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Status |
Public on Aug 05, 2010 |
Title |
IQE3435 |
Sample type |
genomic |
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Source name |
Genomic DNA from Peruvian isolate
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Organism |
Plasmodium falciparum |
Characteristics |
strain: Peruvian isolate
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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.
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Extracted molecule |
genomic DNA |
Extraction protocol |
Genomic DNA was isolated by standard phenol-chloroform extraction.
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Label |
biotin
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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).
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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).
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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).
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Description |
Genomic DNA hybridization of Peruvian isolate
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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.
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Submission date |
Jul 09, 2010 |
Last update date |
Aug 05, 2010 |
Contact name |
Neekesh V Dharia |
E-mail(s) |
ndharia@scripps.edu
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URL |
http://www.scripps.edu/cb/winzeler
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Organization name |
The Scripps Research Institute
|
Lab |
Winzeler Lab
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Street address |
10550 N Torrey Pines Road
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City |
La Jolla |
State/province |
CA |
ZIP/Postal code |
92037 |
Country |
USA |
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Platform ID |
GPL9610 |
Series (1) |
GSE22861 |
Genome-scanning of Amazonian Plasmodium falciparum shows subtelomeric instability and clindamycin resistant parasites |
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