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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptional analysis of AHLs signals add in experiment inYersinia pestis CO92 at 37Â°C

ABSTRACT: Yersinia pestis, the etiological agent of plague, is able to sense cell density by quorum sensing. The function of quorum sensing in Y. pestis is not clear. Here, the process of AHL quorum sensing was investigated by comparing transcript profiles when two AHL quorum-sensing signals are added in. The strain âpgm (pigmentation-negative) mutant R88 was called wild type. The two AHLs signals are N-(3-Oxooctanoyl)-L-homoserine lactone and N-Hexanoyl-DL-homoserine lactone.The control consisted of cells grown and treated under the same conditions without added signals. Six independent RNA samples from R88 cultures were paired with six independent RNA samples from two AHLs added cultures for hybridization to six two-color microarrays. A dye-swap design was used to remove the Cy5 and Cy3 dye bias.

ORGANISM(S): Yersinia pestis

SUBMITTER: Chris Minion

PROVIDER: E-GEOD-22847 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptional analysis of three quorum sensing signals add in experiment inYersinia pestis CO92 at 37M-BM-0C

Project description:Yersinia pestis, the etiological agent of plague, is able to sense cell density by quorum sensing. The function of quorum sensing in Y. pestis is not clear. Here, the process of quorum sensing was investigated by comparing transcript profiles when three quorum-sensing signals are added in. The strain M-bM-^HM-^Fpgm (pigmentation-negative) mutant R88 was used as wild type. The three signals are AI-2, AHLs (N-(3-Oxooctanoyl)-L-homoserine lactone and N-Hexanoyl-DL-homoserine lactone).The control consisted of cells grown and treated under the same conditions without added signals. Six independent RNA samples from Y. pestis CO92 M-bM-^HM-^Fpgm cultures were paired with six independent RNA samples from 3 signals added cultures for hybridization to six two-color microarrays. A dye-swap design was used to remove the Cy5 and Cy3 dye bias.

2013-09-05 | E-GEOD-22846 | biostudies-arrayexpress

Transcription analysis of AI-2 signal add in experiment in Yersinia pestis CO92 at 37M-BM-0C

Project description:Yersinia pestis, the etiological agent of plague, is able to sense cell density by quorum sensing. The function of quorum sensing in Y. pestis is not clear. Here, the process of autoinducer-2 (AI-2) quorum sensing was investigated by comparing transcript profiles when AI-2 quorum-sensing signal is added in. The strain M-bM-^HM-^Fpgm(pigmentation-negative) mutant R88 was used as wild type. The control consisted of cells grown and treated under the same conditions without added signals. Six independent RNA samples from Y. pestis CO92 M-bM-^HM-^Fpgm cultures were paired with six independent RNA samples from AI-2 signal added cultures for hybridization to six two-color microarrays. A dye-swap design was used to remove the Cy5 and Cy3 dye bias.

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Transcriptional analysis of luxS-null strain in Yersinia pestis CO92 at 37M-BM-0C

Project description:Yersinia pestis, the etiological agent of plague, is able to sense cell density by quorum sensing. The function of quorum sensing in Y. pestis is not clear. Here, the process of autoinducer 2 (AI-2) quorum sensing was investigated by comparing transcript profiles when luxS gene was knocked out. The luxS gene encodes S-ribosylhomocysteinase which can produce DPD, a precursor of AI-2. The strain M-bM-^HM-^Fpgm (pigmentation-negative) mutant R88 was called wild type. The M-bM-^HM-^Fpgm M-bM-^HM-^FluxS mutant was called control. Six independent RNA samples from R88 were paired with six independent RNA samples from M-bM-^HM-^Fpgm M-bM-^HM-^FluxS mutant cultures for hybridization to six two-color microarrays. A dye-swap design was used to remove the Cy5 and Cy3 dye bias.

