MC8b-genome
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB40967 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Dichloromethane (DCM, methylene chloride) is a toxic halogenated volatile organic compound massively used for industrial applications, and consequently often detected in the environment as a major pollutant. DCM biotransformation offers a sustainable decontamination strategy of polluted sites. Among methylotrophic bacteria able to use DCM as sole source of carbon and energy for growth, Methylorubrum extorquens DM4 (formerly named Methyobacterium extorquens) is a longstanding reference Alphaproteobacteria strain. Here, its primary transcriptome was obtained using a differential RNA-seq (dRNA-seq) approach to provide the first transcription start site (TSS) genome-wide landscape of a methylotroph using DCM.
2022-06-27 | E-MTAB-11726 | biostudies-arrayexpress
Project description:We conducted chromatin immunoprecipitation followed by sequencing (ChIP-seq) and proximity ligation-assisted ChIP-seq (PLAC-seq) for enhancers and promoters (E-P) using left ventricular tissues from dilated cardiomyopathy (DCM) patients and non-heart failure (NF) donors. Differential active enhancer H3K27ac and promoter H3K4me3 regions were identified between NF and DCM. While the average read density (ARD) for H3K27ac is similar between NF and DCM, the ARD of H3K4me3 is significantly lower in DCM samples than in NF.Super-enhancer (SE) analysis revealed that 929 and 129 genes linked to NF- and DCM-specific SE, respectively, and three unique SE-associated genes between NF and DCM were identified.Moreover, the differential E-P interactions were observed in the known heart failure gene loci and are correlated with the gene expression levels. Motif analysis identified known cardiac factors and possible novel players for DCM. We have established cistrome of four histone modifications and long-range chromatin interaction for enhancers and promoters in NF and DCM tissues. The differential histone modifications and E-P interactions were found in DCM, and these differences were associated with the gene expression level of a subset of disease-associated genes in human heart failure.
2022-01-15 | GSE135954 | GEO
Project description:We conducted chromatin immunoprecipitation followed by sequencing (ChIP-seq) and proximity ligation-assisted ChIP-seq (PLAC-seq) for enhancers and promoters (E-P) using left ventricular tissues from dilated cardiomyopathy (DCM) patients and non-heart failure (NF) donors. Differential active enhancer H3K27ac and promoter H3K4me3 regions were identified between NF and DCM. While the average read density (ARD) for H3K27ac is similar between NF and DCM, the ARD of H3K4me3 is significantly lower in DCM samples than in NF.Super-enhancer (SE) analysis revealed that 929 and 129 genes linked to NF- and DCM-specific SE, respectively, and three unique SE-associated genes between NF and DCM were identified.Moreover, the differential E-P interactions were observed in the known heart failure gene loci and are correlated with the gene expression levels. Motif analysis identified known cardiac factors and possible novel players for DCM. We have established cistrome of four histone modifications and long-range chromatin interaction for enhancers and promoters in NF and DCM tissues. The differential histone modifications and E-P interactions were found in DCM, and these differences were associated with the gene expression level of a subset of disease-associated genes in human heart failure.
2022-01-15 | GSE135953 | GEO
Project description:This study attempts at investigating the changes in cardiac gene expression that occur in Dilated Cardiomyopathy (DCM). DCM in Dobermans and Boxers are the focus of this study. Control heart tissue as well as Pacing tissue used is from mongrel dogs. Keywords: control vs pacing vs disease; strain specific disease 3 Dobermans-DCM, 4 Boxers-DCM, 3 mongrels-control and 3 mongrels-pacing
2008-05-08 | E-GEOD-11015 | biostudies-arrayexpress
Project description:Marine pigment-degrading bacterial genome sequencing
| PRJNA851225 | ENA
Project description:The aniline-degrading strain T1 can efficiently degrade aniline, however, it is not clear which key genes are associated with aniline degradation, and we have adopted a genome-wide and transcriptomic approach to fully understand the microbial degradation mechanism of aniline.
2024-06-25 | GSE269992 | GEO
Project description:This study attempts at investigating the changes in cardiac gene expression that occur in Dilated Cardiomyopathy (DCM). DCM in Dobermans and Boxers are the focus of this study. Control heart tissue as well as Pacing tissue used is from mongrel dogs. Keywords: control vs pacing vs disease; strain specific disease
2008-05-08 | GSE11015 | GEO
Project description:Dichloromethane (DCM, methylene chloride) is a toxic chemical with substantial ozone-depleting capacity that is released by anthropogenic activities and natural processes. Specialized anaerobic bacteria metabolize DCM; however, the genetic basis for this process has remained elusive. Comparative genomics of three known anaerobic DCM-degrading bacteria, including the bacterial isolate, Dehalobacterium formicoaceticum strain DMC (Defo), revealed a homologous gene cluster, designated the methylene chloride catabolism (mec) gene cassette, comprising eight to ten genes with predicted 79.6-99.7% amino acid identity. Functional annotation identified genes encoding a corrinoid-dependent methyltransferase system. To support these observations at the functional level, global proteome analysis of Defo cultures growing with DCM as the sole energy source was performed.
Briefly, axenic cultures (n = 3 biological replicates) of Defo were grown in 100 mL of anoxic mineral basal salt medium with 0.2 mM sodium sulfide, 0.2 mM L-cysteine and 30 mM bicarbonate (pH 7.3) under a headspace of N2/CO2 (80:20, vol/vol) with 156 umol (10 uL) of DCM. Cultures were initiated with a 5% (vol/vol) inoculum, incubated at 30C in the dark without agitation, and provided one additional feeding of DCM once the initial amendment was consumed. Biomass for proteomic analyses was collected after 2 weeks of incubation when approximately 95% of the second DCM feedings were consumed. After protein extraction and digestion, global proteomics analyses of 2 ug peptide solutions were performed with an Orbitrap Q Exactive Plus mass spectrometer (Thermo Fisher Scientific, Waltham, MA, US) equipped with a nano-electrospray source (ESI) interfaced with a Proxeon EASY-nLC 1200 system. Tandem mass spectrometry data (MS/MS) were searched against protein databases from the IMG Defo annotated genome (ID. 2757320304) to which common laboratory contaminant proteins were appended. For standard database searching, the peptide MS/MS data was searched using Proteome Discoverer v2.4. The MS/MS data were searched using the SEQUEST HT algorithm. Peptide spectrum match (PSM) confidence was evaluated with Percolator. PSM and peptides were considered identified at a q value of < 0.01.
The shotgun proteomics analysis reported here revealed high expression of proteins encoded on the mec gene cluster during Defo anaerobic growth with DCM.
2021-04-19 | MSV000087235 | MassIVE
Project description:Enrichment culture DFE is capable of fermenting the toxic pollutant dichloromethane (DCM; CH2Cl2) into environmentally benign acetate. The dominant organism in the enrichment culture is a novel bacterium in the Peptococcaceae family, “Candidatus Formimonas warabiya” strain DCMF. This metaproteomic study analysed culture DFE during growth with four substrates – DCM, glycine betaine, choline, and methanol – all of which are primarily, if not solely, metabolised by strain DCMF.
2023-03-11 | PXD037334 | Pride