Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of hyperthermophilic crenarchaeum Thermoproteus tenax to compare autotrophic growth on CO2/H2 versus heterotrophic growth on glucose using a focussed central carbohydrate metabolism DNA microarray

ABSTRACT: In order to unravel the role of regulation on transcript level in the central carbohydrate metabolism (CCM) of Thermoproteus tenax (glycolytic/gluconeogenic carbon switch), the focused DNA microarray was constructed by using ORFs supposed to be involved in the CCM pathways. Transcriptional profiling was performed comparing autotrophic growth on CO2/H2 versus heterotrophic growth on glucose.

INSTRUMENT(S): GenePix 4000A [Axon Instruments]

ORGANISM(S): Thermoproteus tenax

SUBMITTER: Melanie Zaparty

PROVIDER: E-MEXP-1376 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

DNA microarray analysis of central carbohydrate metabolism: glycolytic/gluconeogenic carbon switch in the hyperthermophilic crenarchaeum Thermoproteus tenax.

Zaparty Melanie M Zaigler Alexander A Stamme Claudia C Soppa Jörg J Hensel Reinhard R Siebers Bettina B

Journal of bacteriology 20080104 6

In order to unravel the role of regulation on transcript level in central carbohydrate metabolism (CCM) of Thermoproteus tenax, a focused DNA microarray was constructed by using 85 open reading frames involved in CCM. A transcriptional analysis comparing heterotrophic growth on glucose versus autotrophic growth on CO2-H2 was performed. ...[more]

PMID: 18178743

Similar Datasets

Transcription profiling of Halobacterium salinarum at different time points after cell cycle synchronization to identify cell cycle dependent transcriptome changes

Project description:Cell cycle dependent transcriptome changes of H. salinarum were analyzed using DNA microarrays. Cells were synchronized by a reversible cell cycle arrest caused by addition of the DNA polymerase inhibitor Aphidicolin. Gene expression of the synchronized cells at different time points after Aphidicolin removal was compared to an unsynchronized control culture (treated identically, but without Aphidicolin addition; time points for the control culture pooled).<br><br>Additional processed data is available from the ArrayExpress FTP site in FGEM format: <a href="ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-1033/E-MEXP-1033.fgem.txt">E-MEXP-1033.fgem.txt</a>

2007-06-15 | E-MEXP-1033 | biostudies-arrayexpress

Measurement of mRNA decay in exponentially growing cultures of the extremely halophilic euryarchaeon Halobacterium salinarum NRC-1 after blocking transcription with actinomycin D

Project description:mRNA half-lives in exponentially growing cultures of the extremely halophilic euryarchaeon Halobacterium salinarum NRC-1

2007-07-31 | E-MEXP-1088 | biostudies-arrayexpress

Profiling of free and polysome-bound mRNA from exponential and stationary growth phase cultures of Haloferax volcanii to identify growth phase dependent translational regulation

Project description:Growth phase dependent translational regulation of Hf. volcanii was analyzed on a genome-wide scale. The relative amounts of free versus polysome-bound mRNA (separated by gradient centrifugation) were quantified in exponential as well as stationary growth phase by the use of shotgun DNA microarrays.

2007-10-31 | E-MEXP-1191 | biostudies-arrayexpress

Profiling of free and polysome-bound mRNA from exponential and stationary growth phase cultures of Halobacterium salinarum to identify growth phase dependent transcriptional and translational changes

Project description:Growth phase dependent transcriptional and translational changes of Hb. salinarum were examined. In the genome-wide transcriptome analysis, gene expression in exponential versus stationary growth phase was monitored on DNA microarrays. In the global study of translational regulation, the relative amounts of free versus polysome-bound mRNA (separated by gradient centrifugation) were quantified in exponential as well as stationary growth phase using DNA microarrays.

2007-10-31 | E-MEXP-1180 | biostudies-arrayexpress

Expression analysis of Clostridium acetobutylicum ATCC 824 grown on different carbohydrates

Project description:Investigation of whole genome gene expression levels in Clostridium acetobutylicum strain 824 grown individually on starch, galactose, lactose, mannose, fructose, glucose, arabinose, xylose, cellobiose, maltose, sucrose A 33 array study using total RNA recovered from three separate wild-type cultures of Clostridium acetobutylicum 824 grown on each of the following sugars: starch, galactose, lactose, mannose, fructose, glucose, arabinose, xylose, cellobiose, maltose, sucrose. RNA extraction, cDNA production, and labeling were performed independently on three separate cultures for each carbohydrate. Each independent sample was hybridized to one array equating to one technical replicate for each biological sample and three biological replicates for each condition tested. Each array contains 2 replicates of 9 probes approximately 60 bp in length for each of the 3,842 open reading frames annotated in the C. acetobutylicum 824 genome.

