Bacteria
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1078343 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Comparison of gene expression in dendritic cells (DCs) isolated from tumors of C57BL/6 obtained from Taconic farms vs DCs isolated from tumor of C57BL/6 mice obtained from Jackson Labortaory vs DCs isolated from tumors of C57BL/6 obtained from Taconic farms and orally gavaged with Bifidobacterium prior to tumor implantation
2015-11-12 | GSE73475 | GEO
Project description:Bacterial genomes of environmental origin in Algeria
| PRJNA540702 | ENA
Project description:Small non-coding RNAs (sRNAs) are widespread effectors of post-transcriptional gene regulation in bacteria. Currently extensive information exists on the sRNAs of Listeria monocytogenes (Lm) expressed during growth in extracellular environments. We used deep sequencing of cDNAs obtained from fractioned RNA (<500nt) isolated from extracellularly growing bacteria and from Lm-infected macrophages to catalog the sRNA repertoire during intracellular bacterial growth. Here we report on the discovery of 150 regulatory RNAs of which 71 have never been previously described. A total of 29 regulatory RNAs, including small non-coding antisense RNAs, are specifically expressed intracellularly. We validated highly expressed sRNAs by Northern blotting and demonstrated by the construction and characterization of isogenic mutants of rli31, rli33-1 and rli50 for intracellular expressed sRNA candidates, that their expression is required for efficient growth of bacteria in macrophages. All three mutants were attenuated when assessed for growth in mouse and insect models of infection. Comparative genomic analysis revealed the presence of lineage specific sRNAs and the absence of sRNA loci in genomes of naturally-occurring infection-attenuated bacteria, with additional loss in non-pathogenic listerial genomes. Our analyses reveal extensive sRNA expression as an important feature of bacterial regulation during intracellular growth.
2011-07-21 | E-MTAB-329 | biostudies-arrayexpress
Project description:Genomes of 49 bacteria species isolated from stool from healthy individuals
| PRJNA496358 | ENA
Project description:Bacterial genomes in TP area, China Genome sequencing and assembly
| PRJNA474356 | ENA
Project description:Gene regulation is one of the most ubiquitous processes in biology. And yet, while the catalogue of 15 bacterial genomes continues to expand rapidly, we remain ignorant about how almost all of the genes in 16 these genomes are regulated. Characterizing the molecular mechanisms by which regulatory sequences 17 operate still requires focused efforts using low-throughput methods. Here we show how a combination of 18 massively parallel reporter assays, mass spectrometry, and information-theoretic modeling can be used 19 to dissect bacterial promoters in a systematic and scalable way. We demonstrate this method on both 20 well-studied and previously uncharacterized promoters in the enteric bacterium Escherichia coli. In all 21 cases we recover nucleotide-resolution models of promoter mechanism. For some promoters, including 22 previously unannotated ones, we can further extract quantitative biophysical models describing 23 input-output relationships. This method opens up the possibility of exhaustively dissecting the 24 mechanisms of promoter function in E. coli and a wide range of other bacteria.
2018-04-13 | PXD007892 | JPOST Repository
Project description:Six bacterial genomes, Geobacter metallireducens GS-15, Chromohalobacter salexigens, Vibrio breoganii 1C-10, Bacillus cereus ATCC 10987, Campylobacter jejuni subsp. jejuni 81-176 and Campylobacter jejuni NCTC 11168, all of which had previously been sequenced using other platforms were re-sequenced using single-molecule, real-time (SMRT) sequencing specifically to analyze their methylomes. In every case a number of new N6-methyladenine (m6A) and N4-methylcytosine (m4C) methylation patterns were discovered and the DNA methyltransferases (MTases) responsible for those methylation patterns were assigned. In 15 cases it was possible to match MTase genes with MTase recognition sequences without further sub-cloning. Two Type I restriction systems required sub-cloning to differentiate their recognition sequences, while four MTases genes that were not expressed in the native organism were sub-cloned to test for viability and recognition sequences. No attempt was made to detect 5-methylcytosine (m5C) recognition motifs from the SMRT sequencing data because this modification produces weaker signals using current methods. However, all predicted m6A and m4C MTases were detected unambiguously. This study shows that the addition of SMRT sequencing to traditional sequencing approaches gives a wealth of useful functional information about a genome showing not only which MTase genes are active, but also revealing their recognition sequences. Examination of the methylomes of six different strains of bacteria using kinetic data from single-molecule, real-time (SMRT) sequencing on the PacBio RS.
2012-10-04 | E-GEOD-40133 | biostudies-arrayexpress
Project description:Genomes of bacterial isolates from IBD patients. Genome sequencing and assembly
| PRJNA512876 | ENA
Project description:human gut bacterial isolate genomes Genome sequencing and assembly
| PRJNA1093465 | ENA