NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1309627 Query DataSets for GSM1309627
Status Public on Jan 17, 2017
Title Primary Breast Cancer4106-250knsp
Sample type genomic
 
Source name genomic [email protected]
Organism Homo sapiens
Characteristics cell type: Primary Breast Cancer
mutation: CHEK2
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from fresh frozen primary breast cancer tissue using Qiagen Dneasy kit . DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.
Label Biotin
Label protocol As per manufacturer (Affymetrix)
 
Hybridization protocol DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Description Hybridized to 250K_Nsp
Data processing The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). .CEL files were imported in Partek Genomics Suite v.6.5. Copy number estimates were calculated in Partek against a reference baseline consisting of 90 female CEPH samples. Copy number segmentation was performed by Parteks Genomic segmentation tool with a minumum number of markers of 20. Threshold for calling gains and losses set to -0.25 < 2 > +25. Signal to noise 0.45.
 
Submission date Jan 17, 2014
Last update date Jan 17, 2017
Contact name Marcel Smid
Organization name Erasmus MC
Department Medical Oncology
Street address Dr. Molewaterplein 50
City Rotterdam
ZIP/Postal code PO Box 2040, 3000CA
Country Netherlands
 
Platform ID GPL3718
Series (2)
GSE54193 Proper genomic profiling of (BRCA1-mutated) basal-like breast carcinomas requires prior removal of tumor infiltrating lymphocytes
GSE54219 Molecular genomic and transcriptomic profiling of familial breast cancer.

Data table header descriptions
ID_REF
VALUE Copy number estimates per SNP

Data table
ID_REF VALUE
SNP_A-1780270 3.6273
SNP_A-1780272 1.99119
SNP_A-1780285 1.54905
SNP_A-1780286 1.32932
SNP_A-1780287 1.84666
SNP_A-1780289 2.47934
SNP_A-1780292 2.0455
SNP_A-1780294 2.11973
SNP_A-1780295 1.73201
SNP_A-1780300 1.94609
SNP_A-1780302 2.60722
SNP_A-1780303 1.4716
SNP_A-1780304 2.80468
SNP_A-1780305 1.84191
SNP_A-1780311 1.83699
SNP_A-1780312 2.14587
SNP_A-1780313 2.49772
SNP_A-1780316 1.77093
SNP_A-1780318 1.60238
SNP_A-1780320 7.21616

Total number of rows: 262264

Table truncated, full table size 5608 Kbytes.




Supplementary file Size Download File type/resource
GSM1309627_EA06018_0214-12C_Nsp250_VER4106_PCRN.CEL.gz 25.2 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap