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Sample GSM649567 Query DataSets for GSM649567
Status Public on Feb 01, 2011
Title HG00174/NA12878
Sample type genomic
 
Channel 1
Source name lymphoblast cell line DNA [test]
Organism Homo sapiens
Characteristics gender: Female
cell line: lymphoblast cell line HG00174
ethnicity: Finnish from Finland (1000 Genomes code: FIN)
Biomaterial provider Coriell cell line HG00174
http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=HG00174
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from lymphoblast cell lines by Coriell Repositories (http://ccr.coriell.org/)
Label Cy3
Label protocol 250 ng of genomic DNA (unsonicated) was labeled by Klenow using random priming with Cy3/Cy5 nonamers (for test and reference samples, respectively) using Nimblegen labelling kit but with the following changes: reagents were scaled to the smaller amount of input DNA and with DNA labeling occurring overnight.
 
Channel 2
Source name lymphoblast cell line DNA [reference]
Organism Homo sapiens
Characteristics gender: female
cell line: lymphoblast cell line NA12878
ethnicity: Northwest European American from Utah (HapMap code: CEU)
Biomaterial provider Coriell cell line NA12878
http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA12878
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from lymphoblast cell lines by Coriell Repositories (http://ccr.coriell.org/)
Label Cy5
Label protocol 250 ng of genomic DNA (unsonicated) was labeled by Klenow using random priming with Cy3/Cy5 nonamers (for test and reference samples, respectively) using Nimblegen labelling kit but with the following changes: reagents were scaled to the smaller amount of input DNA and with DNA labeling occurring overnight.
 
 
Hybridization protocol The hybridization protocol was performed per Agilent protocols (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf) with 5 ug of labelled test sample and 5 ug of labelled reference sample (NA12878)
Scan protocol The scan protocol was performed using the Agilent Scanner per Agilent protocols (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf).
Data processing The data were processed using the Agilent Feature Extraction software 10.5.1.1 using program defaults (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf) except that 3000 probes through out the genome were used for dye normalization.
 
Submission date Jan 05, 2011
Last update date Feb 01, 2011
Contact name Catarina D Campbell
E-mail(s) cdcamp@u.washington.edu
Organization name Univerisity of Washington
Department Genome Sciences
Lab Evan Eichler
Street address 3720 15th Avenue NE
City Seattle
State/province WA
ZIP/Postal code 98103
Country USA
 
Platform ID GPL11387
Series (1)
GSE26450 Population genetic properties of differentiated human copy number polymorphisms

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

Data table
ID_REF VALUE
1 -1.745822321e-002
2 0.000000000e+000
3 0.000000000e+000
4 0.000000000e+000
5 0.000000000e+000
6 0.000000000e+000
7 0.000000000e+000
8 0.000000000e+000
9 0.000000000e+000
10 0.000000000e+000
11 0.000000000e+000
12 0.000000000e+000
13 0.000000000e+000
14 0.000000000e+000
15 0.000000000e+000
16 0.000000000e+000
17 0.000000000e+000
18 0.000000000e+000
19 0.000000000e+000
20 0.000000000e+000

Total number of rows: 180880

Table truncated, full table size 4193 Kbytes.




Supplementary file Size Download File type/resource
GSM649567_252679510293_201008131221_S01_CGH_CNParray_July09_1_2.txt.gz 18.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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