GEO DataSets

(Submitter supplied) The phytopathogen Xylella fastidiosa produces two classes of pili, long type IV pili and short type I pili, which are involved in motility and adhesion. In this work, we have investigated the role of σ54 factor and its involvement in the regulation of fimbrial biogenesis in X. fastidiosa. An rpoN null mutant was constructed from citrus strain J1a12, and analyses of global gene expression profile by microarrays comparing the wild type and rpoN mutant strains showed that few genes exhibited differential expression. more...

Organism:

Xylella fastidiosa

Type:

Expression profiling by array

Platform:

GPL2708

6 Samples

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(Submitter supplied) Genome sequence analysis of the bacterium Xylella fastidiosa revealed the presence of two genes, named rpoE and rseA, predicted to encode an ECF sigma factor and an anti-sigma factor, respectively. In this work, an rpoE null mutant was constructed in the citrus strain J1a12 and shown to be sensitive to exposure to heat shock and ethanol. To identify the X. fastidiosa σE regulon, global gene expression profiles were obtained by DNA microarray analysis of bacterial cells under heat shock identifying 23 sigmaE-dependent genes. more...

Organism:

Xylella fastidiosa

Type:

Expression profiling by array

Platform:

GPL2708

18 Samples

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(Submitter supplied) To investigate the role(s) of a cold shock protein homolog (Csp1) in plant pathogenic bacteria Xylella fastidiosa, we compared transcriptome profiles between wild type and a csp1 deletion mutant (Δcsp1) using long read Nanopore RNA sequencing.

Organism:

Xylella fastidiosa subsp. fastidiosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30664

11 Samples

Download data: TXT

(Submitter supplied) Background: Xylella fastidiosa, a Gram-negative fastidious bacterium, grows exclusively in the xylem of several plants, causing diseases such as citrus variegated chlorosis. As the xylem sap contains low concentrations of amino acids and other compounds, X. fastidiosa needs to cope with nitrogen limitation in its natural habitat. Results: In this work, we performed a whole-genome microarray analysis of the X. more...

Organism:

Xylella fastidiosa

Type:

Expression profiling by array

Platform:

GPL2708

24 Samples

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(Submitter supplied) The aim was to determine the additional genes regulated by PilR in addition to fimA. To determine the additional genes the gene expression profile of a pilR mutant was compared to the wild-type strain. Keywords: genetic modification

Organism:

Dichelobacter nodosus

Type:

Expression profiling by array

Platform:

GPL2981

3 Samples

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(Submitter supplied) To determine the genes in addition to fimA regulated by sigma 54 by analysing the gene expression profiles of an rpoN mutant compared to the D. nodosus wild-type strain. Keywords: genetic modification

Organism:

Dichelobacter nodosus

Type:

Expression profiling by array

Platform:

GPL2981

4 Samples

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(Submitter supplied) Xylella fastidiosa is the etiologic agent of a wide range of plant diseases including citrus variegated chlorosis (CVC), a major threat to the Brazilian citrus industry. Genome sequences of several strains of this phytopathogen are accessible, enabling large-scale functional studies. Transcript levels in different iron availabilities were assessed with DNA microarrays representing 2608 (91.6%) coding sequences (CDS) of X. more...

Organism:

Xylella fastidiosa

Type:

Expression profiling by array

Platform:

GPL2708

22 Samples

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(Submitter supplied) Xylella fastidiosa is the etiologic agent of a wide range of plant diseases including citrus variegated chlorosis (CVC), a major threat to the Brazilian citrus industry. Genome sequences of several strains of this phytopathogen are accessible, enabling large-scale functional studies. Transcript levels in different iron availabilities were assessed with DNA microarrays representing 2608 (91.6%) coding sequences (CDS) of X. more...

Organism:

Xylella fastidiosa

Type:

Expression profiling by array

Platform:

GPL2708

22 Samples

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(Submitter supplied) Xylella fastidiosa regulates traits important to both virulence of grape as well as colonization of sharpshooter vectors via its production of a fatty acid signal molecule known as DSF whose production is dependent on rpfF. While X. fastidiosa rpfF mutants exhibit increased virulence to plants they are unable to be spread from plant to plant by insect vectors. To gain more insight into the traits that contribute to these processes, a DNA microarray for this species was designed and utilized to determine the RpfF-dependent regulon by transcriptional profiling. more...

Organism:

Xylella fastidiosa; Xylella fastidiosa 9a5c; Xylella fastidiosa Temecula1

Type:

Expression profiling by array

Platform:

GPL15652

1 Sample

Download data: TXT

(Submitter supplied) Transcriptomic profiles of Pseudomonas protegens H78 and its rpoN-deleted mutant (H78ΔrpoN), which were grown to the late exponential phase (OD600 = 4.0 to 5.0) in the KMB media at 28 °C, were assessed by deep sequencing (RNA-seq) on BGISEQ-500 (illumina).

