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Sample GSM2301076 Query DataSets for GSM2301076
Status Public on Aug 31, 2018
Title Breast cancer tissue [BaT140]
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 5.844664388
7892502 6.132409121
7892503 4.069759314
7892504 9.730178444
7892505 3.647149319
7892506 5.031417164
7892507 5.580709859
7892508 7.54230449
7892509 11.7084811
7892510 6.46774198
7892511 4.479565317
7892512 8.48773686
7892513 3.574194626
7892514 10.72708189
7892515 10.19944909
7892516 6.897796493
7892517 7.009649712
7892518 3.554154756
7892519 5.577077144
7892520 10.26100101

Total number of rows: 33297

Table truncated, full table size 646 Kbytes.




Supplementary file Size Download File type/resource
GSM2301076_BaT140.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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