Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Clostridium difficile CD630E: growth with 10 mM cysteine in PY vs growth in PY

ABSTRACT: Comparison of Clostridium difficile transcriptome of strain CD630E grown for 10 hours in PY (supplemented with mild concentration of cysteine) versus PYC (PY supplemented with 10 mM of cysteine). Experimental procedure was designed to investigate the influence of cysteine on toxins production and the regulatory network involved. two-conditions experiments, excess of cysteine vs mild concentration of cysteine, 4 biological replicates for each condition Description of the supplementary files: Main - Short description of the experiment Result_all - All significative genes Result_Gold* - High quality significative gene Result_Silver** - Medium quality significative gene All_Raw_data - All genes results significative and non significative Design_Genes-OUT - Genes not present in the platform Design_Genes-Oligos - Number of oligos design per gene * Gold : Nbr significative oligos = Nbr oligos designed for this gene ** Silver : Nbr significative oligos = Nbr oligos designed for this gene -1

ORGANISM(S): [Clostridium] difficile

SUBMITTER: Monot Marc

PROVIDER: E-GEOD-22423 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Comparison of the expression profiles of R20291 strain : a wild type strain, a fliC mutant and a fliC mutant complemented after 14h of growth in PY and a wild type strain and a fliC mutant after 14h of mouse infection in vivo

Project description:Transcriptionnal profiling of C. difficile R20291 strain : a wild type strain, a fliC mutant and a fliC mutant complemented after 14h of growth in PY and a wild type strain and a fliC mutant after 14h of mouse infection in Vivo two-conditions experiments, R20291 strain : a wild type strain, a fliC mutant and a fliC mutant complemented in Vitro and a wild type strain and a fliC mutant in Vivo, 4 biological replicates for each condition, in an direct design.

2013-12-31 | E-GEOD-35727 | biostudies-arrayexpress

Clostridium difficile CD630E: growth with 10 mM cysteine in PY vs growth in PY

Project description:Comparison of Clostridium difficile transcriptome of strain CD630E grown for 10 hours in PY (supplemented with mild concentration of cysteine) versus PYC (PY supplemented with 10 mM of cysteine). Experimental procedure was designed to investigate the influence of cysteine on toxins production and the regulatory network involved.

2013-12-31 | GSE22423 | GEO

Effect of PY-ITC and sulforaphane on gene expression of PC3 and PNT1A prostate cells in the presence and absence of the PI3K inhibitor LY294002

Project description:Non cancerous PNT1A and cancerous PC3 prostate cells were treated with a novel isothiocyanate (PY-ITC) and compared to sulforaphane (SF), an isothiocyanate (ITC) derived from broccoli. Treatments with these ITCs were performed in the presence and absence on the PI3K inhibitor LY294002.

2013-04-24 | E-MEXP-3640 | biostudies-arrayexpress

Comparison of the expression profiles of the 630E strain and a sigE mutant after 14h of growth

Project description:Compartment-specific control of gene expression during Bacillus subtilis sporulation is governed by a cascade of four sigma factors, sigmaF and sigmaG in the forespore and sigmaE and sigmaK in the mother cell. In this work, we combined transcriptional analyses and transcriptional start site mapping to define the sigmaF, sigmaE, sigmaG and sigmaK regulons in Clostridium difficile. A total of about 225 genes were under the control of these sigma factors: 25 in the sigmaF regulon, 97 sigmaE-dependent genes, 50 sigmaG-governed genes and 56 genes specifically controlled by sigmaK. A significant fraction of genes in each regulon are of unknown function and we can propose new candidates for spore coat proteins synthesized under the control of sigmaE and sigmaK among proteins previously detected in the spore proteome (Lawley et al., 2009 (PMID 19542279)). Global analysis of developmental gene expression under the control of these sigma factors indicate deviations from the B. subtilis model regarding the communication between mother cell and forespore in C. difficile. We show that the expression of the sigmaE regulon in the mother cell is not strictly under the control of sigmaF despite the fact that the forespore product SpoIIR is required for the processing of pro-sigmaE. In addition, the sigmaK regulon is not controlled by sigmaG in C. difficile in connection with the lack of pro-sigmaK processing in this bacterium. However, a control of the forespore on sigmaK targets is maintained through a sigmaF-dependent regulation of sigmaK-controlled genes, a process that bypasses sigmaG. Here, transcriptional profiling of the Clostridium difficile 630E strain vs. a sigE mutant after 14h of growth in MS is performed. Two-condition experiment: 630E strain 14h vs. sigE mutant 14h. 4 biological replicates for each condition, including dye-swaps.

2014-02-20 | E-GEOD-43198 | biostudies-arrayexpress

Comparison of the expression profiles of the 630E strain and a sigG mutant after 19h of growth

Project description:Compartment-specific control of gene expression during Bacillus subtilis sporulation is governed by a cascade of four sigma factors, sigmaF and sigmaG in the forespore and sigmaE and sigmaK in the mother cell. In this work, we combined transcriptional analyses and transcriptional start site mapping to define the sigmaF, sigmaE, sigmaG and sigmaK regulons in Clostridium difficile. A total of about 225 genes were under the control of these sigma factors: 25 in the sigmaF regulon, 97 sigmaE-dependent genes, 50 sigmaG-governed genes and 56 genes specifically controlled by sigmaK. A significant fraction of genes in each regulon are of unknown function and we can propose new candidates for spore coat proteins synthesized under the control of sigmaE and sigmaK among proteins previously detected in the spore proteome (Lawley et al., 2009 (PMID 19542279)). Global analysis of developmental gene expression under the control of these sigma factors indicate deviations from the B. subtilis model regarding the communication between mother cell and forespore in C. difficile. We show that the expression of the sigmaE regulon in the mother cell is not strictly under the control of sigmaF despite the fact that the forespore product SpoIIR is required for the processing of pro-sigmaE. In addition, the sigmaK regulon is not controlled by sigmaG in C. difficile in connection with the lack of pro-sigmaK processing in this bacterium. However, a control of the forespore on sigmaK targets is maintained through a sigmaF-dependent regulation of sigmaK-controlled genes, a process that bypasses sigmaG. Here, transcriptional profiling of the Clostridium difficile 630E strain vs. a sigG mutant after 19h of growth in MS is performed. Two-condition experiment: 630E strain 19h vs. sigG mutant 19h. 4 biological replicates for each condition, including dye-swaps.

