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Sample GSM3368783 Query DataSets for GSM3368783
Status Public on Sep 26, 2019
Title breast_cancer_primary_sample_14
Sample type RNA
 
Source name FFPE breast cancer
Organism Homo sapiens
Characteristics er_pos: 1
pgr_pos: 1
her2_pos: 0
grade: 2
systemic therapy: 0
menopause: 1
tumor size (millimeters): <=10
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 0.282982864
MARCH2 -0.066411413
MARCH3 0.088500922
MARCH4 0.126810022
MARCH5 0.208417788
MARCH6 0.99934985
MARCH7 0.709999626
MARCH8 0.092008616
MARCH9 -0.128047593
MARCH10 -0.043307495
MARCH11 0.255273006
SEPT1 0.04588598
SEPT2 0.786682444
SEPT3 -0.036453276
SEPT4 0.017216421
SEPT5 0.055517465
SEPT6 0.218537636
SEPT7 0.433314434
SEPT8 0.394547262
SEPT9 0.222220294

Total number of rows: 46048

Table truncated, full table size 964 Kbytes.




Supplementary file Size Download File type/resource
GSM3368783_GDX-30971-AM068-HuEx-1_0-st-v2-01-1_PR9-003417_.CEL.gz 19.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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