Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

21 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-scale ChIP-on-chip study into the role of AbsA2 in regulating antibiotic biosynthesis in Streptomyces coelicolor

ABSTRACT: Here we report the construction of a absA2 mutant strain which exhibited the classic precocious hyper-production of antibiotics and its complementation by an N-terminal triple-FLAG tagged version of AbsA2. The complemented and non-complemented absA2 mutant strains were used in large-scale time-course experiments to investigate the effect of deleting absA2 on gene expression at multiple time points and identify AbsA2 DNA binding sites in ChIP-on-chip studies using high-density microarrays.

ORGANISM(S): Streptomyces coelicolor A3(2)

SUBMITTER: Colin Smith

PROVIDER: E-MTAB-3527 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Chromosome wide analysis of parental allele specific chromatin and DNA methylation along the central part of mouse chr7

Project description:Imprinted genes are monoallelically expressed according to parental inheritance. The maternally and paternally inherited alleles are distinguished epigenetically by DNA methylation and histone modifications. Chromosome-wide Chromatin immunoprecipitation (ChIP) and MIRA analysis of MatDup.dist7 and PatDup.dist7 MEFs provided a panoramic map of reciprocal allele-specific histone modifications and DNA methylation at imprinted genes along distal chromosome 7 and 15. ChIP-chip and MIRA-chip was done to map histone modifications and DNA methylation along central chr7 in the maternal allele and paternal allele in Matdup.dist7 and Patdup.dist7 MEFs, respectively, using Nimblegen tiling arrays for central chr7.

2011-03-31 | E-GEOD-26892 | biostudies-arrayexpress

Chromosome wide analysis of parental allele specific chromatin and DNA methylation along mouse distal chr15

Project description:Imprinted genes are monoallelically expressed according to parental inheritance. The maternally and paternally inherited alleles are distinguished epigenetically by DNA methylation and histone modifications. Chromosome-wide Chromatin immunoprecipitation (ChIP) and MIRA analysis of MatDup.dist7 and PatDup.dist7 MEFs provided a panoramic map of reciprocal allele-specific histone modifications and DNA methylation at imprinted genes along distal chromosome 7 and 15. ChIP-chip and MIRA-chip was done to map histone modifications and DNA methylation along distal chr15 in the maternal allele and paternal allele in Patdup.dist7=MatDup.dist15 and Patdup.dist7=MatDupdis15 MEFs, respectively, using Nimblegen tiling arrays for chr15.

2011-03-31 | E-GEOD-26893 | biostudies-arrayexpress

3D-printed wound dressings containing a fosmidomycin-derivative prevent Acinetobacter baumannii biofilm formation in vitro and in vivo

Project description:Two Acinetobacter baumannii strains with low susceptibility to fosmidomycin and two reference with high susceptibility to fosmidomycin were DNA-sequenced to investigate the genomic determinants of fosmidomycin resistance.

2022-12-21 | E-MTAB-12357 | biostudies-arrayexpress

Genome-scale transcriptomic study into the role of AbsA2 in regulating antibiotic biosynthesis in Streptomyces coelicolor

Project description:Here we report the construction of a absA2 mutant strain which exhibited the classic precocious hyper-production of antibiotics and its complementation by an N-terminal triple-FLAG tagged version of AbsA2. The complemented and non-complemented absA2 mutant strains were used in large-scale time-course experiments to investigate the effect of deleting absA2 on gene expression at multiple time points and identify AbsA2 DNA binding sites in ChIP-on-chip studies using high-density microarrays.

2019-02-16 | E-MTAB-3528 | biostudies-arrayexpress

Molecular and Functional Characterization of the role of RNA silencing components in Cryptococcus neoformans

Project description:The RNA interference (RNAi) mediated by homology-dependent degradation of the target mRNA with small RNA molecules plays a key role in controlling transcription and translation processes in a number of eukaryotic organisms. The RNAi machinery is also evolutionarily conserved in a wide variety of fungal species, including pathogenic fungi. To elucidate the physiological functions of the RNAi pathway in Cryptococcus neoformans that causes fungal meningitis, here we performed genetic analyses for genes encoding Argonaute (AGO1 and AGO2), RdRP (RDP1), and Dicers (DCR1 and DCR2) in both serotype A and D C. neoformans. The present study shows that Ago1, Rdp1, and Dcr2 are the major components of the RNAi process occurring in C. neoformans. However, the RNAi machinery is not involved in regulation of production of two virulence factors (capsule and melanin), sexual differentiation, and diverse stress response. To further gain insights into the global regulatory circuit governed by the RNAi pathway, comparative transcriptome analysis using the serotype A and D RNAi mutants was performed. Notably, an increase in transcript abundance of active transposons, such as T2 and T3, was observed in the rdp1? mutant. Therefore, this study can improve our understanding of the role of the RNAi genes in human fungal pathogens including C. neoformans. This SuperSeries is composed of the following subset Series: GSE21176: Molecular and Functional Characterization of the role of RNA silencing components in Cryptococcus neoformans [RNAi_Serotype A] GSE21177: Molecular and Functional Characterization of the role of RNA silencing components in Cryptococcus neoformans [RNAi_Serotype D] Refer to individual Series

