|
| Status |
Public on May 01, 2014 |
| Title |
Clinical Breast Cancer Specimen from disease free patient 477_disease.free |
| Sample type |
RNA |
| |
|
| Source name |
Clinical Breast Cancer Specimen
|
| Organism |
Homo sapiens |
| Characteristics |
distant metastasis (0-none): 0
dfs (months): 102
age (y): 69
tumor size: 2
histotype: other
esr1 status (0-negative): 1
erbb2 status (0-negative): 0
tissue: breast cancer specimen
|
| Growth protocol |
Tissue samples collected at time of surgery were stored at -80°C until RNA extraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue was pulverized using a Mikrodismembrator (Braun Biotech International , Germany). Total RNA was extracted with the Trizol reagent (Invitrogen, Carlsbad, CA) according to manufacture instructions and an additional DNase digestion was performed using the RNeasy kit (Qiagen, Valencia, CA).
|
| Label |
biotin
|
| Label protocol |
800 ng of total RNA were reverse transcribed, labeled with biotin and amplified overnight using the Illumina RNA TotalPrep Amplification kit (Ambion, Austin, TX) according to manufacturer’s protocol
|
| |
|
| Hybridization protocol |
One μg of the biotinylated cRNA sample was mixed with the Hyb E1 hybridization buffer containing 37.5% (w/w) formamide and then hybridized at 58 °C overnight to the HumanRef-6_v3 (Illumina, Inc, San Diego, CA)
|
| Scan protocol |
scanned with Illumina BeadArray Reader
|
| Description |
Clinical Breast Cancer Specimen from disease free patient
|
| Data processing |
Microarray raw data where generated using the Illumina BeadStudio 3.8 software and processed using the lumi package of Bioconductor. After quality control, the Robust Spline Normalization was applied.
|
| |
|
| Submission date |
Apr 11, 2012 |
| Last update date |
May 01, 2014 |
| Contact name |
Maurizio Callari |
| E-mail(s) |
maurizio.callari@cruk.cam.ac.uk
|
| Organization name |
Fondazione IRCCS Istituto Nazionale dei Tumori
|
| Street address |
Via Amadeo, 42
|
| City |
Milan |
| ZIP/Postal code |
20133 |
| Country |
Italy |
| |
|
| Platform ID |
GPL6884 |
| Series (1) |
| GSE37181 |
Subtype-dependent prognostic relevance of an interferon-induced pathway metagene in human node negative breast cancer |
|
