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Sample GSM697960 Query DataSets for GSM697960
Status Public on Jun 30, 2011
Title NA18576C genotyping at WTSI (WGTS)
Sample type genomic
 
Channel 1
Source name Input DNA from Coriell Cell Repositories
Organism Homo sapiens
Characteristics cell type: lymphoblastoid cell lines
batch number: 3
genotyping center: WTSI
cell line: GM18576
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM18576
Extracted molecule genomic DNA
Extraction protocol DNA was obtained from Coriell Cell Repositories, extracted from lymphoblastoid cell lines.
Label Cy3
Label protocol The first two replicates were run with the test labeled with Cy5 and reference with Cy3; the third replicate consisted of the dye swap.
 
Channel 2
Source name Input DNA from Coriell Cell Repositories
Organism Homo sapiens
Characteristics cell line: NA10851
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA10851
Extracted molecule genomic DNA
Extraction protocol DNA was obtained from Coriell Cell Repositories, extracted from lymphoblastoid cell lines.
Label Cy5
Label protocol The first two replicates were run with the test labeled with Cy5 and reference with Cy3; the third replicate consisted of the dye swap.
 
 
Hybridization protocol Microarray hybridizations were performed as previously described (Fiegler, H et al, Nature 444, 444-454 2006)
Scan protocol Array images were acquired using a 5-um resolution Agilent Technologies G2505A laser scanner. Fluorescence intensities and log2 ration values were extracted using BlueFuse software.
Data processing After image quantification, log2 ratio calulation and block median normalization, a G+C correction was introduced, consisting of normalizing the log 2 ratios of each clone using the G+C percent of that clone
Copy number variable segments were detected using to CNVfinder algorithm.
 
Submission date Mar 25, 2011
Last update date Sep 06, 2011
Contact name Stephen W Scherer
E-mail(s) stephen.scherer@sickkids.ca
Organization name The Hospital for Sick Children
Department Genetics and Genomic Biology
Street address 686 Bay Street
City Toronto
State/province Ontario
ZIP/Postal code M5G 0A4
Country Canada
 
Platform ID GPL13331
Series (2)
GSE25893 A comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants
GSE28189 A comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants (WGTP)

Data table header descriptions
ID_REF
VALUE normalized log2 red/green

Data table
ID_REF VALUE
1 0.0453
2
3
4 0.0549
5 -0.0235
6 0.0205
7 -0.0192
8 -0.0515
9 0.02
10 0.0507
11 0.0722
12 0.0794
13 0.1426
14 -0.0225
15 0.0438
16 0.084
17 0.0174
18 0.0302
19 -0.0368
20 0.0283

Total number of rows: 28833

Table truncated, full table size 358 Kbytes.




Supplementary file Size Download File type/resource
GSM697960_NA18576C_active_20080222.txt.gz 588.9 Kb (ftp)(http) TXT
Processed data included within Sample table

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