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Sample GSM2301077 Query DataSets for GSM2301077
Status Public on Aug 31, 2018
Title Breast cancer tissue [BaT144]
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

Data table header descriptions
ID_REF
VALUE RMA quantile

Data table
ID_REF VALUE
7892501 6.477122744
7892502 5.962914126
7892503 3.512083158
7892504 9.189465372
7892505 2.651461292
7892506 4.135207299
7892507 4.820526762
7892508 7.567810432
7892509 12.33897599
7892510 6.705678435
7892511 4.663794377
7892512 7.848241735
7892513 3.454790832
7892514 11.15499368
7892515 9.834970594
7892516 6.942858557
7892517 7.169723923
7892518 3.396883381
7892519 5.865950777
7892520 9.99860779

Total number of rows: 33297

Table truncated, full table size 646 Kbytes.




Supplementary file Size Download File type/resource
GSM2301077_BaT144.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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