Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

48 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling by array of Geobacter sulfurreducens and Enterococcus faecium coculture grown in open circuit (control) and closed circuit (current collecting) to observe the difference in extracellular electron transfer (EET) mechanisms.

ABSTRACT: Coculture Geobacter sulfurreducens and Enterococcus faecium were grown in open circuit (control) and closed circuit (current collecting) to observe the difference in extracellular electron transfer (EET) mechanisms. mRNA was extracted, amplified and used on Combimatrix custom arrays to obtain an expression profile. Analysis was performed using R.

ORGANISM(S): Enterococcus faecium

SUBMITTER: Suzanne Read

PROVIDER: E-MTAB-321 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling by array of Clostridium acetobutylicum grown in open circuit (control) and closed circuit (current collecting) to observe the difference in extracellular electron transfer (EET) mechanisms.

Project description:Clostridium acetobutylicum was grown in open circuit (control) and closed circuit (current collecting) to observe the difference in extracellular electron transfer (EET) mechanisms. mRNA was extracted, amplified and used on Combimatrix custom arrays to obtain an expression profile. Analysis was performed using R.

2010-07-09 | E-MTAB-267 | biostudies-arrayexpress

Transcription profiling by array of Pseudomonas aeruginosa and Enterococcus faecium coculture grown in open circuit (control) and closed circuit (current collecting) to observe the difference in extracellular electron transfer (EET) mechanisms.

Project description:Coculture Pseudomonas aeruginosa and Enterococcus faecium were grown in open circuit (control) and closed circuit (current collecting) to observe the difference in extracellular electron transfer (EET) mechanisms. mRNA was extracted, amplified and used on Combimatrix custom arrays to obtain an expression profile. Analysis was performed using R.

2010-08-13 | E-MTAB-320 | biostudies-arrayexpress

Transcription profiling by array of Pseudomonas aeruginosa was grown in open circuit (control) and closed circuit (current collecting) to observe the difference in extracellular electron transfer (EET) mechanisms.

Project description:Pseudomonas aeruginosa was grown in open circuit (control) and closed circuit (current collecting) to observe the difference in extracellular electron transfer (EET) mechanisms. mRNA was extracted, amplified and used on Combimatrix custom arrays to obtain

2010-07-08 | E-MTAB-269 | biostudies-arrayexpress

Transcription profiling by array of Shewanella oneidensis and Enterococcus faecium coculture grown in open circuit (control) and closed circuit (current collecting) to observe the difference in extracellular electron transfer (EET) mechanisms.

Project description:Shewanella oneidensis and Enterococcus faecium were grown in open circuit (control) and closed circuit (current collecting) to observe the difference in extracellular electron transfer (EET) mechanisms. mRNA was extracted, amplified and used on Combimatrix custom arrays to obtain an expression profile. Analysis was performed using R.

2010-08-30 | E-MTAB-319 | biostudies-arrayexpress

Transcription profiling by array of Shewanella oneidensis was grown in open circuit (control) and closed circuit (current collecting) to observe the difference in extracellular electron transfer (EET) mechanisms.

Project description:Shewanella oneidensis was grown in open circuit (control) and closed circuit (current collecting) to observe the difference in extracellular electron transfer (EET) mechanisms. mRNA was extracted, amplified and used on Combimatrix custom arrays to obtain an expression profile. Analysis was performed using R.

2010-07-08 | E-MTAB-266 | biostudies-arrayexpress

Transcription profiling by array of Enterococcus faecium grown in open circuit (control) and closed circuit (current collection) to observe the difference in extracellular electron transfer (EET) mechanisms.

Project description:Enterococcus faecium was grown in open circuit (control) and closed circuit (current collecting) to observe the difference in extracellular electron transfer (EET) mechanisms. mRNA was extracted, amplified and used on Combimatrix custom arrays to obtain a

2010-07-08 | E-MTAB-268 | biostudies-arrayexpress

Revealing impaired pathways in regulatory mutant by high-throughput characterization of Petunia axillaris and Petunia inflata transcriptomes.

