|
| Status |
Public on Feb 01, 2011 |
| Title |
NA19716/NA12878 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
lymphoblast cell line DNA [test]
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
cell line: lymphoblast cell line NA19716
ethnicity: Mexican American from Los Angeles, CA (HapMap code: MEX)
|
| Biomaterial provider |
Coriell cell line NA19716
http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA19716
|
| 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 |
|
