Ontology highlight
ABSTRACT:
PROVIDER: PRJNA577405 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Ruminococcus gauvreauii DSM 19829
| PRJNA188897 | ENA
Project description:Little is known about the bacteria that reside in human gallbladder and the mechanisms that allow them to survive within this harsh environmental niche. Furthermore, certain bacterial species are considered to exhibit antagonistic activities whilst others may form mutualistic interactions through, for example, cross-feeding. We isolated two new strains from healthy human bile samples, one belonging to Ruminococcus gauvreauii, of Lachnospiraceae family, and other constituting a new specie in Ruminococcaceae family, named Ruminocoides biliarensis. The two strains differed markedly in their carbohydrate metabolism as R. gauvreauii mainly metabolised sugar alcohols, including inositol, to form acetate as unique fermentation product, and Rc. biliarensis mainly metabolised resistant starches to mainly form formate and acetate as fermentation end products. Both strains exhibited resistance to different bile salts, and the ability to sporulate. Amino acid and vitamin biosynthesis profiles also markedly differed between the two bile isolates. Finally,RNAseq was used to analyse the co-cultures of both isolates, to analyze the activities involved in the possible cross-feeding relationship.
2022-07-05 | GSE140753 | GEO
Project description:Crossfeeding relationship between Ruminococcus gauvreauii IPLA60001 and Ruminocoides biliarensis IPLA60002
| PRJNA591206 | ENA
Project description:Whole genome shotgun bisulfite sequencing, small RNA sequencing and transcriptome sequencing of wildtype Arabidopsis plants (Col-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer. A comparison was performed with regions of the genome containing cytosine DNA methylation identified by methylcytosine immunoprecipitation and whole-genome oligonucleotide tiling microarrays, for wildtype Col-0. Understanding the epigenetic regulatory mechanisms that mediate control of transcription at multiple levels is critical to understanding how plants develop and respond to their environment. We combined next-generation sequencing by synthesis (SBS) technology with novel methods for direct sequencing of the entire cytosine methylome (methylC-seq), transcriptome (RNA-seq), and the small RNA component of the transcriptome (smRNA-seq) to create a set of highly integrated epigenome maps for Arabidopsis thaliana, in conjunction with a set of informative mutants defective in DNA methyltransferase and DNA demethylase activity. At single-base resolution we discovered extensive, previously undetected, DNA methylation, identified the context and level of methylation at each site, and found that local composition has effects upon DNA methylation state. Deep sequencing of the smRNAome exposed a direct relationship between the location and abundance of smRNAs and DNA methylation, perturbation of smRNA biogenesis upon loss of CpG DNA methylation, and a tendency for smRNAs to direct strand-specific DNA methylation in the region of RNA-DNA homology. Finally, strand-specific RNA-seq revealed changes in the transcript abundance of hundreds of genes upon alteration of the DNA methylation state, and enabled the identification of numerous previously unidentified genes regulated by DNA methylation. Keywords: Whole genome shotgun bisulfite sequencing, small RNA sequencing, transcriptome sequencing, methylcytosine immunoprecipitation, whole-genome oligonucleotide tiling microarrays Whole genome shotgun bisulfite sequencing, small RNA sequencing and transcriptome sequencing of wildtype Arabidopsis plants (Col-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer. A comparison was performed with regions of the genome containing cytosine DNA methylation identified by methylcytosine immunoprecipitation and whole-genome oligonucleotide tiling microarrays, for wildtype Col-0.
2008-04-20 | E-GEOD-10877 | biostudies-arrayexpress
Project description:Part of a set of highly integrated epigenome maps for Arabidopsis thaliana. Keywords: Illumina high-throughput bisulfite sequencing Whole genome shotgun bisulfite sequencing of wildtype Arabidopsis plants (Columbia-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer.
2008-04-21 | E-GEOD-10966 | biostudies-arrayexpress
Project description:Whole-genome sequencing is an important way to understand the genetic information, gene function, biological characteristics, and living mechanisms of organisms. There is no difficulty to have mega-level genomes sequenced at present. However, we encountered a hard-to-sequence genome of Pseudomonas aeruginosa phage PaP1. The shotgun sequencing method failed to dissect this genome. After insisting for 10 years and going over 3 generations of sequencing techniques, we successfully dissected the PaP1 genome with 91,715 bp in length. Single-molecule sequencing revealed that this genome contains lots of modified bases, including 51 N6-methyladenines (m6A) and 152 N4-methylcytosines (m4C). At the same time, further investigations revealed a novel immune mechanism of bacteria, by which the host bacteria can recognize and repel the modified bases containing inserts in large scale, and this led to the failure of the shotgun method in PaP1 genome sequencing. Strategy of resolving this problem is use of non-library dependent sequencing techniques or use of the nfi- mutant of E. coli DH5M-NM-1 as the host bacteria to construct the shotgun library. In conclusion, we unlock the mystery of phage PaP1 genome hard to be sequenced, and discover a new mechanism of bacterial immunity in present study. Methylation profiling of Pseudomonas aeruginosa phage PaP1 using kinetic data generated by single-molecule, real-time (SMRT) sequencing on the PacBio RS.
2013-08-22 | E-GEOD-50100 | biostudies-arrayexpress
Project description:Moniliophthora perniciosa is the causal agent of cacao Witche´s broom disease. This disease has been causing extensive damages to Brazilian cacao plantation, especially in Southern Bahia. Using glass slides microarrays, we analyzed the expression profile of 3872 whole genome shotgun reads from M. perniciosa genome, comparing two stages of development (Biotrophic-like mycelia and saprotrophic mycelia). Keywords: Moniliophthora perniciosa, Witches Broom Disease, Pathogenesis, Cacao
2008-06-13 | GSE9627 | GEO
Project description:Moniliophthora perniciosa is the causal agent of cacao Witche´s broom disease. This disease has been causing extensive damages to Brazilian cacao plantation, especially in Southern Bahia. Using glass slides microarrays, we analyzed the expression profile of 3872 whole genome shotgun reads from M. perniciosa genome, comparing two stages of development (Biotrophic-like mycelia and saprotrophic mycelia). Keywords: Moniliophthora perniciosa, Witches Broom Disease, Pathogenesis, Cacao
2008-06-13 | GSE9626 | GEO
Project description:Whole-genome sequencing is an important way to understand the genetic information, gene function, biological characteristics, and living mechanisms of organisms. There is no difficulty to have mega-level genomes sequenced at present. However, we encountered a hard-to-sequence genome of Pseudomonas aeruginosa phage PaP1. The shotgun sequencing method failed to dissect this genome. After insisting for 10 years and going over 3 generations of sequencing techniques, we successfully dissected the PaP1 genome with 91,715 bp in length. Single-molecule sequencing revealed that this genome contains lots of modified bases, including 51 N6-methyladenines (m6A) and 152 N4-methylcytosines (m4C). At the same time, further investigations revealed a novel immune mechanism of bacteria, by which the host bacteria can recognize and repel the modified bases containing inserts in large scale, and this led to the failure of the shotgun method in PaP1 genome sequencing. Strategy of resolving this problem is use of non-library dependent sequencing techniques or use of the nfi- mutant of E. coli DH5α as the host bacteria to construct the shotgun library. In conclusion, we unlock the mystery of phage PaP1 genome hard to be sequenced, and discover a new mechanism of bacterial immunity in present study.
2013-08-22 | GSE50100 | GEO