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Sample GSM3368825 Query DataSets for GSM3368825
Status Public on Sep 26, 2019
Title breast_cancer_primary_sample_56
Sample type RNA
 
Source name FFPE breast cancer
Organism Homo sapiens
Characteristics er_pos: 0
pgr_pos: 0
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 0.117626526
MARCH2 -0.164936714
MARCH3 0.041125703
MARCH4 0.058881647
MARCH5 0.191795663
MARCH6 0.874052968
MARCH7 0.805151595
MARCH8 0.051688151
MARCH9 -0.193298986
MARCH10 -0.04571201
MARCH11 -0.063620849
SEPT1 0.060860123
SEPT2 0.833293076
SEPT3 0.361877505
SEPT4 0.354214936
SEPT5 0.023476526
SEPT6 0.09941128
SEPT7 0.652964903
SEPT8 0.166910357
SEPT9 0.212614449

Total number of rows: 46048

Table truncated, full table size 967 Kbytes.




Supplementary file Size Download File type/resource
GSM3368825_GDX-31967-AM118-HuEx-1_0-st-v2-01-1_PR9-003594_.CEL.gz 19.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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