|
| Status |
Public on Jun 30, 2011 |
| Title |
NA12239_3 genotyping at HMS (NimbleGen 2.1M) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Input DNA from Coriell Cell Repositories
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GM12239
|
| Biomaterial provider |
Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM12239
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was obtained from Coriell Cell Repositories, extracted from lymphoblastoid cell lines.
|
| Label |
Cy3
|
| Label protocol |
1 ug reactions of each sample were labeled in quadruplicate according to manufacture's instructions using cy3 and cy5-random nonamers
|
| |
|
| Channel 2 |
| Source name |
Input DNA from Coriell Cell Repositories
|
| Organism |
Homo sapiens |
| Characteristics |
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 |
Cy5
|
| Label protocol |
1 ug reactions of each sample were labeled in quadruplicate according to manufacture's instructions using cy3 and cy5-random nonamers
|
| |
|
| |
| Hybridization protocol |
Hybridizations were performed according to manufacture's instructions, carried out on the Maui Hybridization System (BioMicro Systems Inc).
|
| Scan protocol |
Arrays were scanned on a DNA Microarray Scanner with Surescan High-Resolution Technology (G2464CA, Agilent Technologies)
|
| Data processing |
Normalization was performed using the segMNT algorithm at a 1X window averaging a minimum segment difference score of 0.3)
The Nexus rank segmentation software was used for CNV discovery
|
| |
|
| Submission date |
Jun 29, 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 |
GPL9973 |
| Series (2) |
| GSE25893 |
A comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants |
| GSE30312 |
A comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants (NimbleGen 2.1M) |
|
