GEO DataSets

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

Organism:

Moraxella catarrhalis

8 Series

40 Samples

Download data

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Moraxella catarrhalis BBH18

Type:

Expression profiling by array; Other; Genome variation profiling by genome tiling array

Platforms:

GPL16171 GPL16172

100 Samples

Download data: PAIR

(Submitter supplied) Iron-sequestration by the human host is a first line defense against respiratory pathogens like Moraxella catarrhalis, which consequently experiences a period of iron-starvation during colonization and infection. We determined the genetic requirements for M. catarrhalis growth during iron-starvation using the high-throughput genome-wide screening technology genomic array footprinting (GAF). To further characterize the functional consequences of the gene deletions (GAF identified genes), we determined transcriptome profiles of the wild-type and directed mutant strains during exponential growth in BHI medium. more...

Organism:

Moraxella catarrhalis BBH18

Type:

Expression profiling by array

Platform:

GPL16172

76 Samples

Download data: PAIR

(Submitter supplied) Iron-sequestration by the human host is a first line defense against respiratory pathogens like Moraxella catarrhalis, which consequently experiences a period of iron-starvation during colonization and infection. We determined the genetic requirements for M. catarrhalis growth during iron-starvation using the high-throughput genome-wide screening technology genomic array footprinting (GAF). To this end, a large marinerT7 transposon mutant library (~28,000 independent transposon mutants) was grown under iron-limiting conditions, achieved by sequestration of iron by 30 µM Desferal (DF30), and under control growth conditions (brain heart infusion broth, DF0). more...

Organism:

Moraxella catarrhalis BBH18

Type:

Genome variation profiling by genome tiling array; Other

Platform:

GPL16171

24 Samples

Download data: PAIR

(Submitter supplied) Transcriptome analysis of M. catarrhalis RH4 predicted coding sequences and clustered regularly interspaced short palindromic repeats (CRISPRs) regions. The results described in this study are further discussed in De Vries, S.P.W., van Hijum, S.A.F.T., Schueler, W., Riesbeck, K., Hays, J.P., Hermans, P.W.M., Bootsma, H.J.; Genome analysis of Moraxella catarrhalis strain RH4: a human respiratory tract pathogen; Journal of Bacteriology

Organism:

Moraxella catarrhalis RH4; Moraxella catarrhalis BBH18

Type:

Expression profiling by genome tiling array

Platform:

GPL10378

18 Samples

Download data: PAIR

(Submitter supplied) L. helveticus is used to modulate cheese flavor and as a starter organism in certain cheese varieties. Our group has compiled a draft (4x) sequence for the 2.4 Mb genome of an industrial strain L. helveticus CNRZ32. The primary aim was to investigate expression of 168 completely sequenced genes during growth in milk and MRS medium using microarrays. Oligonucleotide probes against each of the completely sequenced genes were compiled on maskless photolithography-based DNA microarrays. more...

Organism:

Lactobacillus helveticus; Lactobacillus helveticus CNRZ32

Type:

Expression profiling by array

Platform:

GPL4817

12 Samples

Download data: DATA, PAIR

(Submitter supplied) High-density microarrays based on Maskless Array Synthesizer technology.

Organism:

Lactobacillus helveticus CNRZ32

1 Series

12 Samples

Download data: TXT

(Submitter supplied) Background: Moraxella catarrhalis, a major nasopharyngeal pathogen of the human respiratory tract, is exposed to rapid downshifts of environmental temperature when humans breathe cold air. The prevalence of pharyngeal colonization and respiratory tract infections caused by M. catarrhalis is greatest in winter. We investigated how M. catarrhalis uses the physiologic exposure to cold air to regulate pivotal survival systems that may contribute to M. more...

Organism:

Moraxella catarrhalis O35E

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17097

6 Samples

Download data: BED, TSV

(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) M. catarrhalis strain O35E.rpsl was inoculated into the nasopharynx of healthy, male adult chinchillas. 24 hours later the nasopharyngeal tissues were extracted and homogenized. Total RNA was extracted from these tissue samples. Subsequently, M. catarrhalis genome directed primers were utilized to synthesize cDNA from the total RNA sample. As a control, M.catarrhalis strain O35E.rpsl was grown in BHI broth to a Klett density of 200 units and underwent RNA extraction per standard protocols. more...

Organism:

Moraxella catarrhalis

Type:

Expression profiling by array

Platform:

GPL7398

5 Samples

Download data: GPR

(Submitter supplied) Series of DNA microarrays (4) comparing the M. catarrhalis strain 035E and M. catarrhalis oxyR mutant response to 50 mM hydrogen peroxide.

Organism:

Moraxella catarrhalis

Type:

Expression profiling by array

Platform:

GPL7398

4 Samples

Download data: GPR

(Submitter supplied) Series of DNA microarrays (4) comparing the M. catarrhalis strain 035E response to 50 mM hydrogen peroxide relative to a water-only control.

Organism:

Moraxella catarrhalis

Type:

Expression profiling by array

Platform:

GPL7398

4 Samples

Download data: GPR

(Submitter supplied) Because many virulence genes in E. coli and other pathogens are regulated by temperature, we wanted to determine on a genome-wide scale which genes are modulated in adapting to both human host temperature (37˚C) and ambient room temperature (23˚C). Overall, 126 genes were found to be more highly expressed at 37˚C (1) whereas 297 genes were more highly expressed at 23˚C (2). Genes involved in the uptake and utilization of amino acids, carbohydrates, and iron dominated the 37˚C list, supporting a model in which temperature serves as a host cue to increase expression of bacterial genes needed for growth. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL5942

5 Samples

Download data: GPR, TXT

(Submitter supplied) Microarray consists of full-length PCR products from all 4,290 annotated open reading frames (ORFs) in E. coli mg1655 (1). PCR products are printed in replicate on standard, 1” X 3”, poly-l-lysine coated glass microscope slides. Greater than 95% have been shown to migrate as a single band, of the predicted molecular weight, as determined by gel electrophoresis and ethidium bromide staining. Also printed on each microarray are >200 control spots consisting of: fragmented E. more...

Organism:

Escherichia coli

1 Series

5 Samples

Download data: TXT

(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

Download data

(Submitter supplied) Transcription profile analysis of a wild type ETSU9 strain and its isogenic non-polar in frame mesR mutant.

Organism:

Moraxella catarrhalis

Type:

Expression profiling by array

Platform:

GPL7398

6 Samples

Download data: GPR

(Submitter supplied) Moraxella catarrhalis contains an N6-adenine DNA-methyltransferase (ModM3), that is subject to phase variable expression (random ON/OFF switching). Phase-variable switching of DNA methyltransferase activity results in the presence or absence of methylation at a specific target sequence, leading to co-ordinated, epigenetically-regulated switching of expression of multiple genes across the genome. The suite of genes thus regulated are known as a phasevarion (phase-variable regulon). more...

Organism:

Moraxella catarrhalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27756

6 Samples

Download data: TXT