|
| Status |
Public on Aug 31, 2018 |
| Title |
Breast cancer tissue [BaT122] |
| Sample type |
RNA |
| |
|
| Source name |
Fresh frozen tumor tissue
|
| Organism |
Homo sapiens |
| Characteristics |
molecular subtype: Basal-like
theraoy: Adjuvant
population: Mexico Hispanic
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA were extracted from the frozen tissue using the AllPrep DNA/RNA mini kit (Qiagen, Valencia, CA)
|
| Label |
Biotin
|
| Label protocol |
cDNA synthesis, amplification, and gene expression profiling were done with the WT PLUS Reagent Kit for fresh samples (Affymetrix) and and labeled with the Genechip hybridization wash and stain kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Samples were hybridized with Gene Chip Human Transcriptome Array (HTA) 2.0 (Affymetrix) and scanned at the INMEGEN Microarray Core Facility.
|
| Scan protocol |
Microarrays were read in a scanner and high-resolution model 7Gimage analysis and quality control was performed using the Affymetrix Expression Console software
|
| Description |
Gene expression data from breast tumor.
|
| Data processing |
The mRNA expression values were normalized with RMA and quantile algorithms in R with the oligo library from Bioconductor. In order to obtain the intrinsic subtype classification the PAM50 algorithm was performed as described by Parker.
|
| |
|
| Submission date |
Sep 01, 2016 |
| Last update date |
Aug 31, 2018 |
| Contact name |
Sandra Lorena Romero-Cordoba |
| E-mail(s) |
sromero_cordoba@hotmail.com
|
| Organization name |
National Instute of Genomic Medicine
|
| Department |
Cancer Genomics
|
| Street address |
Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México, D.F.
|
| City |
Mexico |
| State/province |
Mexico |
| ZIP/Postal code |
14610 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL6244 |
| Series (2) |
| GSE86374 |
Analysis of somatic DNA copy number alterations and frequency of breast cancer intrinsic subtypes from Mexican women [gene expression] |
| GSE87049 |
Analysis of somatic DNA copy number alterations and frequency of breast cancer intrinsic subtypes from Mexican women |
|
