|
| Status |
Public on May 30, 2019 |
| Title |
breast cancer sample, replicate 2 [Anon_15A_R2] |
| Sample type |
RNA |
| |
|
| Source name |
breast cancer sample, replicate 2
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Breast cancer
replicate: 2
cohort: Training
set er_pr rnaseq: 2.111
set er_pr u133a: 2.088996074
|
| Treatment protocol |
Patients prospectively consented to a fine-needle aspiration.
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from tissue using Qiagen RNeasy columns.
|
| Label |
biotin
|
| Label protocol |
A single-round T7 amplification was used to generate biotin-labeled cRNA for hybridization. At least 1 ug of RNA is required for cRNA synthesis.
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized overnight at 46C on Affymetrix U133A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000DX.
|
| Description |
Anon_15A_R2
|
| Data processing |
Probe intensities were quantified with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. CEL files were normalized using global scaling with a trimmed mean target intensity of each array arbitrarily set to 600 using the MAS5 algorithm from the simpleaffy package (http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html).
|
| |
|
| Submission date |
Apr 09, 2019 |
| Last update date |
May 30, 2019 |
| Contact name |
Bruno Valentin Sinn |
| E-mail(s) |
bruno.sinn@charite.de
|
| Organization name |
University of Texas - MD Anderson Cancer Center
|
| Department |
Translational Molecular Pathology
|
| Lab |
W.F. Symmans
|
| Street address |
2130 W Holcombe Blvd
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL96 |
| Series (2) |
| GSE124648 |
SET ER/PR - A robust 18-gene Predictor for Sensitivity to Endocrine Therapy for Metastatic Breast Cancer |
| GSE129560 |
Study to compare SET ER/PR index values from Affymetrix U133A microarrays to values from targeted RNASeq and to validate technical reproducibility on U133A microarrays |
|
