Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Heterologous Microarray Hybridization Between Vesicomyid Symbionts

ABSTRACT: The goal of this study was to use heterologous microarray hybridization to determine genomic content shared among different vesicomyid symbionts. These symbionts are closely related and can be thought of as different strains of bacteria, facilitating the use of heterologous microarray hybridization to determine genomic content. Keywords: comparative genomic hybridization Microarrays were built off the Ruthia magnifica genome and two replicate hybridizations to this organism were used as a baseline for comparisons. Genomic DNA from two other vesicomyid symbionts (Calyptogena kilmeri and C. pacifica symbionts) was also hybridized to the array with three biological replicates for each sample.

ORGANISM(S): Calyptogena magnifica symbiont

SUBMITTER: Irene Newton

PROVIDER: E-GEOD-13447 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Comparative genomics of vesicomyid clam (Bivalvia: Mollusca) chemosynthetic symbionts.

Newton Irene L G IL Girguis Peter R PR Cavanaugh Colleen M CM

BMC genomics 20081204

<h4>Background</h4>The Vesicomyidae (Bivalvia: Mollusca) are a family of clams that form symbioses with chemosynthetic gamma-proteobacteria. They exist in environments such as hydrothermal vents and cold seeps and have a reduced gut and feeding groove, indicating a large dependence on their endosymbionts for nutrition. Recently, two vesicomyid symbiont genomes were sequenced, illuminating the possible nutritional contributions of the symbiont to the host and making genome-wide evolutionary analy ...[more]

PMID: 19055818

Similar Datasets

Heterologous Microarray Hybridization Between Vesicomyid Symbionts

Project description:The goal of this study was to use heterologous microarray hybridization to determine genomic content shared among different vesicomyid symbionts. These symbionts are closely related and can be thought of as different strains of bacteria, facilitating the use of heterologous microarray hybridization to determine genomic content. Keywords: comparative genomic hybridization

2008-11-28 | GSE13447 | GEO

Heterologous Microarray Hybridization Between Vesicomyid Symbionts

Project description:Heterologous Microarray Hybridization Between Vesicomyid Symbionts

| PRJNA110047 | ENA

High throughput ribosome profiling of E. coli expressing a library of heterologous proteins

2022-07-07 | GSE134324 | GEO

Genomic diversity of Escherichia isolates from diverse habitats

Project description:Comparative genomic hybridization between Escherichia coli strains to determine core and pan genome content of clinical and environmental isolates

2012-08-30 | GSE39667 | GEO

Array-based cross-species hybridization between genera of Rhabditidae (Nematoda)

Project description:The objective of this work was to determine the effectiveness of cross-hybridization of gDNA from five native soil nematodes to an Affymetrix Caenorhabditis elegans tiling array. Cross-hybridization experiments using C. briggsae, for which genome information is available, allowed hybridisation intensities to be correlated with known sequence differences. Initial analysis of data by conventional array-based Comparative Genomic Hybridization (aCGH) techniques at the chip level lead to misleading results due to an artefact from the combination of scaling, bandwidth smoothing, and differential GC content in exon and intron regions. To circumvent this artefact, individual probes were instead normalized and centered by adjusting for probe-specific thermodynamic binding affinity. However, cross-hybridization of C. briggsae DNA revealed that the resultant probe intensities alone were still uncorrelated to sequence similarity below 90% identity. Below 90% similarity, all probes hybridize uniformly poorly, and above 90% similarity the hybridization differences are not large enough to detect over background, therefore, no 'threshold' ratio of hybridization intensity was successful at identifying probes with similarity to the heterologous genome. In light of the observations described here, we suggest that the criteria for replication and verification of gene expression profiles generated from cross-species microarray hybridizations be more stringent than typically adopted for con-specific hybridizations. Genomic DNA from Caenorhabditis elegans N2 (Bristol), C. elegans CB4856 (Hawaiian), C. briggsae AF16, Oscheius tipulae KS585, Oscheius FVV-2 KS555, Mesorhabditis sp. KS587, Acrobeloides sp. KS586, and Chiloplacus sp. KS584 were hybridized onto C. elegans Affymetrix tiling array (two replicate chips were performed for each species).

2010-08-17 | E-GEOD-23667 | biostudies-arrayexpress

Independent component analysis of E. coli’s transcriptome reveals the cellular processes which respond to heterologous gene expression

Project description:Heterologous gene expression to expand the native genetic capability of E. coli is the backbone of protein expression and metabolic engineering. The goal of this study was to determine how the identity of the heterologous gene expressed affected the host cell transcriptome. We generated a library of E. coli expressing 46 heterologous genes through an identical rhamnose inducible expression system and perform high throughput RNAseq as well as independent component analysis to elucidate the major variances in the transcriptome. We find that the major variations during heterologous gene expression can be divided into 5 main cellular responses: Fear vs greed, metal homeostasis, respiration, protein folding and amino acid and nucleotide metabolism.

2021-04-09 | GSE133607 | GEO

Systems-level engineering and characterization of Clostridium autoethanogenum through heterologous production of poly-3-hydroxybutyrate (PHB)

Project description:Gas fermentation is emerging as an economically attractive option for the sustainable production of fuels and chemicals from gaseous waste feedstocks. Clostridium autoethanogenum can use CO and/or CO2 + H2 as its sole carbon and energy sources. Fermentation of C. autoethanogenum is currently being deployed on a commercial scale for ethanol production. Expanding the product spectrum of acetogens will enhance the economics of gas fermentation. To achieve efficient heterologous product synthesis, limitations in redox and energy metabolism must be overcome. Here, we engineered and characterised at a systems-level, a recombinant poly-3-hydroxybutyrate (PHB)-producing strain of C. autoethanogenum. Cells were grown in CO-limited steady-state chemostats on two gas mixtures, one resembling syngas (20% H2) and the other steel mill off-gas (2% H2). Results were characterised using metabolomics and transcriptomics, and then integrated using a genome-scale metabolic model reconstruction. PHB-producing cells had an increased expression of the Rnf complex, suggesting energy limitations for heterologous production. Subsequent optimisation of the bioprocess led to a 12-fold increase in the cellular PHB content. The data suggest that the cellular redox state, rather than the acetyl-CoA pool, was limiting PHB production. Integration of the data into the genome-scale metabolic model showed that ATP availability limits PHB production. Altogether, the data presented here advances the fundamental understanding of heterologous product synthesis in gas-fermenting acetogens.

2019-02-03 | GSE115837 | GEO

Strains of increasing genetic divergence to the reference strain

Project description:comparative genomic hybridization between Burkholderia cepacia sequenced strains to determine what are the limits to strain relativity in order to still provide accurate estimations of gene content

2010-02-06 | GSE20096 | GEO

RNA-Seq of Pichia pastoris GS115 to determine the effect of inducing heterologous expression of human lysozyme (HuLy) variants

Project description:To determine the effect of inducing heterologous expression of human lysozyme (HuLy) variants

2017-09-17 | E-MTAB-562 | biostudies-arrayexpress

Comparative Genomic Hybridization of E. coli and Shigella species to determine the relatedness of isolates from Neobladders

Project description:Using comparative genomic hybridization we examined the genome content of 30 isolates of E. coli and Shigella to determine the relative location of E. coli isolates from the human neobladder

2011-07-25 | GSE27326 | GEO

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