|
Status |
Public on Jun 30, 2011 |
Title |
NA15510B 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: 2 genotyping center: WTSI cell line: GM15510
|
Biomaterial provider |
Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM15510
|
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) |
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 |
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) |
|