|
| Status |
Public on Apr 01, 2011 |
| Title |
3D7 SNP Hybe 13 |
| Sample type |
genomic |
| |
|
| Source name |
3D7 DNA
|
| Organism |
Plasmodium falciparum |
| Characteristics |
strain: 3D7
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Phenol-chloroform extraction (Moll et al. 2008. Methods in Malaria Research. MR4/ATCC.)
|
| Label |
Cy3
|
| Label protocol |
Used NimbleGen's standard labeling protocol (http://www.nimblegen.com/products/lit/lit.html) with the following modification: used a custom 65% AT random nonamer mix from TriLink Biotechnologies
|
| |
|
| Hybridization protocol |
Used NimbleGen's standard CGH hybridization protocol (http://www.nimblegen.com/products/lit/lit.html) with the following modification: used 1x Denhardt's Solution in place of sample tracking control
|
| Scan protocol |
Arrays were scanned at 2um on a NimbleGen MS200 scanner with autogain per manufacturer's instructions (http://www.nimblegen.com/products/lit/lit.html)
|
| Data processing |
Arrays were processed using NimbleScan v2.5 per manufacturer's instructions (http://www.nimblegen.com/products/lit/lit.html)
The .bases files were created from scanned images using NimbleGen’s NimbleScan software (Analysis -> Reports -> Sequencing Bases ). These files contain the same information as NimbleGen .pair files but the probes have been collated by SNP locus. Due to this enhanced organization and readability, we use the .bases file instead of the .pair file as our raw data. We do not attempt to normalize between samples or across an entire image within one sample and directly use these intensity values in our secondary analysis, so no processed data is provided.
|
| |
|
| Submission date |
Mar 31, 2011 |
| Last update date |
Apr 01, 2011 |
| Contact name |
Michael Ferdig |
| E-mail(s) |
ferdig.1@nd.edu
|
| Phone |
(574)631-9973
|
| Organization name |
University of Notre Dame
|
| Department |
Biological Sciences
|
| Lab |
Ferdig Lab
|
| Street address |
280 Galvin Life Science
|
| City |
Notre Dame |
| State/province |
IN |
| ZIP/Postal code |
46556 |
| Country |
USA |
| |
|
| Platform ID |
GPL13355 |
| Series (1) |
| GSE28287 |
Plasmodium falciparum CNV-SNP chip optimization |
|
