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Sample GSM2301096 Query DataSets for GSM2301096
Status Public on Aug 31, 2018
Title Breast cancer tissue [BT123]
Sample type RNA
 
Source name Fresh frozen tumor tissue
Organism Homo sapiens
Characteristics molecular subtype: Luminal B
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 8.072078544
7892502 5.765933808
7892503 4.837642475
7892504 9.58741448
7892505 3.988907789
7892506 3.298777046
7892507 4.599391436
7892508 7.376234442
7892509 12.37734927
7892510 6.216982081
7892511 4.012825403
7892512 7.979487761
7892513 4.099971428
7892514 10.88649294
7892515 9.596227133
7892516 6.314374968
7892517 6.081076178
7892518 3.79190984
7892519 5.463500007
7892520 9.855494078

Total number of rows: 33297

Table truncated, full table size 646 Kbytes.




Supplementary file Size Download File type/resource
GSM2301096_BT123.CEL.gz 4.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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