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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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SuperSeries for the study of expression analysis of the T. thermophilus sigE (TTHB211)

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE7165: mRNA expression in wild-type Thermus thermophilus HB8 strain grown on a rich medium. GSE8780: mRNA expression in sigE (TTHB211) deletion mutant of Thermus thermophilus HB8 strain grown on a rich medium Keywords: SuperSeries Refer to individual Series

ORGANISM(S): Thermus thermophilus HB8

SUBMITTER: Akeo Shinkai

PROVIDER: E-GEOD-8781 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Identification of promoters recognized by RNA polymerase-sigmaE holoenzyme from Thermus thermophilus HB8.

Shinkai Akeo A Ohbayashi Naomi N Terada Takaho T Shirouzu Mikako M Kuramitsu Seiki S Yokoyama Shigeyuki S

Journal of bacteriology 20070928 23

Thermus thermophilus sigma(E), an extracytoplasmic function sigma factor from the extremely thermophilic bacterium Thermus thermophilus HB8, bound to the RNA polymerase core enzyme and showed transcriptional activity. With the combination of in vitro transcription assay and GeneChip technology, we identified three promoters recognized by sigma(E). The predicted consensus promoter sequence for sigma(E) is 5'-CA(A/T)(A/C)C(A/C)-N(15)-CCGTA-3'. ...[more]

PMID: 17905996

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SuperSeries for the study of expression analysis of the T. thermophilus CRP (TTHA1437)

Project description:This SuperSeries is composed of the following subset Series: GSE7165: mRNA expression in wild-type Thermus thermophilus HB8 strain grown on a rich medium. GSE7166: mRNA expression in crp (TTHA1437) deletion mutant of Thermus thermophilus HB8 strain grown on a rich medium Keywords: SuperSeries Refer to individual Series

2010-05-27 | E-GEOD-7175 | biostudies-arrayexpress

Time course of the mRNA expression in wild-type Thermus thermophilus HB8 strain grown on a rich medium (labeling:ENZO)

Project description:We observed the expression profile of the total mRNA of wild-type Thermus thermophilus HB8 strain grown in a rich (TT) medium at 70oC. Keywords: time course Three wild-type T. thermophilus HB8 strains were pre-cultured at 70oC for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70oC. Cells were collected after 180, 240, 300, 360, 420, 480, 540, 600, 680, and 760 min, and then crude RNA was extracted. The expression of each mRNA at each time point was analyzed on a GeneChip as described under Sample Description Sheet of each sample in this website.

2010-05-27 | E-GEOD-7165 | biostudies-arrayexpress

Time course of bacteriophage ?YS40 infection in wild-type and crp deletion Thermus thermophilus HB8 strain

Project description:This SuperSeries is composed of the following subset Series: GSE16954: Time course of the mRNA expression after bacteriophage ?YS40 infection in wild-type Thermus thermophilus HB8 strain. GSE16955: Time course of the mRNA expression after phage ?YS40 infection in crp deletion mutant of Thermus thermophilus HB8. Refer to individual Series

2009-11-02 | E-GEOD-16978 | biostudies-arrayexpress

Comparative expression analysis between CRP (TTHA1437) deletion mutant and wild-type of T. thermophilus HB8

Project description:We observed the expression profile of the total mRNA of crp (TTHA1437) deletion mutant of Thermus thermophilus HB8 strain grown in a rich (TT) medium at 70oC compared with that of wild type. Keywords: cell type comparison Three wild-type and mutant T. thermophilus HB8 strains were each pre-cultured at 70oC for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70oC. Cells were collected after 6 h and 8 h, and then crude RNA was extracted. In order to compare mRNA expression in the crp (TTHA1437) deletion mutant with that of wild type, the expression of each mRNA at each time point was analyzed on a GeneChip as described under Sample Description Sheet of each sample in this website.

2010-05-27 | E-GEOD-7166 | biostudies-arrayexpress

Time course of the mRNA expression in wild-type Thermus thermophilus HB8 strain grown in a rich medium (labeling:ENZO)

Project description:In order to observe altered expression profile of wild-type T. thermophilus HB8 strain grown in a rich (TT) medium at 70Â°C. we analyzed time-dependent mRNA expression profile of the total mRNA from the strain, which corresponds the logarithmic phase to the early stationary phase. Three wild-type T. thermophilus HB8 strains were pre-cultured at 70Â°C for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70Â°C. Cells were collected after 180, 240, 300, 360, 420, 480, 540, 600, 680, and 760 min, and then crude RNA was extracted. The expression of each mRNA at each time point was analyzed on a GeneChip.

