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Series GSE6528 Query DataSets for GSE6528
Status Public on Dec 15, 2006
Title NSH57 Tn Library Mouse Pools
Organism Helicobacter pylori
Experiment type Genome variation profiling by array
Summary Microarray Tracking of transposon mutants for a H. pylori mouse colonization screen described in Baldwin DN et al. Screen in NSH57 H. pylori strain background. Original 50,000 clone transposon library was plated and patched to make 25 pools of 48 clones. Clones were infected into 4-8 C57Bl/6 mice and stomach bacteria from at least two mice were harvested at 1 week or one month. Semi-random PCR was used to amplify and label the DNA next to the transposon insertion from the input (Cy3) and output pool (Cy5) genomic DNA for each array. Two arrays were done per mouse. One array labeled from the left side of transposon (primers S, 2C) and one array labeled from the right side of the transposon (primers N3, 2C). Transposon insertions were defined by spots with signal four standard deviations above background in both arrays. We also counted insertions where two adjacent gene spots (after arranging the data in genome order) gave signal from the two different sides of the transposon (but not both).
A pathogenicity experiment design type is where an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed.
Keywords: pathogenicity_design
 
Overall design Computed
 
Contributor(s) Baldwin D
Citation(s) 17101654
Submission date Dec 14, 2006
Last update date Mar 17, 2012
Contact name Nina Reda Salama
E-mail(s) nsalama@fhcrc.org
Phone 206-667-1540
Fax 206-667-6524
Organization name Fred Hutchinson Cancer Research Center
Department Division of Human Biology
Lab Mailstop C3-168
Street address 1100 Fairview Ave. N
City Seattle
State/province WA
ZIP/Postal code 19024
Country USA
 
Platforms (1)
GPL2781 HP_Hutcharray_6-03
Samples (194)
GSM150340 NSH57 6-5 1mo: N3, 2C
GSM150341 NSH57 17-1 1wk: N3, 2C
GSM150342 NSH57 17-2 1wk: N3, 2C
This SubSeries is part of SuperSeries:
GSE6531 Identification of Helicobacter pylori genes contributing to stomach colonization.
Relations
BioProject PRJNA104241

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Supplementary data files not provided
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