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Sample GSM2301155 Query DataSets for GSM2301155
Status Public on Aug 31, 2018
Title Normal adjacent tissue [C39]
Sample type RNA
 
Source name Fresh frozen normal 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 normal adjacent tissue.
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 5.81102681
7892502 5.916868719
7892503 4.388344241
7892504 10.54619225
7892505 3.346860627
7892506 4.599413293
7892507 5.725264315
7892508 7.510927488
7892509 11.08665529
7892510 4.542363492
7892511 4.23336009
7892512 7.87554546
7892513 4.232743156
7892514 10.45772409
7892515 10.0856441
7892516 6.88008729
7892517 6.989874831
7892518 2.831340303
7892519 4.941816193
7892520 9.999371762

Total number of rows: 33297

Table truncated, full table size 646 Kbytes.




Supplementary file Size Download File type/resource
GSM2301155_C39.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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