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Sample GSM696366 Query DataSets for GSM696366
Status Public on Jun 30, 2011
Title NA18576 rep1 genotyping at TCAG (1X1M)
Sample type genomic
 
Channel 1
Source name NA18576
Organism Homo sapiens
Characteristics gender: Female
cell type: lymphoblastoid cell lines
cell line: GM18576
genotyping center: TCAG
Biomaterial provider Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA18576
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 2.217176013e-003
2 -2.232488757e-001
3 -6.788399600e-001
4 -2.024276903e-001
5 -7.808893260e-002
6 -3.127033026e-001
7 -2.486889035e-001
8 -2.081927950e-001
9 -1.083269545e-001
10 -2.327979438e-001
11 -1.136979703e-001
12 -2.197161314e-001
13 -1.939830828e-001
14 -1.444080642e-001
15 -1.788198277e-001
16 -1.267887027e-001
17 -1.016318450e-001
18 -6.284558302e-002
19 -1.207171867e-002
20 -2.650408812e-001

Total number of rows: 974016

Table truncated, full table size 23216 Kbytes.




Supplementary file Size Download File type/resource
GSM696366_H1M_070810R_SS5-2_NA18576_252152921946_S01_CGH_105_Jan09.txt.gz 101.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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