Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative genomics of Collimonas bacteria

ABSTRACT: Collimonas is a genus of soil bacteria which comprises three recognized species: C. fungivorans, C. pratensis and C. arenae. The bacteria belonging to this genus share the ability to lyse chitin (chitinolysis) and feed on living fungal hyphae (mycophagy), but they differ in colony morphology, physiological properties and antifungal activity. In order to gain a better insight into the genetic background underlying this phenotypic variability of collimonads, we investigated the variability in the genomic content of five strains representing the three formally recognized Collimonas species. The genomic content of four test strains was hybridized on an array representing the reference strain C. fungivorans Ter331.

ORGANISM(S): Collimonas arenae

SUBMITTER: Francesca Mela

PROVIDER: E-MTAB-349 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Identification of genes essential for Moraxella catarrhalis growth under iron-limiting conditions using Genomic Array Footprinting (GAF): Expression analysis of directed gene deletion mutants.

Project description:Iron-sequestration by the human host is a first line defense against respiratory pathogens like Moraxella catarrhalis, which consequently experiences a period of iron-starvation during colonization and infection. We determined the genetic requirements for M. catarrhalis growth during iron-starvation using the high-throughput genome-wide screening technology genomic array footprinting (GAF). To further characterize the functional consequences of the gene deletions (GAF identified genes), we determined transcriptome profiles of the wild-type and directed mutant strains during exponential growth in BHI medium. The results described in this study are further discussed in Stefan P.W. de Vries, Peter Burghout, Jeroen D. Langereis, Aldert Zomer, Peter W.M. Hermans, Hester J. Bootsma: Genetic requirements for Moraxella catarrhalis growth under iron-limiting conditions, Molecular Microbiology. M. catarrhalis BBH18 directed mutants (n = 3) and their parental wild-type BBH18 strain (n = 4) were expanded to mid-log phase (OD620nm, 1.2 to 1.4) and RNA was isolated as previously described (de Vries et al., 2010 J Bacteriol 192: 3574-3583). Total RNA was labeled according to standard Nimblegen gene expression array protocols and hybridized to 4x72K custom design Nimblegen arrays for read-out.

2013-06-06 | E-GEOD-41547 | biostudies-arrayexpress

Identification of genes essential for Moraxella catarrhalis growth under iron-limiting conditions

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

2013-06-06 | E-GEOD-41548 | biostudies-arrayexpress

gene mapping in the physical map of the Triticum aestivum chromosome arm 1BS

Project description:To improve our understanding of the organization and evolution of the wheat gene space, we established the first map of genes of the wheat chromosome 1BS by hybridizing the newly developed INRA GDEC Triticum aestivum NimbleGen 12x40k unigenes microarray (A-MEXP-2314) with 3D-pools of MTP BACs of from the 1BS physical map. By hybridizing the BAC pools with the wheat NimbleGen 40K unigenes chip we managed to map almost 1063 unigenes on the wheat chromosome 1BS BACs. By comparison with 454 sequences and Illumina survey sequence contigs from the sorted chromosome 1BS, we confirmed the assignation of 849 unigenes in individual BACs from the chromosome 1BS. This data allowed us to study the organization of the wheat gene space along chromosome 1BS. The sequences of the unigenes helped to perform synteny and evolutionary analyses of these unigenes. DNA from MTP clones were pooled into 3D manner: library of MTP clones was stored in 17 plates of 384 wells (24 columns x 16 rows); plate1 pool consist of mixture of DNA from all MTP clones situated in plate 1, Row A pool consist of mixture of DNA from all MTP clones situated in Rows A (from all 17 plates, etc). The set of positive plate, column and row pools for the unigene (represented in microarray) allow to detect the list of putative positive clones (clones from the intersection of positive pools, cleaned using information on physical intersection clones based on clone fingerprints). Hence, all 57 experiments (17 for plate pools, 24 for column pools, and 16 for row pools) have the same experimental factor.

2013-12-06 | E-MTAB-1912 | biostudies-arrayexpress

Using pooled earthworm RNA to test 244K probes on TA-1, TA-2, TA-3, TA-4 test arrays

Project description:This SuperSeries is composed of the following subset Series: GSE16536: Using pooled earthworm RNA to test 244K probes on TA-1 test array design 2520022 sense 1 GSE16548: Using pooled earthworm RNA to test 244K probes on TA-2 test array design 2520023 antisense 1 GSE16549: Using pooled earthworm RNA to test 244K probes on TA-3 test array design 2520024 sense 2 GSE16550: Using pooled earthworm RNA to test 244K probes on TA-4 test array design 2520025 antisense 2 Refer to individual Series

2010-05-18 | E-GEOD-16551 | biostudies-arrayexpress

BCL6 ChIP on chip using a Nimblegen custom tiling array

Project description:To determine whether BCL6 binds to the certain locus we performed genomic localization studies by chromatin immunoprecipitations (ChIP) using a densely tiled custom oligonucleotide microarray covering the genomic loci of different genes. Keywords: ChIP-chip, Transcription Factor localization The experiment was performed in Ramos cell. Triplicate ChIP with BCL6 or actin (negative control) antibodies were cohybridized to the arrays versus the respective input chromatin.The fold enrichment for each oligonucleotide was calculated as the ratio of Cy5 vs. Cy3. Any peaks involving >5 oligonucleotides and with > 2.5 fold enrichment were considered potentially positive hits.

