|
| Status |
Public on Jun 30, 2016 |
| Title |
Breast tumor sample from patient 1000 |
| Sample type |
RNA |
| |
|
| Source name |
ductal breast adenocarcinoma tissue sample, no metastatic progression
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast tumor
disease status: invasive ductal breast adenocarcinoma
estrogen/progesterone receptor status: negative
her2 status: positive
ki67 status: positive
metastatic progression: no
prognostic: undetermined
population: Brazilian
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Snap-frozen breast tumor tissue samples were macro-dissected (>80% of tumor cells) prior to RNA isolation. Total RNA was extracted using the RNeasy mini Kit.
|
| Label |
biotin
|
| Label protocol |
RNA samples were treated with RNase-free DNase I prior to labeling. 2 μg of total RNA were reverse transcribed using T7-poly-dT primer. Second-strand cDNA was produced using RNase H and E. coli DNA polymerase I. Double-stranded cDNA was column purified (QIAquick, Qiagen) and biotin-labeled cRNA targets were generated by in vitro transcription using T7 RNA polymerase and biotin-11-UTP.
|
| |
|
| Hybridization protocol |
Fragmented cRNA from each sample was hybridized to oligoarrays overnight at 37 °C in a shaking incubator at 300 rpm. After post-hybridization washes, hybridized targets were revealed by incubating the arrays with a Cy5-Streptavidin conjugate.
|
| Scan protocol |
Signal of the Cy5-dye from hybridized targets were detected with an arrayWoRx Biochip Reader (Applied Precision LLC, Issaquah, WA, USA).
|
| Description |
P1000
|
| Data processing |
CodeLink Expression Analysis software (GE Healthcare) was used to extract background-subtracted spot intensities from oligoarray images.
|
| |
|
| Submission date |
Sep 23, 2015 |
| Last update date |
Jun 30, 2016 |
| Contact name |
Eduardo Moraes Reis |
| E-mail(s) |
emreis@iq.usp.br
|
| Phone |
+55-11-30912173
|
| Organization name |
University of São Paulo
|
| Department |
Biochemistry
|
| Street address |
Av. Prof. Lineu Prestes, 748
|
| City |
São Paulo |
| State/province |
SP |
| ZIP/Postal code |
05508-900 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL11010 |
| Series (1) |
| GSE73383 |
Identification of novel biomarkers associated with poor patient outcome in invasive breast carcinoma |
|
