GEO DataSets

(Submitter supplied) Transition of microbial growth from planktonic to biofilm is associated with programmed changes in the global patterns of gene expression. These changes are likely to faciliate the appropriate physiological and metabolic adjustments that bacteria need to make during the development of biofilms. Using microarrays we have examined the changes in pattern of gene expression associated with growth of Mycobacterium smegmatis in various stages of planktonic and biofilm cultures. more...

Organism:

Mycolicibacterium smegmatis

Type:

Expression profiling by array

Platform:

GPL4686

12 Samples

Download data: GPR

(Submitter supplied) Slide Information Array Name : Mycobacterium smegmatis microarray version 2 Elements on Array : 29184 Elements on Array (minus empties): 28904 Grids: 48 Array Type : ss_oligo (70-mer) Surface Coating: Epoxy Printing Buffer(s): Nexterion with .01 CTAB, Schott buffer LEB E2 Arraying Machine(s): Genetix Oligo Replicates : 4x Oligos Designed : 6746 ORFs w/o oligo*: 1 Controls: 480 A. thaliana (70-mers) Strain Information Design Strain : ORFs in Design: Oligos Designed **: MC2 155 6898 6746 TIGR Spotfinder Printing Pattern MetaRow 12 MetaColumn 4 Pix X (pix) 450 Pin Y (pix) 450 Row Number 25 Column Number 25 X Spacing (pix) 17 Y Spacing (pix) 17 The user should remove slides from their packaging as soon as possible and store them at room temperature in a desiccator or a Rubbermaid® or Tupperware® container containing a bottom layer of anhydrous calcium sulfate such as Drierite®. more...

Organism:

Mycolicibacterium smegmatis

1 Series

12 Samples

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(Submitter supplied) The experiment was carried out to study the effect of loss of (p)ppGpp or cyclic di-GMP on the gene expression pattern of Mycobacterium smegmatis MC2 155 strains. The cells were cultured in MB7H9 broth containing 0.2% glycerol and 0.05% Tween 80. The transcriptome analysis was performed using GeneSpring GX12 software. Fold changes were calculated with respect to the median expression of wild type replicates. more...

Organism:

Mycolicibacterium smegmatis MC2 155

Type:

Expression profiling by array

Platform:

GPL20299

6 Samples

Download data: TXT

(Submitter supplied) The plant pathogen Agrobacterium tumefaciens attaches to and forms biofilms on both biotic and abiotic surfaces. The transition between free-living, planktonic A. tumefaciens and multicellular biofilms is regulated by several well-defined environmental and nutritional inputs, including pH, oxygen tension, and phosphate concentration. In many bacterial species limiting iron levels inhibit attachment and biofilm formation. more...

Organism:

Agrobacterium tumefaciens

Type:

Expression profiling by array

Platform:

GPL18993

4 Samples

Download data: GPR, PDF, XLSX

(Submitter supplied) The plant pathogen Agrobacterium tumefaciens attaches to and forms biofilms on both biotic and abiotic surfaces. The transition between free-living, planktonic A. tumefaciens and multicellular biofilms is regulated by several well-defined environmental and nutritional inputs, including pH, oxygen tension, and phosphate concentration. In many bacterial species limiting iron levels inhibit attachment and biofilm formation. more...

Organism:

Agrobacterium tumefaciens

Type:

Expression profiling by array

Platform:

GPL18993

4 Samples

Download data: GPR, XLS

(Submitter supplied) In vitro comparative transcriptome analysis was carried to determine genes that are differentially expressed in S. mutans biofilm compared with free-living cells. DNA-microarray analyses indicated that about 12 % of genes showed significant differential expression: 139 were activated and 104 were repressed in biofilm vs. planktonic environment. Keywords: cell type comparison

Organism:

Streptococcus mutans

Type:

Expression profiling by array

Platform:

GPL4745

3 Samples

Download data: GPR

(Submitter supplied) In many bacteria, the ability to modulate biofilm production relies on specific signaling molecules that are either self-produced or made by neighboring microbes within the ecological niche. We analyzed the potential interspecies signaling effect of the Burkholderia diffusible signal factor (BDSF) on Francisella novicida, a model organism for Francisella tularensis, and demon- strated that BDSF both inhibits the formation and causes the dispersion of Francisella biofilm. more...

