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Sample GSM3368801 Query DataSets for GSM3368801
Status Public on Sep 26, 2019
Title breast_cancer_primary_sample_32
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): 11-20
age: >=70
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 0.103549894
MARCH2 0.200553806
MARCH3 0.258188186
MARCH4 0.126595371
MARCH5 0.341363641
MARCH6 1.134858616
MARCH7 0.746362144
MARCH8 0.096322148
MARCH9 -0.241714187
MARCH10 -0.050931129
MARCH11 0.047867295
SEPT1 0.124934969
SEPT2 0.769685417
SEPT3 0.35957971
SEPT4 0.16811887
SEPT5 0.093450334
SEPT6 0.304716374
SEPT7 0.506005531
SEPT8 0.418899465
SEPT9 0.385114049

Total number of rows: 46048

Table truncated, full table size 968 Kbytes.




Supplementary file Size Download File type/resource
GSM3368801_GDX-26052-AL415-HuEx-1_0-st-v2-01-1_PR9-002429_.CEL.gz 19.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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