|
Status |
Public on Jun 30, 2011 |
Title |
NA18576 rep1 genotyping at TCAG (1X1M) |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
NA18576
|
Organism |
Homo sapiens |
Characteristics |
gender: Female cell type: lymphoblastoid cell lines cell line: GM18576 genotyping center: TCAG
|
Biomaterial provider |
Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA18576
|
Extracted molecule |
genomic DNA |
Extraction protocol |
DNA was obtained from Coriell Cell Repositories, extracted from lymphoblastoid cell lines.
|
Label |
Cy5
|
Label protocol |
Invitrogen BioPrime CGH labeling kit was used (cat. No. 18094011), with an extended labeling time and increased cy3/cy5 concentrations compared to the manufactures protocol.
|
|
|
Channel 2 |
Source name |
GM10851
|
Organism |
Homo sapiens |
Characteristics |
gender: Male cell type: lymphoblastoid cell lines 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 |
Cy3
|
Label protocol |
Invitrogen BioPrime CGH labeling kit was used (cat. No. 18094011), with an extended labeling time and increased cy3/cy5 concentrations compared to the manufactures protocol.
|
|
|
|
Hybridization protocol |
On each slide, a total combined 55ug of DNA was hybridized according to the 40-hour manual protocol described by manufacturer.
|
Scan protocol |
Arrays were scanned at 5 micron resolution in an Agilent Scanner
|
Description |
Genomic DNA extracted was analyzed using Illumina's BeadStudio software
|
Data processing |
Images were processed with Agilent Feature Extraction v9.5.1.1, and were required to show derivative Log Ratio spread (DLRS) values < 0.3. CNV detection was performed using Agilent's ADM-2 and also with the Nexus rank segmentation software.
|
|
|
Submission date |
Mar 22, 2011 |
Last update date |
Jun 30, 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 |
GPL8736 |
Series (2) |
GSE25893 |
A comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants |
GSE28112 |
A comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants (1X1M) |
|