Acinetobacter baumannii AB5075
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA168474 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| JHUI01.dat.gz | Other | |||
| JHUI01.fasta.gz | Fasta.gz | |||
| JHUI01.master.dat | Other | |||
| JHUI01.dat.gz | Other |
Items per page: 5 1 - 4 of 4 |
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Project description:The experiment contains native Tn-seq data for Acinetobacter baumannii strain AB5075 with different genetic alterations. The strain was grown at 37 degrees in LB medium and genomic DNA was isolated. We then used PCR to select for DNA regions containing a junction between ISAba13 and chromosomal DNA. Libraries were then prepared using these DNA fragments.
2024-07-15 | E-MTAB-13792 | biostudies-arrayexpress
Project description:The experiment contains ChIP-seq data for Acinetobacter baumannii strain AB5075 encoding 3xFLAG tagged H-NS. Experiments were done with or without ectopic expression of the truncated H-NS-39 protein (corresponding to the H-NS multimerization surface). The strain was grown at 37 degrees in LB medium and crosslinked with 1 % (v/v) formaldehyde. After sonication, to break open cells and fragment DNA, immunoprecipitations were done using anti-FLAG antibodies against. Libraries were prepared using DNA remaining after immunoprecipitation.
2024-07-15 | E-MTAB-13790 | biostudies-arrayexpress
Project description:The experiment contains 3C-seq data for Acinetobacter baumannii strain AB5075 with different genetic alterations. The strain was grown at 37 degrees in LB medium and nucleoprotein was cross-linked using formaldehyde. Genomic DNA was isolated and digested with NlaIII before being ligated with T4 ligase. Sequencing was then used to identify junctions between ligated DNA sequences.
2024-07-15 | E-MTAB-13800 | biostudies-arrayexpress
Project description:Acinetobacter baumannii AB5075 Genome sequencing
| PRJNA1074270 | ENA
Project description:We perform RNA-seq comparing a treatment with 0.375 mM Kaempferol to a mock treatment (DMSO) in A. baumannii AB5075 in order to describe the alterations in global transcription produced by this phytochemical. A. baumannii AB5075 cultures were grown in LB medium in the presence of 0.375 mM Kaempferol or a DMSO control (3 biological replicates per condition) until reaching mid-exponential phase. At this point, cells were harvested, treated with RNAlater for preservation of total RNA and stored at -80 C. After that, total RNA was extracted from each sample. As a result, 99 genes appeared upregulated in the presence of Kaempferol whereas 18 were downregulated. In highlights, the gene functional groups showing the strongest transcriptional alterations were those related to iron acquisition, siderophore biosynthesis and iron transport genes.
2023-09-20 | GSE212989 | GEO
Project description:Acinetobacter baumannii strain:AB5075-UW Genome sequencing and assembly
| PRJNA1003928 | ENA
Project description:Acinetobacter baumannii strain:AB5075-UW Genome sequencing
| PRJNA243297 | ENA
Project description:In recent years, the Gram-negative bacterium Acinetobacter baumannii has garnered considerable attention for its unprecedented capacity to rapidly develop resistance to antibacterial therapeutics. This is coupled with the seemingly epidemic emergence of new hyper-virulent strains. Although strain-specific differences for A. baumannii isolates have been well described, these studies have primarily focused on proteinaceous factors. At present, only limited publications have investigated the presence and role of small regulatory RNA (sRNA) transcripts. Herein, we perform such an analysis, describing the RNA-seq-based identification of 78 A. baumannii sRNAs in the AB5075 background. Together with six previously identified elements, we include each of these in a new genome annotation file, which will serve as a tool to investigate regulatory events in this organism. Our work reveals that the sRNAs display high expression, accounting for >50 % of the 20 most strongly expressed genes. Through conservation analysis we identified six classes of similar sRNAs, with one found to be particularly abundant and homologous to regulatory, C4 antisense RNAs found in bacteriophages. These elements appear to be processed from larger transcripts in an analogous manner to the phage C4 molecule and are putatively controlled by two further sRNAs that are strongly antisense to them. Collectively, this study offers a detailed view of the sRNA content of A. baumannii, exposing sequence and structural conservation amongst these elements, and provides novel insight into the potential evolution, and role, of these understudied regulatory molecules. This study is based on the annotation of novel sRNAs on basis of an Acinetobacter baumannii RNA sequencing dataset. Each sample was generated by pooling three independent biological replicate RNA preps
2016-03-30 | E-GEOD-75708 | biostudies-arrayexpress
Project description:We perform RNA-seq for comparison of deleted cavA wiht empty vector and complemented strains in A. baumannii AB5075 in order to assess the transcription regulation uder the control of this cyclase. A. baumannii AB5075 ΔcavA EV and ΔcavA+cavA cultures were grown in LB medium with 1mM IPTG (3 biological replicates per strain) until reaching mid-exponential phase. At this point, cells were harvested, treated with RNAlate for preservation of total RNA and stored at -80 C. After that, total RNA was extracted from each sample. The results showed 234 differentially expressed genes of which 143 were upregulated and 91 were downregulated in the ΔcavA+cavA complemented strain compared to the deleted cavA mutant harbouring empty vector (ΔcavA EV). The gene functional groups showing the strongest transcriptional alterations were those related to twitching motility (upregulation of genes involves in biogenesis and control of Type IV pili and com genes) as well as biofilm formation, exopolysaccharides production and fimbriae biogenesis (downregulation of csu operon, pga operon and ABUW_2052-2055). Also, genes related to inter- and intracellular signalling were differentially expressed. Cyclic AMP response regulator vfr and genes involved in c-di-GMP synthesis (ABUW_2135) and degradation (ABUW_1138) were upregulated while another gene linked to c-di-GMP degradation (ABUW_2631) and autoinducer synthase encoding gene abaI (part of the quorum sensing signalling system) were downregulated.
2024-08-30 | GSE250425 | GEO
Project description:Acinetobacter baumannii AB5075 isolate:grey variant Genome sequencing
| PRJNA1074272 | ENA