Project description:Petunia is an excellent model system, especially for genetic, physiological and molecular studies. Thus far, however, genome-wide expression analysis has been rarely applied because of the lack of sequence information. We applied next-generation sequencing to generate, through de novo read assembly, a large catalogue of transcripts for Petunia axillaris and Petunia inflata. On the basis of the transcriptome of each species, comprehensive microarray chips for gene expression analysis were established and used for the analysis of global- and organ-specific gene expression in both species. In addition, microarray analysis was applied to explore the molecular basis of the seed coat defects in Petunia hybrida mutants, homozygous for a null allele of the AN11 gene, encoding a WDR transcription regulator. Among the transcripts differentially expressed in an11 seeds compared to wild type, many expected targets of AN11 were found but also several interesting new candidates that might play a role in morphogenesis of the seed coat. Our results validate the combination of next-generation sequencing with microarray analyses strategies to identify the transcriptome of two petunia species without previous knowledge of their genome, and to develop comprehensive chips as useful tools for the analysis of gene expression in P. axillaris, P. inflata and P. hybrida. The manuscript describes the creation by next generation sequencing of a large catalogue of the transcriptome of the two Petunia species, that are considered to represent the natural material from which the breeders selected their varieties. This submission represents the transcriptome component of study. The high throughput sequencing data were submitted to SRA (accession numbers: SRA027293, SRP004866.1, SRX036999.2, SRX036998.2).

2012-02-29 | E-GEOD-28120 | biostudies-arrayexpress

Generation of a transcriptome catalog for global analysis of gene expression in Ampelomyces quisqualis during mycoparasitization

Project description:In this work, 454 pyrosequencing was used to build up a 3M-bM-^@M-^Y cDNA fragment library from a normalized library constructed from pooled RNA samples extracted at different stages of A. quisqualis mycoparasitization process (recognition, early and late parasitization). An extensive catalogue of unique transcripts was compiled and used to develop a microarray for large-scale analysis of genes involved in this mycoparasitism. We examined the transcriptomic changes that occur during the first stage of mycoparasitism (conidial germination). Our results showed that 1,776 transcripts are regulated during germination in the presence of powdery mildew. A striking feature of the gene catalogue was the presence of a number of genes predicted to encode proteins involved in the production of, glucanases, chitinases and extracellular proteases. This suggests that A. quisqualis causes the degradation of powdery mildew macromolecular constituents to provide the carbon skeletons and energy for the synthesis of proteins and other components destined for the developing of the mycelium. Microarray oligo probes were designed based on 454 sequencing of 3'-ends of transcripts of a sample constituted by pooling RNAs extracted at different stages of A. quisqualis mycoparasitization process (recognition, early and late parasitization)

2014-07-11 | E-GEOD-22888 | biostudies-arrayexpress

Exploring the function of the grape regulators VvMYB5a and MYB5b by heterologous expression in anthocyanin petunia mutants

Project description:To obtain insights about the roles of VvMYB5a and VvMYB5b, here we perform complementation analyses using petunia regulatory mutants impaired in pigment accumulation in flower epidermis, proven to be a valid tool for gene functional studies. We created three transgenic petunia lines overexpressing VvMYB5a, VvMYB5b and VvMYBA1 and we compared petal transcriptomes of each overexpressors with the untransformed one.

2013-12-19 | E-GEOD-48058 | biostudies-arrayexpress

Identification of reference genes for quantitative Real-Time PCR in Bifidobacterium bifidum PRL2010 based on transcriptome analysis

Project description:In this study, we investigated the transcriptome of Bifidobacterium bifidum PRL2010 during in vitro growth by micro array technology. When B. bifidum PRL2010 was grown in liquid broth, 425 of the 1644 PRL2010 genes represented on the array were expressed in at least one of the three investigated growth phases, i.e., lag-, exponential and stationary phase. These transcriptional analyses identified a core in vitro transcriptome encompassing 150 genes, which resulted expressed in all phases. A proportion of the latter genes were further investigated as potential reference genes by Quantitative Real Time PCR (qRT-PCR) assays. Their expression stability was evaluated under different growth conditions, encompassing cultivation on different carbon sources, exposure to environmental stresses (thermal, acidic and osmotic) and growth phases. Our analyses validated six reference genes suitable for normalizing mRNA expression levels in qRT-PCR experiments applied to bifidobacteria. Transcriptional profiling of B.bifidum PRL2010 at different growth phases (lag phase, early exponential phase, late exponential phase, early stationary phase).

2012-01-05 | E-GEOD-30832 | biostudies-arrayexpress

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