|
| Status |
Public on Jun 18, 2015 |
| Title |
breast cancer_relapse [Patient 23] |
| Sample type |
RNA |
| |
|
| Source name |
patients with local relapse after breast conserving therapy in early stage breast cancer
|
| Organism |
Homo sapiens |
| Characteristics |
patient id: Patient 23
gender: female
tissue type: primary tumor
sample type: FFPE material
|
| Treatment protocol |
breast cancer tissue from surgical procedure
|
| Extracted molecule |
total RNA |
| Extraction protocol |
slices from FFPE samples were sent to the comprehensive biomarker center (cbc™) in Heidelberg, RNA was extracted according to cbc standard procedures
|
| Label |
Cy3
|
| Label protocol |
100 ng total RNA input per array, for labeling Agilent's microRNA Complete labeling and Hybridization Kit was used; the protocol followed cbc™ standard procedures
|
| |
|
| Hybridization protocol |
hybridization time was 20h at 55° with 20rpm following cbc™ standard procedures
|
| Scan protocol |
Scanning and image acquisition followed cbc™ standard procedures; Scanner: Latest High-Resolution Microarray Scanner GS2505_C
|
| Data processing |
The scanned images were analyzed with the latest Agilent Feature Extraction software (10.7.3.1) according to cbc™ standard procedures. To detect outliers in the samples, Hampel's rule was applied. For this purpose all correlation coefficients were transformed using the Fisher transformation and then applied the robust test for detecting outliers. The RMA (robust multi-arra average) was used for normalization.
The RMA algorithm calculates an own background, normalizes by quantile and summarizes the data. The first step is a background correction by fitting a normal and exponential convolution model to the vector of observed intensities. The normal part represents the background, the exponential part represents the signal intensities. After background subtraction the arrays are normalized by quantile across a set of hybridizations at the probe level. Finally an estimate of the microRNA gene signal is obtained by fitting a linear model to log 2 transformed intensities. This procedure was carried out by cbcT.
|
| |
|
| Submission date |
Jun 17, 2015 |
| Last update date |
Jun 18, 2015 |
| Contact name |
Franz Zehentmayr |
| E-mail(s) |
f.zehentmayr@salk.at
|
| Organization name |
RadArt
|
| Street address |
Müllner Hauptstraße
|
| City |
Salzburg |
| ZIP/Postal code |
5020 |
| Country |
Austria |
| |
|
| Platform ID |
GPL16770 |
| Series (1) |
| GSE69951 |
Hsa-miR-375 in early breast cancer |
|
