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Sample GSM699997 Query DataSets for GSM699997
Status Public on Apr 01, 2011
Title HB3 vs. 3D7 CGH Hybe 2
Sample type genomic
 
Channel 1
Source name HB3 DNA
Organism Plasmodium falciparum
Characteristics strain: HB3
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
 
Channel 2
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 Cy5
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)
 
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

Data table header descriptions
ID_REF
VALUE NimbleScan log2 Cy3/Cy5 (test/reference) ratio

Data table
ID_REF VALUE
10055_0250_0774 -0.768
10055_0861_0749 0.821
10055_0241_0891 -0.609
10055_0805_1147 -0.85
10055_0463_0895 0.155
10055_0827_1007 -0.114
10055_0389_1007 -0.881
10055_0729_0853 -0.739
10055_0497_1269 -0.916
10055_0091_1215 -1.226
10055_0075_0773 -1.252
10055_0238_0902 -0.235
10055_0154_0834 -0.441
10055_0861_0775 -0.049
10055_0037_0829 0.504
10055_0188_1126 -1.369
10055_0332_1064 -0.627
10055_0032_0896 -0.83
10055_0789_1243 -1.63
10055_0221_0977 -0.287

Total number of rows: 355803

Table truncated, full table size 7748 Kbytes.




Supplementary file Size Download File type/resource
GSM699997_HB3v3D7_2_Cy3.pair.gz 6.5 Mb (ftp)(http) PAIR
GSM699997_HB3v3D7_2_Cy5.pair.gz 6.5 Mb (ftp)(http) PAIR
Processed data included within Sample table

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