Map transformed DNA into W6G from VCXB21
Ontology highlight
ABSTRACT:
ORGANISM(S): Vibrio cholerae
PROVIDER: GSE8791 | GEO | 2007/08/16
SECONDARY ACCESSION(S): PRJNA102093
REPOSITORIES: GEO
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Project description:Vibrio cholerae isolate W6G transformed with DNA from VCXB21 and selected for chitosan metabolism. Nine independent transformants compared to parental W6G on microarrays containing probes for all N16961 ORFs. Regions acquired from VCXB21 hybridize more strongly to the array. A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's. Using regression correlation
2007-08-16 | E-GEOD-8791 | biostudies-arrayexpress
Project description:Environmental isolates of Vibrio cholerae from California coastal water compared to reference strain N16961. A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's. Keywords: genotyping_design; array CGH
2007-07-17 | GSE8499 | GEO
Project description:These experiments were performed to show a serogroup conversion in Vibrio cholerae from O1 to O139. For this purpose, V. cholerae O1 WT = A1552 was grown on crab shell fragments to induce natural competence for transformation. Purified DNA (2 ug each) from strain VC73-orf6/7-Kan-A was added after 24h and the cells grown further for 24h. The VC73-orf6/7-Kan-A strain is a ATCC25873 derivative (both O37 serogroup) which harbors a Kanamycin cassette in the O37 region (as part of the operon between orf6 and orf7 w/o own promotor) for better selection. Transformants were selected on LB+Kan plates. Three clones were selected from each experiment and analyzed by microarray hybridization (BioPrime. Array CGH Genomic Labeling from Invitrogen). Two microarray replicates were done per clone. Comparison of A1552 versus VC73-orf6/7-Kan-A is shown as control. A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's. Keywords: genotyping_design
2007-04-26 | GSE5935 | GEO
Project description:These experiments were performed to show serogroup conversion in Vibrio cholerae from O1 to O139 in a mixed communities / biofilms. For this purpose, V. cholerae O1 El Tor A1552 and VCO139-Kan strain (a MO10 derivative; O139 serogroup) were grown on crab shell fragments to induce natural competence for transformation. Transformants were selected on LB+Kan+Rif plates. O139 positive transformants have undergone a full exchange of the O1 region by the O139 region. This implies an exchange of an at least 32 kb spanning O1 genomic region by more than 42 kb of the O139 region. The transformation experiment was done at least five independent times; data from four experiments are shown; per experiment one to three clones were analysed by CGH with two experimental replicates each. A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's. Keywords: all_pairs, array CGH
2007-04-25 | GSE5932 | GEO
Project description:These experiment were performed to show a serogroup conversion in Vibrio cholerae from O1 to O139. For this purpose, V. cholerae O1 WT = A1552 was grown on crab shell fragments to induce natural competence for transformation. Purified DNA (2 ug each) from strain VCO139-Kan was added after 24h and the cells grwon further for 24h. The VCO139-Kan strain is a MO10 derivative (both O139 serogroup) which harbors a Kanamycin cassette in the O139 region (as part of the operon between wbfA and wbfB w/o own promotor) for better selection. Transformants were selected on LB+Kan plates. Two groups of transformants were gained: Group I had a full exchange of the O1 region by the O139 region (clones serogroup-converted: SGC#1-3); the crossovers for the homologous recombination event had occurred within or upstream of the gmhD gene and in most instances within or downstream of the homolog gene of VC0271. This implies an exchange of an at least 33 kb spanning O1 genomic region by more than 42 kb of the O139 region. Group II had only half of the O139 region transfered and therefore half of the O1 region kept (clones HSGC#4-6). We analyzed their genotype and found that all of them had undergone a homologous recombination event with one crossover in or upstream of the gmhD gene and the second one inside the VC0254 and IS1358 gene. The transformation experiment was done three independent times (I - III). Three clones from group I and group II were selected from each experiment and analyzed by microarray hybridization (BioPrime. Array CGH Genomic Labeling from Invitrogen). Two microarray replicates were done per clone. A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's. Strain Name: -III for experimental replicates (transformation); clones #1 -#3 full region exchanged; clones #4-#6 half region exchanged. Two MA replicates for each clone Keywords: genotyping_design, array CGH
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Project description:Array CGH analysis of Helicobacter pylori strains isolated from a North American cohort of symptomatic pediatric patients. Keywords: genotyping_design A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's. Patients enrolled under Benjamin Gold's Emory IRB protocol. Initial strain isolation from antral biopsies performed at Emory and culture sweeps sent to FHCRC (Seattle) for analysis. Single colony isolates (4) from each patient antral biopsy were isolated and profiled using RAPD. A single clone of each RAPD type detected in each patient (1-2) were analyzed on duplicate arrays. For analysis 500 ng of genomic DNA of each test strain was labeled with Cy5 and 500 ng of genomic DNA of a reference sample (equimolar mix of 26695 and J99) was labeled with Cy3. Strains identified as Em-patient#-clone#.
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Project description:These experiments were performed to show a serogroup conversion of Vibrio cholerae from O1 to 37. For this purpose, V. cholerae O1 El Tor (A1552) was grown on crab shell fragments to induce natural competence for transformation. Purified DNA (4 ug each) from strain ATCC25872, an O37 serogroup strain, was added after 24h and the cells were further grown for 24h. After detachment from the crab shell fragments, bacteria were poured into soft-agar and overlaid onto LB plates. Mukerjee's El Tor phage III (a gift of Dr. M.S. Islam) was dropped onto the surface of the bacteria containing soft-agar. The plaques formed by killing non-transformed A1552 cells possessed resistant clones which were picked and further selected by non-agglutination with O1-specific antiserum. One to four clones were selected from each independent experiment and analyzed by microarray hybridization (BioPrime. Array CGH Genomic Labeling from Invitrogen). Two microarray replicates were done per clone. Strain Names: AIpO37#1 / AIpO37#4 / AIpO37#6 / AIpO37#8 are clones analyzed from the first experiment; AIIpO37#9 / AIIpO37#13 / AIIpO37#16 are clones analyzed from the second independent experiment; AIIIpO37#9A is a clone analyzed from the third independent experiment; AIVpO37#1A / AIVpO37#3A / AIVpO37#4A / AIVpO37#8A are clones analyzed from the fourth independent experiment. Two MA replicates per clone were done. CGHs of A1552 versus ATCC25872 are provided as control. A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's. Keywords: genotyping_design
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Project description:Investigation of whole genome gene expression level changes in a Vibrio cholerae O395N1 delta-nqrA-F mutant, compared to the wild-type strain. Total RNA recovered from wild-type cultures of VIbrio cholerae O395N1 and its nqrA-F mutant strain. Each chip measures the expression level of 3,835 genes from Vibrio cholerae O1 biovar eltor str. N16961 with twenty average probes/gene, with five-fold technical redundancy.
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Project description:Environmental isolates of Vibrio cholerae from California coastal water compared to reference strain N16961.
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Project description:The pha-4 locus encodes a forkhead box A (FoxA/HNF3) transcription factor homolog that specifies organ identity for Caenorhabditis elegans pharyngeal cells. We used microarrays to identify pharyngeal genes and analyzed those genes to determine which were direct PHA-4 targets. Our data suggest that PHA-4 directly activates most or all pharyngeal genes. Furthermore, the relative affinity of PHA-4 for different TRTTKRY (R = A/G, K = T/G, Y = T/C) elements modulates the onset of gene expression, providing a mechanism to activate pharyngeal genes at different developmental stages. We suggest that direct transcriptional regulation of entire gene networks may be a common feature of organ identity genes. A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's. Keywords: genotyping_design
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