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TranscriptomicsVariation in genomic islands contribute to genome plasticity in Cupriavidus metallidurans
Different Cupriavidus metallidurans strains isolated from metal-contaminated and other anthropogenic environments were genotypically and phenotypically compared with C. metallidurans type strain CH34. The latter is well-studied for its resistance to a wide range of metals, which is carried for a sub...
ORGANISM(S): Cupriavidus metallidurans CH34 
2014-01-23 | E-GEOD-36303 | biostudies-arrayexpress
TranscriptomicsDeep Sequence Analysis of the Relationship between Gene Expression, CpG Island Methylation, and Gene Copy Number in Breast Cancer Cells
We used deep sequencinge technology to profile the transcriptome, gene copy number, and CpG island methylation status simultaneously in eight commonly used breast cell lines to develop a model for how these genomic features are integrated in estrogen receptor positive (ER+) and negative breast cance...
ORGANISM(S): Homo sapiens 
2011-03-16 | E-GEOD-27003 | biostudies-arrayexpress
ProteomicsA strain-specific genomic island encodes regulatory proteins to activate type VI secretion system expression in the squid symbiont Vibrio fischeri.
We used the bioluminescent squid symbiont, Vibrio fischeri, to identify essential regulatory factors that control expression and function of a strain-specific T6SS encoded within a genomic island. Random transposon mutagenesis revealed that three genes located on the T6SS2-encoding genomic island ar...
ORGANISM(S): Aliivibrio fischeri 
2021-08-24 | PXD017722 | Pride
Aliivibrio fischeri Squid-vibrio symbiosis Genomic island Symbiosis Vibrio fischeri 1d-lc-ms/ms Type vi secretion system 
TranscriptomicsGenomic comparison in Vibrio parahaemolyticus strains by comparative genomic hybridization.
Vibrio parahaemolyticus is a Gram-negative marine bacterium. A limited population of the organisms causes acute gastroenteritis in humans. Almost all of the clinical V. parahaemolyticus isolates exhibit a beta-type hemolysis on Wagatsuma agar, known as the Kanagawa phenomenon (KP). KP is induced by ...
ORGANISM(S): Vibrio parahaemolyticus 
2010-05-25 | E-GEOD-10020 | biostudies-arrayexpress
TranscriptomicsIsocitrate dehydrogenase 1 (IDH1) mutant gliomas demonstrate a distinct global CpG island methylation profile compared to IDH1 wildtype gliomas using MRSE
In order to identify other molecular aberrations that may cooperate with IDH1R132MUT in gliomagenesis, we performed CpG-island methylation profiling analysis using MSRE (Tran et al. Front. Neurosci. 3:57. Doi: 10.3389/neuro.15.005.2009) on a subset of IDH1R132MUT and IDH1R132WT GBMs and found a dist...
ORGANISM(S): Homo sapiens 
2011-10-24 | E-GEOD-28271 | biostudies-arrayexpress
TranscriptomicsVariation in the Genomic islands of porcine enteropathogenic E. coli strains of serogroup O45 revealed by CGH and PCR.
Background: Members of E. coli serogroup O45 are porcine enteropathogenic E. coli (PEPEC) strains which cause post-weaning diarrhea and produce characteristic attaching and effacing (A/E) lesions. Most of O45 PEPEC strains possess the locus of enterocyte effacement (LEE), encoding the virulence fact...
ORGANISM(S): Escherichia coli 
2010-05-16 | E-GEOD-17036 | biostudies-arrayexpress
TranscriptomicsComparative Genomic Analysis of Clinical Strains of Campylobacter jejuni from South Africa
Background. The bacterial foodborne pathogen Campylobacter jejuni is a common cause of acute gastroenteritis and is also associated with the postinfectious neuropathies, Guillain-Barré and Miller Fisher syndromes. This study described the use of multilocus sequence typing and DNA microarrays to e...
ORGANISM(S): Campylobacter jejuni 
2010-05-27 | E-GEOD-9862 | biostudies-arrayexpress
TranscriptomicsComparative genomic analysis of 93 Bp strains using K96243 as the reference
Natural isolates of Burkholderia pseudomallei (Bp), the causative agent of melioidosis, are known to exhibit diverse phenotypic traits, suggesting significant intraspecies genetic heterogeneity. Using whole-genome Bp microarrays, we experimentally mapped patterns of large-scale genomic variation in ...
ORGANISM(S): Burkholderia pseudomallei K96243 
2008-12-25 | E-GEOD-9491 | biostudies-arrayexpress
TranscriptomicsAnalysis of ToxT regulon in Vibrio cholerae El Tor
Using a combination of ChIP-seq and RNA-seq we show that ToxT regulates expression of the small RNA TarB. TarB modulates the expression level of the transcriptioanl repressor VC0177. VC0177 controls expression of several genes including VC0179. The function of the Vibrio 7th pandemic island-1 (VSP-1...
ORGANISM(S): Vibrio cholerae O1 str. C6706 
2012-04-13 | E-GEOD-36373 | biostudies-arrayexpress
TranscriptomicsDetection of transcription factor NRF1, YY1 and SP1 bound regions in human peripheral blood monocytes
To study the correlation between sequence motif appearance, transcription factor binding and aberrant hypermethylation in the cell lines, we performed ChIP-on-chip analyses (on CpG island microarrays) for the transcription factors Sp1, NRF1 and YY1 in normal peripheral blood monocytes. Keywords: Ch...
ORGANISM(S): Homo sapiens 
2010-06-05 | E-GEOD-16078 | biostudies-arrayexpress
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