Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

53 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Differential expression analysis of T. thermophilus HB8 csoR deficient strain in response to copper.

ABSTRACT: We observed the expression profile of the total mRNA in Thermus thermophilus HB8 csrR deficient strain at 0 and 30 min after the addition of CuSO4. Three csoR deficient strain of T. thermophilus HB8 were pre-cultured at 70 degC for 16 hours 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 (1 mL) were inoculated into 250 mL of the synthetic medium and then cultivated at 70°C for 8 hours (A600 value being ~0.4). Then the 1.25 mM of CuSO4 was added into the medium, and continued cultivation. Cells were collected at 0 and 30 min time point after the addition of copper ion, 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.

ORGANISM(S): Thermus thermophilus HB8

SUBMITTER: Akeo Shinkai

PROVIDER: E-GEOD-19509 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Structural and functional characterization of the transcriptional repressor CsoR from Thermus thermophilus HB8.

Sakamoto Keiko K Agari Yoshihiro Y Agari Kazuko K Kuramitsu Seiki S Shinkai Akeo A

Microbiology (Reading, England) 20100415 Pt 7

The TTHA1719 gene from Thermus thermophilus HB8 encodes an orthologue of the copper-sensing transcriptional repressor CsoR. X-ray crystal structure analysis of T. thermophilus CsoR indicated that it forms a homotetramer. The structures of the CsoR monomer and dimer are similar to those of Mycobacterium tuberculosis CsoR. In the absence of copper ions, T. thermophilus CsoR bound to the promoter region of the copper-sensitive operon copZ-csoR-copA, which encodes the copper chaperone CopZ, CsoR and ...[more]

PMID: 20395270

Publication: 1/2

Similar Datasets

SuperSeries for the analysis of transcriptional regulation by Thermus themophilus CsoR (TTHA1719)

Project description:We observed the copper response of Thermus thermophilus HB8 wild-type and csoR deficient strain at 0 and 30 min after the addition of 1.25 mM CuSO4, and zinc response of T. thermophilus HB8 wild-type strain at 0 and 30 min after the addition of 1.0 mM ZnSO4. Three wild-type and three csoR deficient strain of T. thermophilus HB8 were pre-cultured at 70 degC for 16 hours 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 (1 mL) were inoculated into 250 mL of the synthetic medium and then cultivated at 70M-BM-0C for 8 hours. Then the 1.25 mM of CuSO4 or 1.0 mM ZnSO4 was added into the medium cultivating wild type, and 1.25 mm CuSO4 was added into the medium cultivating csoR deficient strain, and continued cultivation. Cells were collected at 0 and 30 min time point after the addition of copper or zinc ion, 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.

2010-04-12 | E-GEOD-19521 | biostudies-arrayexpress

Differential expression analysis of Thermus thermophilus HB8 wild-type strain in response to zinc

Project description:We observed the expression profile of the total mRNA in Thermus thermophilus HB8 wild-type strain at 0 and 30 min after the addition of ZnSO4. Three wild-type strain of T. thermophilus HB8 were pre-cultured at 70 degC for 16 hours 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 (1 mL) were inoculated into 250 mL of the synthetic medium and then cultivated at 70°C for 8 hours (A600 value being ~0.52). Then the 1.0 mM of ZnSO4 was added into the medium, and continued cultivation. Cells were collected at 0 and 30 min time point after the addition of zinc ion, 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.

2010-04-13 | E-GEOD-20900 | biostudies-arrayexpress

Differential expression analysis of T. thermophilus HB8 TTHA0995-deficient strain in response to iron

Project description:We observed the expression profile of the total mRNA in Thermus thermophilus HB8 TTHA0995 deficient strain at 0 and 30 min after the addition of FeSO4. Three TTHA0995 deficient strain of T. thermophilus HB8 were pre-cultured at 70 degC for 16 hours 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 L of the same medium and then cultivated at 70Â°C for 5.5 hours (A600 value being ~1.53). Then the 1.0 mM of FeSO4 was added into the medium, and continued cultivation. Cells were collected at 0 and 30 min time point after the addition of iron ion, 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.

2010-10-15 | E-GEOD-21470 | biostudies-arrayexpress

Differential expression analysis of T. thermophilus HB8 wild-type strain in response to copper.

Project description:We observed the expression profile of the total mRNA in Thermus thermophilus HB8 wild-type strain at 0 and 30 min after the addition of CuSO4. Three wild-type strain of T. thermophilus HB8 were pre-cultured at 70 degC for 16 hours 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 (1 mL) were inoculated into 250 mL of the synthetic medium and then cultivated at 70°C for 8 hours (A600 value being ~0.44). Then the 1.25 mM of CuSO4 was added into the medium, and continued cultivation. Cells were collected at 0 and 30 min time point after the addition of copper ion, 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.

2010-04-13 | E-GEOD-19508 | 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

Transcriptional profiling of the T. thermophilus HB8 response to hydrogen peroxide

Project description:We observed the expression profile of the total mRNA in Thermus thermophilus HB8 wild-type strain at 0, 5, 15 and 30 min after the addition of 10 mM H2O2. Three wild-type strain of T. thermophilus HB8 were pre-cultured at 70 degC for 16 hours in 2 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 (1 mL) were inoculated into 1000 mL of the same medium and then cultivated at 70Â°C for 6.5 hours (A600 value being ~0.55). Then the 10 mM of H2O2 was added into the medium, and continued cultivation. Cells were collected at 0, 5, 15 and 30 min time point after the addition of H2O2, 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-21430 | 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 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

Transcriptional profiling of the T. thermophilus HB8 response to tetracycline

Project description:We observed the expression profile of the total mRNA in Thermus thermophilus HB8 wild-type strain at 10 min after the addition of 50 mM tetracycline. Three wild-type strain of T. thermophilus HB8 were pre-cultured at 70 degC for 16 hours in 4 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 L of the same medium and then cultivated at 70Â°C for 6 hours (A600 value being ~0.62). Then the 50 mM of tetracycline was added into the medium, and continued cultivation. Cells were collected at 0 and 10 min time point after the addition of tetracycline, 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-21432 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data