2010-06-10 | E-GEOD-7673 | biostudies-arrayexpress

ISBP mapping in the physical map of the Triticum aestivum chromosome arm 1BL

Project description:To improve the resources for map-based cloning and sequencing of the wheat genome, we established a physical map of the wheat chromosome 1BL with a high density of markers by hybridizing the newly developed INRA GDEC Triticum aestivum NimbleGen 12x17k ISBP microarray (A-MEXP-2312) with BAC pools from the 1BL physical map. Then, we managed to map 3912 ISBP on the wheat chromosome 1BL BACs. The values in the 'Factor Value[individual]' column represent the BAC pool that have been hybridized on the array. For example, the assay 1 correspond to the hybridization of a bulk of all DNA BAC of the plate 1 of the MTP (Minimum Tilling path) BAC library of the chromosome 1BL.

2013-06-01 | E-MTAB-1657 | biostudies-arrayexpress

Identification of genes essential for Moraxella catarrhalis growth under iron-limiting conditions using Genomic Array Footprinting (GAF)

Project description:Iron-sequestration by the human host is a first line defense against respiratory pathogens like Moraxella catarrhalis, which consequently experiences a period of iron-starvation during colonization and infection. We determined the genetic requirements for M. catarrhalis growth during iron-starvation using the high-throughput genome-wide screening technology genomic array footprinting (GAF). To this end, a large marinerT7 transposon mutant library (~28,000 independent transposon mutants) was grown under iron-limiting conditions, achieved by sequestration of iron by 30 M-BM-5M Desferal (DF30), and under control growth conditions (brain heart infusion broth, DF0). Mutants were recovered at exponential- and the early-stationary growth phase and used for the generation of mutant-specific cDNA probes that were hybridized to custom-designed NimbleGen GAF microarrays. The results described in this study are further discussed in Stefan P.W. de Vries, Peter Burghout, Jeroen D. Langereis, Aldert Zomer, Peter W.M. Hermans, Hester J. Bootsma: Genetic requirements for Moraxella catarrhalis growth under iron-limiting conditions, Molecular Microbiology. cDNA probes generated from mutants recovered during the exponential growth phase, or early-stationary phase under challenge (iron-limiting, DF30) or control conditions (DF0). Hybridization on GAF 4x72K custom design Nimblegen GAF arrays for read-out.

2013-06-06 | E-GEOD-41546 | biostudies-arrayexpress

Chip-chip from mouse olfactory epithelium (OE) and liver with antibodies against H3K9me3 and H4K20me3

Project description:The Olfactory Receptor (OR) genes are specifically expressed in the MOE in a monogenic and monoallelic fashion. Only 1 out of 2800 alleles is expressed in each olfactory sensory neuron in mice. ChIP-chip from mouse olfactory epithelium (OE) and liver for H3K9me3 and H4K20me3 revealed that the ORs are highly enriched for these modifications in OE but not in liver. 24 samples were analyzed (20 from OE and 4 from liver) with matching inputs as controls. For the OE samples, there were 2-3 replicates for each array.

2011-05-03 | E-GEOD-24420 | biostudies-arrayexpress

gene mapping in the physical map of the Triticum aestivum chromosome arm 1BL

2013-06-01 | E-MTAB-1650 | biostudies-arrayexpress

Identification by ChIP-on-Chip of ARX target genes, a transcription factor implicated in mental retardation and epilepsy

Project description:Genetic investigations of X-linked intellectual disabilities have implicated the ARX (Aristaless-related homeobox) gene in a wide spectrum of disorders extending from phenotypes characterised by severe neuronal migration defects such as lissencephaly, to mild or moderate forms of mental retardation without apparent brain abnormalities but with associated features of dystonia and epilepsy. Analysis of Arx spatio-temporal localisation profile in mouse revealed expression in telencephalic structures, mainly restricted to populations of GABAergic neurons at all stages of development. Furthermore, studies of the effects of ARX loss of function in humans and animal models revealed varying defects, suggesting multiple roles of this gene during brain development. However, to date, little is known about how ARX functions as a transcription factor and the nature of its targets. To better understand its role, we combined chromatin immunoprecipitation and mRNA expression with microarray analysis and identified a total of 1006 gene promoters bound by Arx in transfected neuroblastoma (N2a) cells and in mouse embryonic brain. Some of these promoters were enriched for a sequence very similar to a motif previously identified as Arx-binding motif and approximately 24% of Arx-bound genes were found to show expression changes following Arx overexpression or knock-down. Several of the Arx target genes we identified are known to be important for a variety of functions in brain development, including axonal guidance and synaptic plasticity and some of them suggest new functions for Arx. Overall, these results identified multiple new candidate targets for Arx and should help to better understand the pathophysiological mechanisms of intellectual disability and epilepsy associated with ARX mutations. ChIP-Chip experiments were performed with either Arx transfected N2a cells or mouse embryonic brains (E15.5). Three replicates were performed for each condition.

2011-12-22 | E-GEOD-29985 | 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