Organism:

Pseudomonas protegens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24866

6 Samples

Download data: XLS

(Submitter supplied) A 4608-spot DNA microarray was printed containing unique internal fragments of 2572 CDS representing 90.3% of all of the 2848 CDS annotated by Simpson et al. (2000, Nature) (http://aeg.lbi.ic.unicamp.br/xf). PCR primers were designed to amplify unique internal fragments of 200-1000 bp of each predicted CDS described in the annotated genome sequence of X. fastidiosa strain 9a5c (http://aeg.lbi.ic.unicamp.br/xf). more...

Organism:

Xylella fastidiosa

1 Series

8 Samples

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(Submitter supplied) A 4608-spot DNA microarray was printed containing unique internal fragments of 2692 CDS representing 94.5% of all of the 2848 CDS annotated by Simpson et al. (2000, Nature) (http://aeg.lbi.ic.unicamp.br/xf). PCR primers were designed to amplify unique internal fragments of 200-1000 bp of each predicted CDS described in the annotated genome sequence of X. fastidiosa strain 9a5c (http://aeg.lbi.ic.unicamp.br/xf). more...

Organism:

Xylella fastidiosa

8 Series

178 Samples

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(Submitter supplied) Gene expression changes between outside and inside of biofilms were investigated. The gene expression was compared between the outside and inside of the biofilms. At the same time, the gene expressions were also compared with exponential phase and stationary phase in planktonic cells. The gene expression analysis showed that the physiological activities were higher at the outside of the biofilms than those at the inside of the biofilms. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

12 Samples

Download data: CEL, DCP

(Submitter supplied) In the xylem vessels of susceptible hosts, such as citrus trees or grapevines, Xylella fastidiosa forms biofilm like-colonies that can block water transport, which appears to correlate to disease symptoms. Besides helping host colonization, bacterial biofilms play an important role in resistance against antimicrobial agents, for instance antimicrobial peptides (AMP). Here we show that gomesin, a potent AMP from a Brazilian tarantula spider, modulates X. more...

Organism:

Xylella fastidiosa

Type:

Expression profiling by array

Platform:

GPL9024

20 Samples

Download data: TXT

(Submitter supplied) Xylella fastidiosa is a phytopathogenic bacterium responsible for diseases in many economically important crops. Although different strains have been studied, little is known about X. fastidiosa stress responses. One of the best characterized stresses in bacteria is the heat shock response, which induces the expression of specific genes to prevent protein misfolding and aggregation, and to promote degradation of the irreversibly denatured polypeptides. more...

Organism:

Xylella fastidiosa

Type:

Expression profiling by array

Platforms:

GPL3409 GPL2708

52 Samples

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(Submitter supplied) Analyses of the Wild type and the sigma 54 mutant strain NZ7306 with and without peroxide treatment: A Lactobacillus plantarum strain with a deletion in the alternative sigma factor 54 (?54) encoding gene rpoN, displayed a 100 fold higher sensitivity to peroxide as compared to its parental strain. This feature could be due to ?54-dependent regulation of genes involved in peroxide stress response. However, transcriptome analyses of the wild type and the mutant strain during peroxide exposure did not support such a role for ?54. more...

Organism:

Lactiplantibacillus plantarum; Lactiplantibacillus plantarum WCFS1

Type:

Expression profiling by array

Platform:

GPL6368

10 Samples

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(Submitter supplied) In this experiment two strains were compared. The control strain was the wild type strain containing the plasmid, pCD341. pCD341 is an inducible expression vector, a plasmid which can be used to make a bacterium produce a protein of interest. It is called inducible, because the protein of interest will only be produced if an inducer, in this case, IPTG, is present. In the control strain pCD341 is "empty", meaning the gene encoding the protein of interest has not been inserted into the vector, so when you add IPTG nothing will be produced. more...

Organism:

Geobacter sulfurreducens

Type:

Expression profiling by array

Platform:

GPL4897

6 Samples

Download data: GPR

(Submitter supplied) Transcriptional analysis of Clostridium difficile R20291 in biofilm formation, planktonic state and grown on blood agar

Organism:

Clostridioides difficile R20291

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20211

9 Samples

Download data: TXT

(Submitter supplied) The role of rpoS gene in the formation of Escherichia coli biofilms were investigated. The gene expression was compared among E. coli MG1655 wild type strain and rpoS knock-out strain in the biofilms, the planktonic exponential phase, and the planktonic stationary phase. The analysis revealed that the wild type bilfilms (WBF) showed similar pattern of gene expression with the WT planktonic stationary phase (WS), whereas the rpoS knock-out biofilms (MBF) showed similar pattern of gene expression with the wild type planktonic exponential phase (WE). more...

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL199

18 Samples

Download data: CEL

(Submitter supplied) Investigation of whole genome gene expression level changes in Xylella fastidiosa 9a5c biofilm, submitted to treatments with sub inhibitory and inhibitory concentrations of copper and tetracycline.

Organism:

Xylella fastidiosa 9a5c

Type:

Expression profiling by array

Platform:

GPL10380

15 Samples

Download data: PAIR