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Expression analysis of A. actinomycetemcomitans wild type (JP2) vs. Mlc deletion mutant both grown aerobically and anaerobically

ABSTRACT: The goal of this analysis is to define the aerobic and anaerobic regulons for the transcription factor Mlc (Makes Large Colonies) in the periodontal pathogen Aggregatibacter actinomycetemcomitans. The objectives were met by comparing the mRNA profile of a wild type strain, JP2, to that of an isogenic mutant deleted of the Mlc gene. Both strains were grown aerobically and anaerobically. The results show that Mlc is involved in the regulation of dozens of genes in both growth conditions.

ORGANISM(S): Aggregatibacter actinomycetemcomitans Aggregatibacter actinomycetemcomitans HK1651

PROVIDER: GSE38868 | GEO | 2013/06/01

SECONDARY ACCESSION(S): PRJNA169082

REPOSITORIES: GEO

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Expression analysis of A. actinomycetemcomitans wild type (JP2) vs. Mlc deletion mutant both grown aerobically and anaerobically

Project description:The goal of this analysis is to define the aerobic and anaerobic regulons for the transcription factor Mlc (Makes Large Colonies) in the periodontal pathogen Aggregatibacter actinomycetemcomitans. The objectives were met by comparing the mRNA profile of a wild type strain, JP2, to that of an isogenic mutant deleted of the Mlc gene. Both strains were grown aerobically and anaerobically. The results show that Mlc is involved in the regulation of dozens of genes in both growth conditions. Half of the study (anaerobic samples) was a four biological replicates study using total RNA recovered from four separate anaerobic cultures of wild-type Aggregatibacter (formerly Actinobacillus) actinomycetemcomitans strain JP2 and four separate anaerobic cultures of strain AAM155, an isogenic deletion mutant in which the gene for Mlc (Makes Large Colonies) has been replaced by a spectinomycin resistance gene cassette. The cells were grown anaerobically in pairs (wild type paired with mutant). The second half of the study (aerobic samples) was a four biological replicates study using total RNA recovered from four separate aerobic cultures of wild-type Aggregatibacter actinomycetemcomitans strain JP2 and four separate anaerobic cultures of strain AAM155, an isogenic deletion mutant of Mlc. The cells were grown aerobically in pairs (wild type paired with mutant). Each chip measures the expression level of 2,116 genes from A. actinomycetemcomitans strain HK1651. There were 11 different 60-mer probes /gene for 94% of the genes, and the entire probe set (22,537 probes) was replicated (technical replicates) three times on each array. Each probe set is contained on a quarter of a chip and there were also 4,426 random probes per array. A total of four chips were used in these experiments.

2013-06-01 | E-GEOD-38868 | biostudies-arrayexpress

Expression analysis, A. actinomycetemcomitans wild type (JP2) vs CRP deletion mutant both grown anaerobically.

2011-06-01 | GSE25459 | GEO

Expression analysis, A. actinomycetemcomitans wild type (JP2) vs CRP deletion mutant both grown anaerobically.

Project description:The goal of this analysis is to define the anaerobic regulon for the global transcription factor CRP (catabolite repressor protein) in the periodontal pathogen Aggregatibacter actinomycetemcomitans. The objectives were met by comparing the mRNA profile of a wild type strain, JP2, to that of an isogenic mutant deleted of the CRP gene. Both strains were grown anaerobically. A three biological replicates study using total RNA recovered from three separate cultures of wild-type Aggregatibacter actinomycetemcomitans strain JP2 and three separate cultures of strain AAM167, an isogenic deletion mutant in which the gene for cAMP-Receptor-Protein (CRP) has been replaced by a spectinomycin resistance gene cassette. The cells were grown anaerobically in pairs (wild type paired with mutant). Each chip measures the expression level of 2,116 genes from A. actinomycetemcomitans strain HK1651. There were 11 different 60-mer probes /gene for 94% of the genes, and the entire probe set (22,537 probes) was replicated (technical replicates) three times on each array. Each probe set is contained on a quarter of a chip and there were also 4,426 random probes per array. Wild type and mutant RNAs from cultures #1 and #2 were hybridized to the same chip and the RNAs from cultures #3 were hybridized in different quadrants of a second chip.

2011-06-01 | E-GEOD-25459 | biostudies-arrayexpress

Comparative genomic analysis of Aggregatibacter actinomycetemcomitans of JP2 and non-JP2 genotypes using a pan-genome microarray

Project description:To assess the performance of our custom-designed pan-genome microarray and characterize the differences in gene content between JP2 and non-JP2 genotypes of A. actinomycetemcomitans. Comparative genomic hybridization reactions were carried out to assess the performance of our pan-genome microarray by using genomic DNA of 11 previously sequenced Aggregatibacter actinomycetemcomitans strains (I23C, SCC1398, ANH9381, HK1651, D7S-1, D11S-1, I63B, SCC393, D18P-1, SCC2302, and D17P-2). The microarray was subsequently used for comparative genomic hybridization of 6 strains of JP2 (S067, A26, G111-1, G121-2, D41S-1, and HK1651) and 6 strains non-JP2 (I23C, SCC1398, ANH9381, ATCC29524, 194, and G104-2) genotypes of Aggregatibacter actinomycetemcomitans. Two biological duplicates were carried out for each strain.

2012-09-28 | E-GEOD-39143 | biostudies-arrayexpress

Transcriptome analysis of Aggregatibacter actinomycetemcomitans serotype b strains of JP2 and non-JP2 genotypes using a pan-genome microarray

2012-09-28 | GSE38943 | GEO

Comparative genomic analysis of Aggregatibacter actinomycetemcomitans of JP2 and non-JP2 genotypes using a pan-genome microarray

2012-09-28 | GSE39143 | GEO

Aggregatibacter actinomycetemcomitans

Project description:Expression analysis of A. actinomycetemcomitans wild type (JP2) vs. Mlc deletion mutant both grown aerobically and anaerobically

| PRJNA169082 | ENA

Transcriptome analysis of Aggregatibacter actinomycetemcomitans serotype b strains of JP2 and non-JP2 genotypes using a pan-genome microarray

Project description:To characterize the differences in pattern of gene expression between JP2 and non-JP2 genotypes of A. actinomycetemcomitans. Transcriptome analysis of 3 strains of JP2 and 2 strains of non-JP2 genotypes of A. actinomycetemcomitans was performed Transcripome of three strains of JP2 genotype (HK1651, D28S-1 and D41S-1) and two strains of non-JP2 genotype (SCC1398 and ANH9381) were examined where two biological duplicates were carried out for each strain.

2012-09-28 | E-GEOD-38943 | biostudies-arrayexpress

Transcriptome of aerobically/anaerobically grown Actinobacillus succinogenes strain 130Z on fumarate/glucose

Project description:Transcriptome of aerobically/anaerobically grown Actinobacillus succinogenes strain 130Z on fumarate/glucose

2016-12-22 | GSE92722 | GEO

Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically

Project description:Transcriptome analysis using RNA-Seq of E. coli REL4536 grown aerobically and anaerobically was undertaken to investigate the activities of various DNA replication and repair pathways involved in maintaining genome integrity, and to assess if their expression is consistent with observed patterns of mutation in the aerobic and anaerobic environments. Consistent with mutation rate and spectra observations, genes for recombination repair, associated with SVs, were generally up-regulated during anaerobic growth.

2016-04-26 | GSE80451 | GEO

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