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Sample GSM2301144 Query DataSets for GSM2301144
Status Public on Aug 31, 2018
Title Breast cancer tissue [T175]
Sample type RNA
 
Source name Fresh frozen tumor tissue
Organism Homo sapiens
Characteristics molecular subtype: NA
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 3.686264347
7892502 5.371054136
7892503 4.531442758
7892504 9.689754543
7892505 3.98621035
7892506 4.452963636
7892507 5.677978535
7892508 7.22756929
7892509 11.73946052
7892510 3.734183676
7892511 3.806529621
7892512 7.180877409
7892513 2.591977523
7892514 11.0592948
7892515 9.475069864
7892516 3.11173145
7892517 5.10264858
7892518 3.050614273
7892519 5.388053721
7892520 9.712405785

Total number of rows: 33297

Table truncated, full table size 646 Kbytes.




Supplementary file Size Download File type/resource
GSM2301144_T175.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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