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Sample GSM696392 Query DataSets for GSM696392
Status Public on Jun 30, 2011
Title NA18517 rep2 genotyping at HMS (1X1M)
Sample type genomic
 
Channel 1
Source name NA18517
Organism Homo sapiens
Characteristics gender: Female
cell type: lymphoblastoid cell lines
cell line: GM18517
genotyping center: HMS
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA18517
Extracted molecule genomic DNA
Extraction protocol DNA was obtained from Coriell Cell Repositories, extracted from lymphoblastoid cell lines.
Label Cy5
Label protocol Invitrogen BioPrime CGH labeling kit was used (cat. No. 18094011), with an extended labeling time and increased cy3/cy5 concentrations compared to the manufactures protocol.
 
Channel 2
Source name GM10851
Organism Homo sapiens
Characteristics gender: Male
cell type: lymphoblastoid cell lines
cell line: GM10851
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM10851
Extracted molecule genomic DNA
Extraction protocol DNA was obtained from Coriell Cell Repositories, extracted from lymphoblastoid cell lines.
Label Cy3
Label protocol Invitrogen BioPrime CGH labeling kit was used (cat. No. 18094011), with an extended labeling time and increased cy3/cy5 concentrations compared to the manufactures protocol.
 
 
Hybridization protocol On each slide, a total combined 55ug of DNA was hybridized according to the 40-hour manual protocol described by manufacturer.
Scan protocol Arrays were scanned at 5 micron resolution in an Agilent Scanner
Description Genomic DNA extracted was analyzed using Illumina's BeadStudio software
Data processing Images were processed with Agilent Feature Extraction v9.5.1.1, and were required to show derivative Log Ratio spread (DLRS) values < 0.3. CNV detection was performed using Agilent's ADM-2 and also with the Nexus rank segmentation software.
 
Submission date Mar 22, 2011
Last update date Jun 30, 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 GPL8736
Series (2)
GSE25893 A comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants
GSE28112 A comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants (1X1M)

Data table header descriptions
ID_REF
VALUE normalized log10 ratio Cy5/Cy3

Data table
ID_REF VALUE
1 1.545034014e-004
2 0.000000000e+000
3 0.000000000e+000
4 -1.130002372e-001
5 1.207969776e-002
6 -9.384710045e-002
7 8.573722619e-002
8 -1.669639208e-001
9 -8.058874452e-002
10 9.309848671e-002
11 8.615787182e-002
12 -1.127620071e-001
13 -6.686810614e-003
14 4.426266954e-002
15 -1.273908203e-001
16 -1.188149608e-001
17 -7.433357241e-002
18 -1.260211679e-003
19 -8.932905340e-002
20 -3.289315615e-001

Total number of rows: 974016

Table truncated, full table size 23267 Kbytes.




Supplementary file Size Download File type/resource
GSM696392_NA18517-US85003610_252152923744_S01_CGH_105_Jan09.txt.gz 100.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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