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Acinetobacter baumannii AB5075

ABSTRACT: Transcriptomic analysis of A. baumannii AB5075 following the treatments of polymyxin and analogs

PROVIDER: PRJNA748873 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15235700_1.fastq.gz	Fastqsanger.gz
	SRR15235700_2.fastq.gz	Fastqsanger.gz
	SRR15235701_1.fastq.gz	Fastqsanger.gz
	SRR15235701_2.fastq.gz	Fastqsanger.gz
	SRR15235702_1.fastq.gz	Fastqsanger.gz

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native Tn-seq analysis of ISAba13 in Acinetobacter baumannii AB5075

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

Alteration of global transcription by the phytochemical Kaempferol in Acinetobacter baumannii AB5075

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

Transcription regulation by CavA cyclase in Acinetobacter baumannii AB5075

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

ChIP-seq analysis of H-NS in Acinetobacter baumannii AB5075

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

Transcriptomic analysis of Acinetobacter baumannii biofilm

Project description:Differential expression of A. baumannii strain AB5075 biofilm compared to planktonic counterparts after 24 h of growth.

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Alteration of global transcription by the artificial sweetener acesulfame K in Acinetobacter baumannii AB5075

Project description:We perform RNA-seq comparing a treatment with 1.33% acesulfame K to a mock treatment in A. baumannii AB5075 in order to describe the alterations in global transcription produced by this artificial sweetener. A. baumannii AB5075 cultures were grown in LB medium in the presence of 1.33% acesulfame K or a water control (3 biological replicates per condition) 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. As a result, 212 genes appeared upregulated in the presence of acesulfame K, whereas 252 were downregulated. In highlights, the gene functional groups showing the strongest transcriptional alterations were those related to twtching motility and natural transformation (downregulation of genes involves in biogenesis and control of Type IV pili and com genes), as well as genes involved in iron acquisition and siderophore biosynthesis and an uncharacterised gene cluster that might be involved in detoxification of sulfonamide compounds.

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3C-seq analysis of Acinetobacter baumannii AB5075 in the presence and absence of H-NS-39

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

RNA-seq analysis of Acinetobacter baumannii AB5075 and grey colony variants having a copy of ISAba13 in the K-locus

Project description:RNA-seq was used to compare the transcriptomes of wild type A. baumannii AB5075 and a spontaneously arising grey colony variant that carries a copy of the insertion sequence ISAba13 within the gtr52 gene.

2024-07-15 | E-MTAB-13791 | biostudies-arrayexpress

Acinetobacter baumannii AB5075

Project description:Acinetobacter baumannii AB5075 Genome sequencing and assembly

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