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Sample GSM3368955 Query DataSets for GSM3368955
Status Public on Sep 26, 2019
Title breast_cancer_primary_sample_186
Sample type RNA
 
Source name FFPE breast cancer
Organism Homo sapiens
Characteristics er_pos: 1
pgr_pos: 1
her2_pos: 0
grade: 3
systemic therapy: 0
menopause: 1
tumor size (millimeters): <=10
age: 60-69
Sex: female
Extracted molecule total RNA
Extraction protocol After pathologic review, FFPE tissue was harvested with a 1 mm punch. RNA was extracted from tissue punches using the RNeasy FFPE kit (Qiagen, Hilden, Germany).
Label biotin
Label protocol cDNA was amplified using the Ovation FFPE WTA system (NuGEN, San Carlos, CA). Amplified cDNA was fragmented and labeled using the Encore Biotin Module (NuGEN, San Carlos, CA).
 
Hybridization protocol Samples were hybridized using Affymetrix hybridization kit materials and protocols
Scan protocol Affymetrix GeneChip Scanner 3000 7G
Description breast cancer primary tumor
Data processing Data was normalized using SCAN (SCAN.UPC package from Bioconductor)
 
Submission date Aug 30, 2018
Last update date Sep 28, 2019
Contact name Laura Chang
Organization name PFS Genomics
Street address 1152 Mainland St, Suite 430
City Vancouver
State/province BC
ZIP/Postal code V6B 4X2
Country Canada
 
Platform ID GPL22995
Series (1)
GSE119295 Comprehensive transcriptomic profiling of breast cancer patients in SweBCG 91-RT

Data table header descriptions
ID_REF
VALUE SCAN normalized expression

Data table
ID_REF VALUE
MARCH1 0.164422351
MARCH2 -0.069664108
MARCH3 0.014261353
MARCH4 0.103735887
MARCH5 0.34106193
MARCH6 0.666573487
MARCH7 0.916662035
MARCH8 0.385463237
MARCH9 -0.141969129
MARCH10 -0.082058185
MARCH11 -0.034599994
SEPT1 0.193115302
SEPT2 0.96837834
SEPT3 -0.085503329
SEPT4 0.05611088
SEPT5 0.09837753
SEPT6 0.066109328
SEPT7 0.403031501
SEPT8 0.200395804
SEPT9 0.250738817

Total number of rows: 46048

Table truncated, full table size 967 Kbytes.




Supplementary file Size Download File type/resource
GSM3368955_GDX-37112-AM712-HuEx-1_0-st-v2-01-1_PR9-004877_.CEL.gz 20.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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