2013-09-05 | E-GEOD-22849 | biostudies-arrayexpress

Transcriptional analysis of quorum sensing null strain in Yersinia pestis CO92 at 30Â°C

Project description:Yersinia pestis is the etiology of plague that is able to sense cell density by quorum sensing. The function of quorum sensing in Y.pestis is not clear. Here, the process of quorum sensing was investigated by comparing transcript profiles when three quorum sensing synthase genes are knocked out. Two strains, â??pgm (pigmentation-negative) mutant R88 as treatment and 3XQS mutant with mutation (â??pgm, â??ypeIR, â??yspIR, and â??luxS) R115 as control are used in this analysis. Six independent RNA samples from R115 cultures were paired with six independent RNA samples from R88 cultures for hybridization to six two-color microarrays. Dye-swap design was used to remove the Cy5 and Cy3 dye bias.

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Project description:Yersinia pestis, the etiological agent of plague, is able to sense cell density by quorum sensing. The function of quorum sensing in Y. pestis is not clear. Here, the process of quorum sensing was investigated by comparing transcript profiles when three quorum-sensing synthase genes are knocked out. Two strains, M-bM-^HM-^Fpgm (pigmentation-negative) mutant R88 as treatment and quorum sensing null strain R115 with mutations (M-bM-^HM-^Fpgm, M-bM-^HM-^FypeIR, M-bM-^HM-^FyspIR, and M-bM-^HM-^FluxS) as control, are used in this analysis. Six independent RNA samples from R115 cultures were paired with six independent RNA samples from R88 cultures for hybridization to six two-color microarrays. A dye-swap design was used to remove the Cy5 and Cy3 dye bias.

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Transcriptional analysis of AHLs signal treatment at 30Â°C

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2016-07-03 | E-GEOD-30238 | biostudies-arrayexpress

3 quorum sensing signals add in microarray comparison in Yersinia pestis at 30Â°C

Project description:The quorum-sensing system has been linked to diverse phenotypes and regulatory changes in pathogenic bacteria. In strain CO92, the AI-2 signal is produced in a luxS-dependent manner, reaching maximal levels of 2.5 Î¼M in late logarithmic growth, and both wild type and pigmentation mutant strains made equivalent levels of AI-2. Yersinia pestis CO92 possesses a chromosomal lsr locus encoding factors involved in the binding and import of AI-2, and confirming this assignment, an lsr deletion increased extracellular pools of AI-2. To assess the functional role of 3 quorum sensing singlas in Y. pestis, microarray study was conducted comparing the 3 quorum sensing signals added in to control at 30Â°C to mimic the flea gut. Here, the ÎPgm (pigmentation-negative) R88 strain was used. The three signals are one AI-2 and two AHLs (N-(3-Oxooctanoyl)-L-homoserine lactone and N-Hexanoyl-DL-homoserine lactone).The control consisted of cells grown and treated under the same conditions without added signals. Six independent RNA samples from 3 signals add in cultures were paired with six independent RNA samples from control cultures for hybridization to six two-color microarrays. A dye-swap design was used to remove the Cy5 and Cy3 dye bias.

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Outlier detection of biologically significant genes from combinatorial microarray data

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

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Transcriptional analysis of AI-2 treatment in Yersinia pestis at 30Â°C

Project description:Yersinia pestis, the etiological agent of plague, is able to sense cell density by quorum sensing. The function of quorum sensing in Y. pestis is not clear. Here, the process of autoinducer-2 (AI-2) quorum sensing was investigated by comparing transcript profiles when AI-2 quorum-sensing signal is added in to control. The strain Îpgm (pigmentation-negative) mutant was used as wild type.The control consisted of cells grown and treated under the same conditions without added signals. Six independent RNA samples from Y. pestis CO92 Îpgm cultures were paired with six independent RNA samples from AI-2 signal added in cultures for hybridization to six two-color microarrays. A dye-swap design was used to remove the Cy5 and Cy3 dye bias.

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