Ontology highlight
ABSTRACT:
PROVIDER: PRJNA662334 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13094569_1.fastq.gz | Fastqsanger.gz | |||
| SRR13094569_2.fastq.gz | Fastqsanger.gz | |||
| SRR13094570_1.fastq.gz | Fastqsanger.gz | |||
| SRR13094570_2.fastq.gz | Fastqsanger.gz | |||
| SRR13094571_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 1146 |
Similar Datasets
Project description:Genomic content of Bordetella pertussis clinical isolates circulating in Senegal
2009-01-08 | E-MEXP-1674 | biostudies-arrayexpress
Project description:454 sequences from EMBRYOME collaboration, INRA-Orleans
| PRJNA206749 | ENA
Project description:2020 P. falciparum whole genome sequences from Kedougou, Senegal and Thies, Senegal
| PRJNA882774 | ENA
Project description:The obligate intracellular bacterium, Ehrlichia ruminantium (ER) is the causal agent of Heartwater, a fatal disease in ruminants. It is transmitted by ticks of the genus Amblyomma. Here, we report the genomic comparative and the global transcriptional profile of 4 strains of ER, Gardel and Senegal, two distant virulent strains with their corresponding attenuated strains. Our results showed a higher metabolic activity in attenuated strains compared to virulent strains, suggesting a better adaptation in vitro of attenuated strains to the host cells. There was a strong modification of membrane protein encoding genes expression for the 4 strains. A major over-expression of map1-related genes was observed for virulent strains, whereas attenuated strains over-expressed genes encoding for hypothetical membrane proteins. This result suggests that in vivo, MAP-1 related proteins could induce non-protective immune responses for virulent strains. For the attenuated strains, the lack of expression of map1-related genes and over-expression of other membrane proteins encoding genes could be important in induction of efficient immune responses.The diminution of expression of many genes in attenuated Senegal was caused by severe mutation. One of them, the gene recO is involved in DNA repair and its mutation could explain the higher proportion of mutated genes in attenuated Senegal, inducing the faster attenuation of Senegal compared to Gardel.
2016-05-01 | GSE55726 | GEO
Project description:Specification and propagation of the centromeres of eukaryotic chromosomes is determined by epigenetic mechanisms. Unfortunately, the epigenetic characteristics of centromeric DNA and chromatin are difficult to define because the centromeres are composed of highly repetitive DNA sequences in most eukaryotic species. Several rice centromeres have been fully sequenced, making rice an excellent model for centromere research. We conducted genome-wide mapping of cytosine methylation using methylcytosine immunoprecipitation combined with Illumina sequencing. The DNA sequences in the core domains of rice Cen4, Cen5, and Cen8 showed elevated methylation levels compared to the sequences in the pericentromeric regions. In addition, elevated methylation levels were associated with the DNA sequences in the CENH3-binding subdomains compared to the sequences in the flanking H3 subdomains. In contrast, the centromeric domain of Cen11, which is composed exclusively of centromeric satellite DNA, is hypomethylated compared to the pericentromeric domains. Thus, the DNA sequences associated with functional centromeres can be either hypomethylated or hypermethylated. The methylation patterns of centromeric DNA appear to be correlated with the composition of the associated DNA sequences. We propose that both hypomethylation and hypermethylation of CENH3-associated DNA sequences can serve as epigenetic marks to distinguish where CENH3 deposition will occur within the surrounding H3 chromatin. mCIP-seq of one sample of rice seedling
2010-04-22 | E-GEOD-21414 | biostudies-arrayexpress
Project description:Histones are among the most conserved proteins known, but organismal differences do exist. In this study we examined the contribution that divergent amino acids within histone H3 make to cell growth and chromatin structure in S. cerevisiae. We show that, while amino acids that define histone H3.3 are dispensable for yeast growth, substitution of residues within the histone H3 alpha 3 helix with the human counterparts results in a severe growth defect. Mutations within this domain also result in altered nucleosome positioning, both in vivo and in vitro, which is accompanied by increased preference for nucleosome favoring sequences. These results suggest that divergent amino acids within the histone H3 alpha 3 helix play organismal roles in defining chromatin structure. Mnase-seq for two replicates each of wildtype and H3 c-terminal mutants.
2015-11-10 | E-GEOD-73425 | biostudies-arrayexpress
Project description:The G9a mediates mono- and dimethylation of Lys9 of histone H3 at specific gene loci, which is associated with transcriptional repression. ZNF644 and WIZ contain multiple zinc finger motifs that recognize consensus DNA sequences.
2015-03-20 | GSE62616 | GEO
Project description:This study investigated the microbial community of rock varnish Based on consensus sequences for 16S OTUs
2013-04-26 | E-GEOD-46347 | biostudies-arrayexpress
Project description:The transcription factor (TF) interferon regulatory factor 8 (IRF8) controls both developmental and inflammatory stimulus-inducible genes in macrophages, but the mechanisms underlying these two different functions are largely unknown. One possibility is that these different roles are linked to the ability of IRF8 to bind alternative DNA sequences. We found that IRF8 is recruited to distinct sets of DNA consensus sequences before and after lipopolysaccharide (LPS) stimulation. In resting cells, IRF8 was mainly bound to composite sites together with the master regulator of myeloid development PU.1. Basal IRF8M-bM-^@M-^SPU.1 binding maintained the expression of a broad panel of genes essential for macrophage functions (such as microbial recognition and response to purines) and contributed to basal expression of many LPS-inducible genes. After LPS stimulation, increased expression of IRF8, other IRFs, and AP-1 family TFs enabled IRF8 binding to thousands of additional regions containing low-affinity multimerized IRF sites and composite IRFM-bM-^@M-^SAP-1 sites, which were not premarked by PU.1 and did not contribute to the basal IRF8 cistrome. While constitutively expressed IRF8-dependent genes contained only sites mediating basal IRF8/PU.1 recruitment, inducible IRF8-dependent genes contained variable combinations of constitutive and inducible sites. Overall, these data show at the genome scale how the same TF can be linked to constitutive and inducible gene regulation via distinct combinations of alternative DNA-binding sites. Chromatin immuno-precipitations of transcription factors IRF8, IRF1, PU.1, STAT1, STAT2 and of H3 lysine 27 acetylated followed by multiparallel sequencing, performed in bone marrow-derived macrophages from wild type (WT) and BXH2/TyJ mice. Cells were treated with lipopolysaccharide (LPS) for 2 or 4 hours, or interferon b (IFNb) for 30 or 60 minutes, 2 or 4 hours, or left unstimulated.
2015-01-30 | E-GEOD-56121 | biostudies-arrayexpress