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Sample GSM2301057 Query DataSets for GSM2301057
Status Public on Aug 31, 2018
Title Breast cancer tissue [AT172]
Sample type RNA
 
Source name Fresh frozen tumor tissue
Organism Homo sapiens
Characteristics molecular subtype: Luminal A
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

Data table header descriptions
ID_REF
VALUE RMA quantile

Data table
ID_REF VALUE
7892501 5.381626778
7892502 4.989028626
7892503 4.40335188
7892504 9.843307892
7892505 4.64450615
7892506 4.62797844
7892507 4.819356904
7892508 6.218246806
7892509 11.98596207
7892510 3.579527775
7892511 3.251047886
7892512 8.07892173
7892513 2.672050641
7892514 10.44810436
7892515 9.364713183
7892516 6.11837511
7892517 7.355971913
7892518 4.062582446
7892519 5.960381495
7892520 9.623431163

Total number of rows: 33297

Table truncated, full table size 646 Kbytes.




Supplementary file Size Download File type/resource
GSM2301057_AT172.CEL.gz 4.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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