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Sample GSM2301154 Query DataSets for GSM2301154
Status Public on Aug 31, 2018
Title Normal adjacent tissue [C38]
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 6.366465821
7892502 4.311725493
7892503 4.442847459
7892504 10.43161295
7892505 3.579055154
7892506 3.395239301
7892507 4.957013193
7892508 4.771151507
7892509 11.47425548
7892510 4.110461545
7892511 3.371916743
7892512 8.100039741
7892513 2.840492789
7892514 10.88744719
7892515 10.53165496
7892516 5.126360964
7892517 5.654015986
7892518 3.1147827
7892519 6.075445686
7892520 9.877952482

Total number of rows: 33297

Table truncated, full table size 646 Kbytes.




Supplementary file Size Download File type/resource
GSM2301154_C38.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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