2014-02-20 | E-GEOD-43200 | biostudies-arrayexpress

Comparison of the expression profiles of the 630E strain and a sigF mutant after 14h of growth

Project description:Compartment-specific control of gene expression during Bacillus subtilis sporulation is governed by a cascade of four sigma factors, sigmaF and sigmaG in the forespore and sigmaE and sigmaK in the mother cell. In this work, we combined transcriptional analyses and transcriptional start site mapping to define the sigmaF, sigmaE, sigmaG and sigmaK regulons in Clostridium difficile. A total of about 225 genes were under the control of these sigma factors: 25 in the sigmaF regulon, 97 sigmaE-dependent genes, 50 sigmaG-governed genes and 56 genes specifically controlled by sigmaK. A significant fraction of genes in each regulon are of unknown function and we can propose new candidates for spore coat proteins synthesized under the control of sigmaE and sigmaK among proteins previously detected in the spore proteome (Lawley et al., 2009 (PMID 19542279)). Global analysis of developmental gene expression under the control of these sigma factors indicate deviations from the B. subtilis model regarding the communication between mother cell and forespore in C. difficile. We show that the expression of the sigmaE regulon in the mother cell is not strictly under the control of sigmaF despite the fact that the forespore product SpoIIR is required for the processing of pro-sigmaE. In addition, the sigmaK regulon is not controlled by sigmaG in C. difficile in connection with the lack of pro-sigmaK processing in this bacterium. However, a control of the forespore on sigmaK targets is maintained through a sigmaF-dependent regulation of sigmaK-controlled genes, a process that bypasses sigmaG. Here, transcriptional profiling of the Clostridium difficile 630E strain vs. a sigE mutant after 14h of growth in MS is performed. Two-condition experiment: 630E strain 14h vs. sigF mutant 14h. 4 biological replicates for each condition, including dye-swaps.

2014-02-20 | E-GEOD-43199 | biostudies-arrayexpress

Comparison of the expression profiles of the 630E strain and a sigK mutant after 24h of growth

Project description:Compartment-specific control of gene expression during Bacillus subtilis sporulation is governed by a cascade of four sigma factors, sigmaF and sigmaG in the forespore and sigmaE and sigmaK in the mother cell. In this work, we combined transcriptional analyses and transcriptional start site mapping to define the sigmaF, sigmaE, sigmaG and sigmaK regulons in Clostridium difficile. A total of about 225 genes were under the control of these sigma factors: 25 in the sigmaF regulon, 97 sigmaE-dependent genes, 50 sigmaG-governed genes and 56 genes specifically controlled by sigmaK. A significant fraction of genes in each regulon are of unknown function and we can propose new candidates for spore coat proteins synthesized under the control of sigmaE and sigmaK among proteins previously detected in the spore proteome (Lawley et al., 2009 (PMID 19542279)). Global analysis of developmental gene expression under the control of these sigma factors indicate deviations from the B. subtilis model regarding the communication between mother cell and forespore in C. difficile. We show that the expression of the sigmaE regulon in the mother cell is not strictly under the control of sigmaF despite the fact that the forespore product SpoIIR is required for the processing of pro-sigmaE. In addition, the sigmaK regulon is not controlled by sigmaG in C. difficile in connection with the lack of pro-sigmaK processing in this bacterium. However, a control of the forespore on sigmaK targets is maintained through a sigmaF-dependent regulation of sigmaK-controlled genes, a process that bypasses sigmaG. Here, transcriptional profiling of the Clostridium difficile 630E strain vs. a sigE mutant after 24h of growth in MS is performed. Two-conditions experiments, 630E strain 24h vs sigK mutant 24h, 4 biological replicates for each condition

2014-02-20 | E-GEOD-43201 | biostudies-arrayexpress

Comparison of the expression profiles of the 630E JIR8094 strain and sporulation sigma factor mutants (sigE, sigF, sigG, sigK, spoIIID) in MS

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

2014-02-20 | E-GEOD-43202 | biostudies-arrayexpress

Comparison of the expression profiles of 630E strain and hfQ mutants

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

2014-07-15 | E-GEOD-55274 | biostudies-arrayexpress

Phosphorylation ratio of pT vs pY ERK in MEK phosphorylation reaction determined by mass spectrometry

Project description:The purpose of this experiment is to determine the phosphorylation ratio of pT vs pY ERK present in ERK phosphorylation reaction by activated MEK E203K or MEK WildType. Aliquots were collected at 3 minutes 15 seconds, the time at which the mono-phosphorylated ERK is at its maximal. To determine the ratio between pT and pY ERK, synthetic AQUA peptides corresponding to the pY- and the pT-phosphorylated ERK were spiked into the sample. The two peptides have identical mass but they can be umabiguguously distinguished by their elution times and fragmentation spectra.

2020-01-14 | PXD016580 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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