2010-10-15 | E-GEOD-21473 | biostudies-arrayexpress

Time course of the mRNA expression after bacteriophage ÏYS40 infection in wild-type Thermus thermophilus HB8 strain.

Project description:We observed the expression profile of the total mRNA of wild-type Thermus thermophilus HB8 strain during infection of bacteriophage ÏYS40. Keywords: time course, bacteriophage, infection, wild type Three wild-type T. thermophilus HB8 strains were pre-cultured at 70Â°C for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70Â°C until A600 value being ~0.8 (1.7 Ã 108 cells/ml) that corresponds to logarithmic growth phase. Then the Î¦YS40 phage was infected to the medium at multiplicity of infection (m.o.i.) being ~1, and continued cultivation. Cells were collected after 0, 25, 50, 75 and 100 min infection, and then crude RNA was extracted. The expression of each mRNA at each time point was analyzed on a GeneChip as described under Sample Description Sheet of each sample.

2010-06-20 | E-GEOD-16954 | biostudies-arrayexpress

Time course of the mRNA expression after phage ÏYS40 infection in crp deletion mutant of Thermus thermophilus HB8

Project description:We observed the expression profile of the total mRNA in crp (TTHA1437) deletion mutant strain of Thermus thermophilus HB8 during infection of bacteriophage ÏYS40. Three crp (TTHA1437) delection mutant strain of T. thermophilus HB8 were pre-cultured at 70 C for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70Â°C until A600 value being ~0.8 (1.7 108 cells/ml) that corresponds to logarithmic growth phase. Then the FYS40 phage was infected to the medium at multiplicity of infection (m.o.i.) being ~1, and continued cultivation. Cells were collected after 0, 75 and 100 min infection, and then crude RNA was extracted. The expression of each mRNA at each time point was analyzed on a GeneChip..

2010-10-15 | E-GEOD-21474 | biostudies-arrayexpress

Time course of the mRNA expression after phage ϕYS40 infection in crp deletion mutant of Thermus thermophilus HB8.

Project description:We observed the expression profile of the total mRNA in crp (TTHA1437) deletion mutant strain of Thermus thermophilus HB8 during infection of bacteriophage ϕYS40. Keywords: time course, bacteriophage, infection, CRP, cAMP receptor protein, deletion mutant Three crp (TTHA1437) delection mutant strain of T. thermophilus HB8 were pre-cultured at 70 C for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C until A600 value being ~0.8 (1.7 108 cells/ml) that corresponds to logarithmic growth phase. Then the FYS40 phage was infected to the medium at multiplicity of infection (m.o.i.) being ~1, and continued cultivation. Cells were collected after 0, 75 and 100 min infection, and then crude RNA was extracted. The expression of each mRNA at each time point was analyzed on a GeneChip as described under Sample Description Sheet of each sample.

2009-11-02 | E-GEOD-16955 | biostudies-arrayexpress

Comparative expression analysis between sigE (TTHB211) deletion mutant and wild-type of T. thermophilus HB8

Project description:We observed the expression profile of the total mRNA of sigE (TTHB211) deletion mutant of Thermus thermophilus HB8 strain grown in a rich (TT) medium at 70oC compared with that of wild type. Keywords: cell type comparison Three wild-type and mutant T. thermophilus HB8 strains were each pre-cultured at 70oC for 16 h in 3 ml of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70oC. Cells were collected after 8 h, and then crude RNA was extracted. In order to compare mRNA expression in the sigE (TTHB211) deletion mutant with that of wild type, the expression of each mRNA at the time point was analyzed on a GeneChip as described under Sample Description Sheet of each sample in this website.

2007-09-04 | E-GEOD-8780 | biostudies-arrayexpress

SuperSeries for the study of expression analysis of the PfmR (TTHB023) in T. thermophilus HB8

Project description:This SuperSeries is composed of the following subset Series: GSE21290: Time course of the mRNA expression in wild-type Thermus thermophilus HB8 strain grown in a rich medium (labeling:Affymetrix) GSE36881: Expression profile of PfmR (TTHB023)-deficient Thermus thermophilus HB8 strain GSE36883: Expression profile of wild-type Thermus thermophilus HB8 strain cultured in TT medium for 6 h, reproduced in 2010 GSE36884: Expression profile of wild-type Thermus thermophilus HB8 strain cultured in TT medium for 6 h, reproduced in 2011 Refer to individual Series

2012-06-19 | E-GEOD-36912 | biostudies-arrayexpress

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