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Sample GSM3368840 Query DataSets for GSM3368840
Status Public on Sep 26, 2019
Title breast_cancer_primary_sample_71
Sample type RNA
 
Source name FFPE breast cancer
Organism Homo sapiens
Characteristics er_pos: 0
pgr_pos: 0
her2_pos: 0
grade: 2
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 0.255366854
MARCH2 -0.059114445
MARCH3 0.139913207
MARCH4 -0.027778833
MARCH5 0.309735108
MARCH6 0.992120816
MARCH7 0.93413575
MARCH8 0.169241037
MARCH9 -0.256285879
MARCH10 0.013428386
MARCH11 -0.028438382
SEPT1 0.210211203
SEPT2 0.91738784
SEPT3 0.203287672
SEPT4 0.071619443
SEPT5 -0.004293447
SEPT6 0.634444721
SEPT7 0.713768646
SEPT8 0.185688631
SEPT9 0.374881285

Total number of rows: 46048

Table truncated, full table size 967 Kbytes.




Supplementary file Size Download File type/resource
GSM3368840_GDX-31954-AM105-HuEx-1_0-st-v2-01-1_PR9-003569_.CEL.gz 20.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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