2010-05-15 | E-GEOD-18471 | biostudies-arrayexpress

Transcription profiling of Paxillus involutus, Betula pendula mycorrhizal tissue at five different time points after initial contact between the symbionts

Project description:Mycorrhizal tissue was analyzed at five different time points after initial contact between the symbionts had occurred. The experimental design also included reference material grown axenically in parallel during the time course, with the purpose of detecting differential regulation of genes not related to the mycorrhizal interaction. For the mycorrhizal tissue, we sequentially and directly compared time points, including one loop-back hybridization, whereas the reference material was directly compared with mycorrhizal tissue within each time point. For the mycorrhizal material three biological replicates were included (Rep 1-3) whereas for the reference material only two were included (Rep 1 and 2), which equals 25 individual samples used. In total 40 separate labeling reactions and 20 microarray hybridizations were performed.

2005-08-30 | E-MEXP-180 | biostudies-arrayexpress

Transcription profiling of four human prostate cancer cell lines and seven prostate cancer xenografts

Project description:Gene expression profiling of four prostate cancer cell lines and seven prostate cancer xenografts. The experiment was done to see which genes were over- or underexpressed in the samples. The results were combined with aCGH results of the same samples (experiment prostate cancer CGH) to see, whether the copy number status had any effect on gene expression.

2005-12-30 | E-MEXP-336 | biostudies-arrayexpress

Transcription profiling of strains of Paxillus involutus that show different abilities in formation of ectomycorrhizal associations with birch (Betula pendula)

Project description:A microarray analysis was conducted to investigate transcriptional differences between strains of Paxillus involutus that show different abilities in formation of ectomycorrhizal associations with birch (Betula pendula). Our goal was to identify genes that showed differential regulation from comparing incompatible (not mycorrhiza forming) (Nau) and compatible (mycorrhiza forming) strains (ATCC200175 and Maj) of P. involutus, in association with birch. The entire design involved 11 slides (ME01-M11), 13 labelled extracts, and 3 biological replicates (Rep1-Rep3). The experiment was designed as a simple loop (all-pairwise comparisons) of all three strains including dye-swap, biological and technical replication. Additional information: In our pre-processing of data, 4 channels were excluded for further analyses due to overall poor quality and are listed below. Slide ME03, Cy5(635nm) (strain Nau, Rep2) Slide ME04, Cy5(635nm) (strain Nau, Rep2) Slide ME06, Cy5(635nm) (strain Maj, Rep2) Slide ME09, Cy5(635nm) (strain Nau, Rep2)

2004-10-05 | E-MEXP-179 | biostudies-arrayexpress

DNA-seq of mitochondrial DNA from mouse heart that is both heart SOD2 knockout and deficient for mitochondrial DNA repair

Project description:To study whether increase in mitochondrial oxidative stress (SOD2 removal) and decrease in mitochondrial DNA repair (Ogg1 dMTS) results into increase in mitochondrial DNA mutation load. Oxidative stress has been suggested to induce mutations in mtDNA. To verify this, we extracted and sequenced (Illumina) mitochondrial DNA from heart Sod2 knockout animals that were also deficient for mitochondrial base-excision repair. The repair deficiency was induced by removing the genomic region encoding for the predicted mitochondrial targeting sequence from endogenous OGG1 (L2 to W23) called Ogg1 dMTS mice, thus excluding the protein from mitochondria. OGG1 is a DNA glycosylase that recognizes and repairs 8-oxo-dG damage from DNA. Oxidative stress can induce 8-oxo-dG lesions, thus we removed the mitochondrial matrix localized superoxide dismutase (SOD2) from these mice to increase the level of oxidative stress. 8-oxo-dG lesion can be mutagenic because some DNA repair polymerases are known to erroneously incorporate adenosine opposite to 8-oxo-dG during replication leading to GC>TA transversion mutations.

2018-07-13 | E-MTAB-6533 | biostudies-arrayexpress

An antibiotic-sensing leader peptide regulates translation and premature Rho-dependent transcription termination of the topAI gene in Escherichia coli

Project description:The SHAPE-Seq experiment was used to determine accessible nucleotides in the 5' UTR of the topAI gene in the presence and absence of 0.2 ug/ml of tetracycline.

2019-10-03 | E-MTAB-8365 | 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