|
| Status |
Public on Jun 28, 2013 |
| Title |
278a |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Breast tumor tissue
|
| Organism |
Homo sapiens |
| Characteristics |
menopause_status: Postmenopausal
age: 55
tumor_size: 24
who: Invasive ductal carcinoma
grade: 3
er_dbcg: 0
pr_dbcg: 0
group: Sporadic
pam50agilent: Basal
her2_dbcg: 0
er: 0
pr: 0
her2: 0
general_brca1_pred_agilent: BRCA1
general_brca2_pred_agilent: Sporadic
basal_brca1_pred_agilent: Sporadic
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from freshly frozen tumor tissue using Trizol Reagent (Invitrogen) and RNeasy Micro Kit (Qiagen).
|
| Label |
Cy5
|
| Label protocol |
RNA was amplified and labeled using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion) according to the manufacturer’s protocol.
|
| |
|
| Channel 2 |
| Source name |
Universal Human Reference RNA (Stratagene)
|
| Organism |
Homo sapiens |
| Characteristics |
reference: Universal Human Reference RNA (Stratagene)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from freshly frozen tumor tissue using Trizol Reagent (Invitrogen) and RNeasy Micro Kit (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
RNA was amplified and labeled using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion) according to the manufacturer’s protocol.
|
| |
|
| |
| Hybridization protocol |
Hybridization and washing were performed according to manufacture’s recommendations in a low ozone environment.
|
| Scan protocol |
Scanned using a Agilent G2565CA Microarray scanner
|
| Description |
K085
|
| Data processing |
Scanned images were quantified using Agilent Feature Extraction Software (version 10.7.3.1). Bad quality features flagged during feature extraction were removed and the remaining data were pre-processed. Data were background corrected (normexp, offset=50), then within-array normalized by loess normalization method and between-array normalizatized by the quantile method. The normalized values were used to calculate log2 transformed Cy5/Cy3 ratios. Replicate probes were collapsed by calculating the median. Probes without gene symbol annotation were filtered out. In cases of multiple probes per gene symbol only the probe with the maximum mean (Cy5) intensity was kept. Missing expression values were imputed by k-nearest neighbors averaging (k = 10).
|
| |
|
| Submission date |
Aug 14, 2012 |
| Last update date |
Aug 05, 2013 |
| Contact name |
Martin Jakob Larsen |
| E-mail(s) |
martin.larsen@rsyd.dk
|
| Organization name |
Odense University Hospital
|
| Department |
Dept. of Clinical Genetics
|
| Street address |
Sdr. Boulevard 29
|
| City |
Odense C |
| ZIP/Postal code |
5000 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL15931 |
| Series (3) |
| GSE40115 |
Classifications within Molecular Subtypes Enables Identification of BRCA1/BRCA2 Mutation Carriers by RNA Tumor Profiling |
| GSE49481 |
RNA Profiles Reveals Familial Aggregation of Molecular Subtypes in non-BRCA1/2 Breast Cancer Families |
| GSE54275 |
Microarray gene expression analysis: Batch effect removal improves the cross-platform consistency |
|
