|
| Status |
Public on Jun 30, 2011 |
| Title |
NA18980C 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: GM18980
|
| Biomaterial provider |
Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM18980
|
| 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) |
[email protected]
|
| 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) |
|
