MATT mapping of Transposon insertions sites of strain G27 GPS-cat library
Ontology highlight
ABSTRACT:
ORGANISM(S): Helicobacter pylori
PROVIDER: GSE3197 | GEO | 2005/08/26
SECONDARY ACCESSION(S): PRJNA92859
REPOSITORIES: GEO
Similar Datasets
Project description:Genomic DNA from pools of H. pylori strain G27 Clones as indicated (pools of 300 (300p) or insertions in specific mapped genes) were amplifed using the MATT method to label DNA adjacent to the site of transposon insertion with the primer pairs indicated. The left side of the transposon was labeled in the Cy3 channel (Primer S) and the right side of the transposon was labeled in the Cy5 channel (Primer N). Computed
2005-08-26 | E-GEOD-3197 | biostudies-arrayexpress
Project description:Genomic DNA from pools of H. pylori strain G27 Clones as indicated (pools of 300 (300p) or insertions in specific mapped genes) were amplifed using the MATT method to label DNA adjacent to the site of transposon insertion with the primer pairs indicated. The left side of the transposon was labeled in the Cy3 channel (Primer S) and the right side of the transposon was labeled in the Cy5 channel (Primer N). The results of these experiments are published in Salama et al. 2004. J Bact. 186(23):7926-7935.
2005-08-23 | E-SMDB-3048 | biostudies-arrayexpress
Project description:Microarray Tracking of transposon mutants for a H. pylori mouse colonization screen described in Baldwin DN et al. 2007. Screen in NSH79 H. pylori strain background. Original 2000 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
2006-12-15 | GSE6529 | GEO
Project description: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
2006-12-15 | GSE6528 | GEO
Project description:Microarray Tracking of transposon mutants for a H. pylori mouse colonization screen described in Baldwin DN et al. 2007, I&I, 75(2):??, doi:10.1128/IAI.01176-06. 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).
2006-12-15 | E-SMDB-3900 | biostudies-arrayexpress
Project description:Microarray Tracking of transposon mutants for a H. pylori mouse colonization screen described in Baldwin DN et al. 2007, I&I, 75(2):??, doi:10.1128/IAI.01176-06. Screen in NSH79 H. pylori strain background. Original 2000 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).
2006-12-15 | E-SMDB-3901 | biostudies-arrayexpress
Project description:Wildtype G27 and it's Fur mutant derivative were exposed to pH 5.0 for the indicated length of time. Bacterial cells in the exponential phase of growth (denoted log) and stationary phase of growth were used. fur1 denotes a single fur mutant while fur2 denotes an additional fur mutant. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. Keywords: all_pairs
2006-02-03 | GSE4160 | GEO
Project description:RNA from 11 individual mouse cell lines were reverse-transcribed to cDNA, labeled with Cy5 and cohybridized with Cy3-labeled UMRR onto 7,500-spot mouse oligo microarrays (UNC). The data was analyzed using GeneTraffic software. 300-1000 spots out of 8,000 were flagged on each microarray and excluded from further analysis. Spots with hybridization signals in Cy5 channel higher than 1000 and with Cy5/Cy3 ratio greater than 2 were collected and the number of spots with these characteristics on only one microarray was determined. A reference experiment design type is where all samples are compared to a common reference. Keywords: reference_design
2006-01-05 | GSE3974 | GEO
Project description:Total RNA isolated from 10 individual human cell lines were reverse-transcribed to cDNA, labeled with Cy5 and co-hybridized with Cy3-labeled UHRR onto 43,000-spot cDNA microarrays (Stanford University). The data was analyzed using GeneTraffic software. Approximately 6000-8000 spots out of 43,000 (14-18 %) were flagged on each microarray and excluded from further analysis. Spots with hybridization signals in Cy5 channel higher than 1000 and with Cy5/Cy3 ratio greater than 2 were collected and the number of spots with these characteristics in only one cell line was determined. A reference experiment design type is where all samples are compared to a common reference. Keywords: reference_design
2006-01-05 | GSE3972 | GEO
Project description:Wildtype G27 and it's Fur mutant derivative were exposed to pH 5.0 for the indicated length of time. Bacterial cells in the exponential phase of growth (denoted log) and stationary phase of growth were used. fur1 denotes a single fur mutant while fur2 denotes an additional fur mutant. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. Computed
2006-02-02 | E-GEOD-4160 | biostudies-arrayexpress