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Sample GSM564878 Query DataSets for GSM564878
Status Public on Aug 05, 2010
Title IQE3435
Sample type genomic
 
Source name Genomic DNA from Peruvian isolate
Organism Plasmodium falciparum
Characteristics strain: Peruvian isolate
Growth protocol 3D7 (MRA-151) was obtained from the Malaria Research and Reference Reagent Resource Center (MR4; American Type Culture Collection, Manassas, VA, USA). 3D7 and Peruvian P. falciparum patient isolates were propagated in human erythrocytes as previously described (Trager and Jenson 1978) with media for 3D7 containing 5% human serum and 1.2% GIBCO™ AlbuMAX II (Invitrogen) while the media for patient isolates contained 10% human serum.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated by standard phenol-chloroform extraction.
Label biotin
Label protocol Fifteen micrograms of genomic DNA from each isolate and 2.5 ng each of Bio B, Bio C, Bio D, and Cre Affymetrix control plasmids (Affymetrix Inc., Santa Clara, CA, USA) were fragmented with DNaseI and end-labeled with biotin (Winzeler et al. 1998).
 
Hybridization protocol The samples were hybridized to the microarrays overnight at 45°C in Affymetrix buffers, washed, and scanned using a modified protocol with wash temperatures of 23°C to account for the high AT content of P. falciparum (Supplementary File 6 from this publication) (Dharia et al. 2009).
Scan protocol The samples were hybridized to the microarrays overnight at 45°C in Affymetrix buffers, washed, and scanned using a modified protocol with wash temperatures of 23°C to account for the high AT content of P. falciparum (Supplementary File 6 from this publication) (Dharia et al. 2009).
Description Genomic DNA hybridization of Peruvian isolate
Data processing Briefly, for polymorphism detection, using a sliding window of three overlapping probes we scanned for sets probes that had significantly lower hybridization when compared to the reference indicative of a polymorphism as determined by z-test using a p-value cutoff of 1´10-5 and a reference 3D7 hybridization. Gene copy number variation scanning was performed by calculating the log2 ratio of the mean intensity for probes to a gene divided by the mean intensity of the probes for a reference 3D7 hybridization as previously described (Dharia et al. 2009).
The arrays were analyzed using our custom software available at http://www.scripps.edu/cb/winzeler/software and described in Dharia et al Genome Biology 2009, 10:R21.
 
Submission date Jul 09, 2010
Last update date Aug 05, 2010
Contact name Neekesh V Dharia
E-mail(s) ndharia@scripps.edu
URL http://www.scripps.edu/cb/winzeler
Organization name The Scripps Research Institute
Lab Winzeler Lab
Street address 10550 N Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL9610
Series (1)
GSE22861 Genome-scanning of Amazonian Plasmodium falciparum shows subtelomeric instability and clindamycin resistant parasites

Supplementary file Size Download File type/resource
GSM564878.CEL.gz 50.1 Mb (ftp)(http) CEL
Processed data are available on Series record

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