Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The primary transcriptome of Acinetobacter baumannii ATCC 17978

ABSTRACT: Transcriptomics by RNA-seq provides unparalleled insight into bacterial gene expression networks, enabling a deeper understanding of the regulation of pathogenicity, mechanisms of antimicrobial resistance, metabolism, and other cellular processes. Here we present the transcriptome architecture of Acinetobacter baumannii ATCC 17978, a species emerging as a leading cause of antimicrobial resistant nosocomial infections. Differential RNA-seq (dRNA-seq) examination of model strain ATCC 17978 in 16 laboratory conditions identified 3731 transcriptional start sites (TSS), and 110 small RNAs, including the first identification of 22 sRNA encoded at the 3′ end of mRNA.

ORGANISM(S): Acinetobacter baumannii

PROVIDER: GSE103244 | GEO | 2018/06/25

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of Acinetobacter baumannii ATCC 17978: deleted effects of dna adenine methylase

Project description:Comparison for gene expression of Acinetobacter baumannii ATCC 17978 by deleted effects of dna adenine methylase

2022-01-31 | GSE195621 | GEO

Comparative transcriptional analysis of Acinetobacter baumannii strain ATCC 17978 and strain 17978hm

Project description:In this study the transcriptomes of Acinetobacter baumannii strains ATCC 17978 and 17978hm were compared. Strain 17978hm is a hns knockout derivative of strain ATCC 17978. Strain 17978hm displays a hyper-motile phenotype on semi-solid Mueller-Hinton (MH) media (0.25% agar). ATCC 17978 and 17978hm from an 37C overnight culture were transferred to the centre of the semi-solid MH plate and incubated at 37C for 8 hours. Only 17978hm cells displayed a motile phenotype and covered the complete surface of the plate. These motile 17978hm cells and the non-motile wild-type ATCC 17978 cells were harvested and RNA was isolated. The comparative transcriptome analysis was performed using the FairPlay labeling kit and a custom made Agilent MicroArray with probes designed to coding regions of the ATCC 17978 genome. The data was analyzed using Agilent GeneSpring GX9 and the significance analysis of microarray MS Excel add-on. The motile 17978hm cells and the non-motile wild-type ATCC 17978 cells were harvested and RNA was isolated. The comparative transcriptome analysis was performedThe probes on the microarray cover all predicted open reading frames (at least 4 per ORF) and additional replicates of housekeeping genes of the A. baumannii ATCC 17978 genome .

2013-08-05 | E-GEOD-40681 | biostudies-arrayexpress

Comparative transcriptional analysis of Acinetobacter baumannii strain ATCC 17978 and strain 17978hm

2013-08-05 | GSE40681 | GEO

RNA-Seq of Acinetobacter baumannii ATCC 17978 and a gene knockout strain of putative response regulator gene A1S_2006 from the ATCC 17978 background

Project description:The putative response regulator gene A1S_2006 of Acinetobacter baumannii ATCC 17978 was knocked out using a homologous recombination method to assess the effects of that gene knockout in a global transcriptome landscape. This was done with an objective to better understand the cellular processes that are regulated by the response regulator protein encoded by A1S_2006 gene.

2019-04-04 | E-MTAB-7815 | biostudies-arrayexpress

Transcriptional responses of Acinetobacter baumannii ATCC 17978 to limiting iron availability

Project description:A. baumannii ATCC 17978 cells were incubated under iron replete (mueller-hinton) and iron limiting (MH + 200 ÂµM 2,2'-dipyridyl) conditions, total RNA was extracted when cultures reached OD600=0.7. The probes on the microarray cover all predicted open reading frames (at least 4 per ORF) and additional replicates of housekeeping genes of the A. baumannii ATCC 17978 genome

2013-10-18 | E-GEOD-24921 | biostudies-arrayexpress

Expression Data from Acinetobacter baumannii strain ATCC 17978 and isogenic lpsB mutant cells

Project description:lpsB encodes a glycosyltransferase involved in lipopolysaccharide (LPS) synthesis. LPS is a major component of the Gram-negative bacterial outer membranes. We used custom-made Affymetrix A. baumannii strain ATCC 17978 derived GeneChips to compare the gene expression properties of wild type and isogenic lpsB mutant cells. Two mutants were evaluated; A. baumannii strain 5A7 is a ATCC 17978 derivative harboring a transposon (Tn5) within lpsB (A1S_0430 locus); A. baumannii strain containing a deletion of lpsB (A1S_0430). A. baumannii strain ATCC 17978, 5A7 (lpsB:Tn5) or IH1∆lpsB (∆lpsB) were grown to mid-exponential phase growth, total bacterial RNA was isolated and subjected to GeneChip hybridization and analysis. We sought to determine the transcription profile of lpsB mutated cells.

2012-12-01 | E-GEOD-40771 | biostudies-arrayexpress

Expression Data from Acinetobacter baumannii strain ATCC 17978 and isogenic lpsB mutant cells

2012-12-01 | GSE40771 | GEO

Resistance to pentamidine is mediated by AdeAB, regulated by AdeRS, and influenced by growth conditions in Acinetobacter baumannii ATCC 17978

Project description:The goal of this study was to assess the role of the AdeRS two component signal transduction system in Acinetobacter baumannii ATCC 17978 and its impact on the virulence potential of this bacterial organism. Specific gene deletion strains targeting the adeRS system were generated and compared to wildtype for a number of phenotypic in vitro assays as well as transcriptomic profiling via RNA-sequencing.

2018-05-13 | GSE102711 | GEO

Transcriptional responses of Acinetobacter baumannii ATCC 17978 to limiting iron availability

Project description:A. baumannii ATCC 17978 cells were incubated under iron replete (mueller-hinton) and iron limiting (MH + 200 µM 2,2'-dipyridyl) conditions, total RNA was extracted when cultures reached OD600=0.7.

2013-10-18 | GSE24921 | GEO

Comparison of the gene expression profiles of different strains of A. baumannii by microarrays

Project description:In the present work we compare the gene expression profile of A. baumannii and a mutant knock-out strain of A. baumannii lacking a small RNA gene 13573 and the corresponding small RNA 13573 over-producing strain. The main objective is to recognize the main pathways in which the small RNA 13573 is involved. Moreover, the same wild type strain was used to infect mice and was further analyzed after the infection with the aim of finding genes differentially expressed in vivo. Three biological replicates have been performed for each comparison. The RNA collection from Acinetobacter baumannii strain over-expresing the small RNA (sample 13573) was compared with this isolated from A. baumannii harboring the empty vector (PETRA sample) while gene expression in the knock-out strain (KO sample) was compared with the wild type strain Acinetobacter baumannii ATCC 17978 (ATCC sample). The RNA from A.baumannii recovered from the infected animals (INF sample) was compared with the wild type (ATCC).

2016-08-01 | E-GEOD-60348 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data