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Sample GSM700004 Query DataSets for GSM700004
Status Public on Apr 01, 2011
Title 3D7 SNP Hybe 1
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

Supplementary file Size Download File type/resource
GSM700004_3D7_1.bases.gz 3.9 Mb (ftp)(http) BASES
Processed data not applicable for this record

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