2010-05-01 | E-GEOD-21178 | biostudies-arrayexpress

Chromosome wide analysis of parental allele specific chromatin and DNA methylation in mouse

Project description:This SuperSeries is composed of the following subset Series: GSE26720: Chromosome wide analysis of parental allele specific chromatin and DNA methylation GSE26891: Chromosome wide analysis of parental allele specific chromatin and DNA methylation along mouse distal chr7 GSE26892: Chromosome wide analysis of parental allele specific chromatin and DNA methylation along the central part of mouse chr7 GSE26893: Chromosome wide analysis of parental allele specific chromatin and DNA methylation along mouse distal chr15 Refer to individual Series

2011-03-31 | E-GEOD-26947 | biostudies-arrayexpress

Chromosome copy number analysis (WGS) of repair-proficient and repair-deficient yeast strains (S. cerevisiae) after genotoxic treatment with camptothecin or X-ray irradiation

Project description:We investigated how yeast cells deficient in performing homologous recombination-mediated DNA repair due to a deletion of the critical RAD52 gene respond to irreparable DNA damage inflicted by genotoxic treatment commonly applied in cancer therapy (camptothecin and irradiation). We found that upon persistence of irreparable DNA damage, yeast rad52 mutants readily undergo checkpoint adaptation accompanied by the acquisition of resistance to further genotoxic insults as well as the development of aneuploidy. Together, our findings can be used to elucidate how repair-defective cancer cells can become treatment-resistant thereby providing a way to target these resistant cell clones by tackling their aneuploidy-associated phenotypes. To investigate these characteristics commonly present in aneuploid cells in our experimental set-up, we treated yeast cells with genotoxic agents and performed whole genome sequencing. We could identify frequent whole chromosome loss events manifesting in a sensitivity of cells to aneuploidy-targeting agents.

2019-10-22 | E-MTAB-7380 | biostudies-arrayexpress

ChIP on chip data for AbrC3 binding sites in S. coelicolor M145

Project description:ChIP on chip assay of AbrC3 to determine its binding sites in S. coelicolor M145 genome using purified anti-AbrC3 polyclonal antibodies. Samples from nutrient broth (NB) cultures were collected at 36, 48 and 60 hours, cross-linked, and finally hybridized to DNA 104K microarrays designed by University of Surrey.

2014-01-04 | E-MTAB-1451 | biostudies-arrayexpress

Molecular and Functional Characterization of the role of RNA silencing components in Cryptococcus neoformans [RNAi_Serotype D]

Project description:The RNA interference (RNAi) mediated by homology-dependent degradation of the target mRNA with small RNA molecules plays a key role in controlling transcription and translation processes in a number of eukaryotic organisms. The RNAi machinery is also evolutionarily conserved in a wide variety of fungal species, including pathogenic fungi. To elucidate the physiological functions of the RNAi pathway in Cryptococcus neoformans that causes fungal meningitis, here we performed genetic analyses for genes encoding Argonaute (AGO1 and AGO2), RdRP (RDP1), and Dicers (DCR1 and DCR2) in both serotype A and D C. neoformans. The present study shows that Ago1, Rdp1, and Dcr2 are the major components of the RNAi process occurring in C. neoformans. However, the RNAi machinery is not involved in regulation of production of two virulence factors (capsule and melanin), sexual differentiation, and diverse stress response. To further gain insights into the global regulatory circuit governed by the RNAi pathway, comparative transcriptome analysis using the serotype A and D RNAi mutants was performed. Notably, an increase in transcript abundance of active transposons, such as T2 and T3, was observed in the rdp1Δ mutant. Therefore, this study can improve our understanding of the role of the RNAi genes in human fungal pathogens including C. neoformans. RNAi_D: 6 slides are used in this analysis, 3 biological replicate experiments are performed, total RNAs are extracted from 4 strains (NE519 MAT alpha, NE520 MAT a backcrossed Wild type strain, NE517 rdp1 mutant MAT alpha, NE518 rdp1 mutant MAT a). We use Cy5 as rdp1 mutant dye and Cy3 as a WT dye

2010-05-01 | E-GEOD-21177 | biostudies-arrayexpress

Global distribution of RNA polymerase in Streptomyces coelicolor

Project description:Genome wide ChIP-chip analysis of RNA Polymerase binding sites in Streptomyces coelicolor MT1110 cultures grown in SMM + 0.5% casaminoacids at 30C up to mid exponential and stationary phase. Chromatin extracted from rifampicin and formaldehyde treated cultures was incubated with anti ? subunit of core RNA polymerase of E.coli monoclonal antibodies and the DNA purified from anti RNA Polymerase IP and mock IP samples was labelled with either Cy3 or Cy5- dCTP and hybridized in an direct type of microarray experiment onto SCO-Chip2-v2 High Density IJISS arrays

2020-08-01 | E-MAXD-60 | 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