affymetrix; 900494) according to the manufacturer's instructions (www.affymetrix.com/products/reagents/specific/cdna2.affx).
|
| |
|
| Hybridization protocol |
Hybridisation solution (1 mol/l NaCl, 20 mmol/1 EDTA, 100 mmol/1 2-(N-morpholino) ethanesulfonic acid, and 0.01% Tween 20) was used to pre-hybridise Affymetrix U133 Plus 2.0 oligonucleotide microarrays for 10 minutes at 45°C and 60 rpm. The pre-hybridisation solution was removed and replaced with 200 μl hybridisation solution containing 0.05 μg/μl fragmented cRNA. The arrays were hybridised for 16 hours at 45°C and 60 rpm. Arrays were subsequently washed (Affymetrix Fluidics Station 400) and stained with streptavidin-phycoerythrin (Stain Buffer, 2 mg/ml acetylated BSA and 10 μg/ml streptavidin R-phycoerythrin; Molecular Probes, Inc., Eugene, OR).
|
| Scan protocol |
Arrays were scanned on an Affymetrix GCS GeneChip GeneArray scanner. Resulting data was analysed using GCOS, dCHIP, and GeneSpring (Agilent Technologies).
|
| Description |
Normal breast tissue data.
|
| Data processing |
All microarray data were called using the GC robust multichip average method (GC-RMA). R and Bioconductor - GCRMA package.
|
| |
|
| Submission date |
Nov 27, 2012 |
| Last update date |
Jul 30, 2013 |
| Contact name |
Colin Clarke |
| E-mail(s) |
colin.clarke@dcu.ie
|
| Organization name |
Dublin City University
|
| Department |
NICB
|
| Street address |
Collin's Av.
|
| City |
Dublin |
| ZIP/Postal code |
Dublin 9 |
| Country |
Ireland |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE42568 |
Breast Cancer Gene Expression Analysis |
|