Organism:

Francisella tularensis subsp. novicida U112

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20815

2 Samples

Download data: TXT

(Submitter supplied) Streptococcus pneumoniae is a Gram positive bacterium that causes severe invasive infection such as pneumonia, septicemia, meningitis and otitis media especially in children, the elderly and immune-compromised patients. Pneumococcal colonization and disease is often associated with biofilm formation. Bacteria in biofilms exhibit elevated resistance both to antibiotics and to host defense systems, which often results in persistent and difficult-to-treat infections. more...

Organism:

Streptococcus pneumoniae D39

Type:

Expression profiling by array

Platform:

GPL19709

6 Samples

Download data: GPR

(Submitter supplied) Otitis media, pneumonia, sinusitis and as well as severe diseases such as meningitis and bacteraemia are related to biofilm-like diseases, in which Streptococcus pneumoniae demonstrated differential and tissue specific gene expressions. In this study, we reported the differential gene expression profile of early in vitro biofilm and planktonic cell in c-DNA microarray analysis. The microarray analysis was performed on total RNA extracted from biofilms grown in 24-well microtiter plate and mid-log grown planktonic cells. more...

Organism:

Streptococcus pneumoniae R6

Type:

Expression profiling by array

Platform:

GPL15071

3 Samples

Download data: GPR

(Submitter supplied) Compare the gene expression difference between MSMEG_2225 knockout strains and wild-type strains by RNA sequencing in Mycobacterium smegmatis. The goal of this study is that detection MSMEG_2225 acts as a transcriptional factor and regulates the target genes expression.

Organism:

Mycolicibacterium smegmatis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22662

6 Samples

Download data: XLS

(Submitter supplied) Total RNA samples were isolated from M. catarrhalis grown in the planktonic state (i.e., in broth) and in a biofilm. Biofilms were generated by growing this strain in the continuous-flow Sorbarod filter system for three days. Total RNA samples and M. catarrhalis genome-directed primers (GDPs) were used for synthesis of Cy3- or Cy5-labeled cDNA samples. Five independent M. catarrhalis growth experiments and total RNA isolations were used for the synthesis of cDNA samples, and a total of six DNA microarray hybridizations were performed in this study. more...

Organism:

Moraxella catarrhalis

Type:

Expression profiling by array

Platforms:

GPL3478 GPL3479

6 Samples

Download data: GPR

(Submitter supplied) Total RNA samples were isolated from M. catarrhalis grown in BHI (iron-replete condition, designated DF0) and in BHI containing 30 mM Desferal (iron-limiting condition, designated DF30). Total RNA and M. catarrhalis genome-directed primers (GDPs) were used for synthesis of Cy3- or Cy5-labeled cDNA samples. Three independent M. catarrhalis growth experiments and total RNA isolations were used for synthesis of cDNA samples, and a total of six DNA microarray hybridizations were performed in this study. more...

Organism:

Moraxella catarrhalis

Type:

Expression profiling by array

Platforms:

GPL3478 GPL3479

6 Samples

Download data: GPR

(Submitter supplied) The oligonucleotides were synthesized by Qiagen and spotted in triplicate on Corning UltraGapII slides

Organism:

Moraxella catarrhalis

8 Series

40 Samples

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(Submitter supplied) Initial attachment to a surface marks the onset of a bacterial life style switch from planktonic to biofilm mode of growth. Among dissimilatory iron reducing bacteria, S. oneidensis MR-1 is notable due to its extensive respiratory versatility. It has been hypothesized that direct interaction of Shewanella cells with, or close proximity to, an appropriate surface facilitates the deposition of electrons. more...

Organism:

Shewanella oneidensis MR-1

Type:

Expression profiling by array

Platform:

GPL10101

8 Samples

Download data: TXT

(Submitter supplied) To investigate the gene expression profile of pellicle cells of Pseudomonas aeruginosa, microarray analysis was performed. Transcriptome profiles of pellicle cells and planktonic cells grown in LB medium were determined by Affymetrix GeneChip. Gene expression pattern that is specific to pellicle cells was evaluated by comparing the data set with that of planktonic cells.

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by array

Platform:

GPL84

4 Samples

Download data: CEL

(Submitter supplied) We investigated the gene expression responses of Candidatus Pelagibacter ubique cultures to iron limitation. Differential expression was observed for genes in iron acquisition and incorporation operons. SfuC in particular was 16 times higher in iron-limited cultures and encodes a periplasmic iron-binding protein.

Organism:

Candidatus Pelagibacter ubique HTCC1002; Candidatus Pelagibacter ubique HTCC1062; Candidatus Pelagibacter sp. HTCC7211

Type:

Expression profiling by array

Platform:

GPL7330

18 Samples

Download data: CEL