Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative expression profile of Porphyromonas gingivalis parent strain W83 and the HU protein (PG0121) mutant during exponential growth in rich medium.

ABSTRACT: HU protein regulates expression of genes involved in cell-division, iron acquisition, and transcriptional regulation in Porphyromonas gingivalis Analysis involved RNA extracted from the parent strain W83 and the PG0121 (HU protein) mutant during exponential growth in rich medium. Each of the four experiments used a different preparation of RNA. Comparative expression profiles were determined by hybridizing the microarray slide with a mixture containing equal amount of cDNA generated from each strain. Dye swap experiments were performed.

ORGANISM(S): Porphyromonas gingivalis

SUBMITTER: Mary Davey

PROVIDER: E-GEOD-34009 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Comparative Genome Hybridization of Porphyromonas gingivalis strains

Project description:CGH was used to compare the genomes of a non-invading P. gingivalis strain to the database W83 strain (invader). For hybridization and scanning, TIGR microarrays and protocols were used. The results were independently processed using two different software packages. We used P. gingivalis microarrays in comparative genomics to specifically address the P. gingivalis invasive genotype using invasive and non-invasive phenotypes.

2011-07-27 | E-GEOD-18169 | biostudies-arrayexpress

IHF and HU gene expression in E coli K12

Project description:IHF and HU are two heterodimeric nucleoid associated proteins (NAP) that belong to the same protein family but interact differently with the DNA. IHF is a sequence-specific DNA-binding protein that bends the DNA by over 160o. HU is the most conserved NAP which binds non-specifically to duplex DNA with a particular preference for targeting nicked and bent DNA. Despite their importance, the in-vivo interactions of the two proteins to the DNA remain to be described at a high resolution and on a genome-wide scale. Further, the effects of these proteins on gene expression on a global scale remain contentious. Finally, the contrast between the functions of the homo- and heterodimeric forms of these proteins deserves the attention of further study. Here we present a genome-scale study of HU- and IHF-binding to the E. coli K12 chromosome using ChIP-seq. We also perform microarray analysis of gene expression in single- and double-deletion mutants of each protein to identify their regulons. This data is for microarrays measuring gene expression changes in the various ihf mutants when compared to the wildtype.<br>

2011-11-30 | E-MEXP-3461 | biostudies-arrayexpress

FTO: gene expression and function in skeletal muscle

Project description:We identified the target genes of FTO ("fat mass and obesity associated") in primary cultures of human skeletal muscle cells using adenoviral vectors expressing FTO or GFP and oligonucleotide microarrays. Human myotubes were prepared from 4 different skeletal muscle biopsies. After differentiation, myotubes were infected for 48 hours with recombinant adenovirus expressing either GFP or FTO. Each FTO-infected myotubes culture was compared to GFP-infected myotubes culture. GFP-infected myotubes were regarded as the control. Four biological replicates were processed.

2011-07-05 | E-GEOD-22857 | biostudies-arrayexpress

Transcription profiling of Legionella pneumophila letS insertion mutants

Project description:L. pneumophila Lp02 (thyA hsdR rpsL; MB110) is a virulent thymine auxotroph derived from the Philadelphia 1 clinical isolate and was the parental strain for all constructed mutants. To construct a letS (lpg1912) insertion mutant that lacks pflaG, the letS locus containing the transposon insertion was amplified from MB417 and transferred to Lp02 by natural competence, resulting in strain MB416 (27). Within each experiment, similar culture densities were used to analyze strain phenotypes.

2010-04-01 | E-MTAB-200 | biostudies-arrayexpress

Consequences of an in utero TCDD exposure on the male reproductive function in 28 postnatal days rat

Project description:Our project focuses on the effects of an in utero TCDD exposure on the male reproductive function. Keywords: transcriptionnal analysis Pregnant rats were given either one oral dose of 2,3-7,8 TCDD (200 ng/kg) or equal volume of vehicule (sesame oil). Male rats were sacrified 28 postnatal days and testes were harvested. RNA were extracted with Rneasy mini kit. A pool of RNA from vehicule group was used as the reference group. Each rat submitted to TCDD was compared to reference group. Four biological replicates were processed in a dye swap experimental plan.

2010-12-01 | E-GEOD-13838 | biostudies-arrayexpress

Consequences of an in utero TCDD exposure on the male reproductive function in 5 and 28 postnatal days rat

Project description:This SuperSeries is composed of the following subset Series: GSE13812: Consequences of an in utero TCDD exposure on the male reproductive function in 5 postnatal days rat GSE13838: Consequences of an in utero TCDD exposure on the male reproductive function in 28 postnatal days rat Refer to individual Series

2010-12-01 | E-GEOD-13839 | biostudies-arrayexpress

Consequences of an in utero TCDD exposure on the male reproductive function in 5 postnatal days rat

Project description:Our project focuses on the effects of an in utero TCDD exposure on the male reproductive function. Keywords: transcriptionnal analysis Pregnant rats were given either one oral dose of 2,3-7,8 TCDD (200 ng/kg) or equal volume of vehicule (sesame oil). Male rats were sacrified 5 postnatal days and testes were harvested. RNA were extracted with Rneasy mini kit. A pool of RNA from vehicule group was used as the reference group. Each rat submitted to TCDD was compared to reference group. Four biological replicates were processed in a dye swap experimental plan.

2010-12-01 | E-GEOD-13812 | biostudies-arrayexpress

Loss of tight junction integrity induces loss of epithelial phenotype: case of Claudin11 knock out in testis.

Project description:Epithelium barrier integrity is assumed at least in part by the presence of junctions between cells. Tight-junction formation may be necessary for Sertoli cells to cease dividing and to support germ cell development. Microarray analysis of P20 Cldn11 +/- and Cldn11-/- testes confirmed the impact od Cldn11 deficiency on cell cytoskeleton and junction-related genes. Keywords: transcriptomic analysis Two-condition experiment: P20 Cldn11 +/- vs. P20 Cldn11 -/- testes. A pool of RNA from P20 Cldn11 +/- group was used as the reference group. Each P20 Cldn11 -/- was compared to reference group. Three biological replicates were processed in dye swap.

2010-04-11 | E-GEOD-15492 | biostudies-arrayexpress

Gene expression changes in Porphyromonas gingivalis W83 after inoculation in rat oral cavity

Project description:The aim of this study is to investigate the alterations in gene expression in Porphyromonas gingivalis W83 after inoculation in rat oral cavity. P.gingivalis W83 inoculation in rat oral cavity caused inflammatory responses in gingival tissues and destroyed host alveolar bone. Microarray analysis revealed that 42 genes were upregulated, and 22 genes were downregulated in the detected 1786 genes in the inoculated P.gingivalis W83. Products of these upregulated and downregulated genes are mainly related to transposon functions, cell transmembrane transportation, protein and nucleic acid metabolism, energy metabolism, cell division and bacterial pathogenicity.P.gingivalis W83 has a pathogenic effect on host oral cavity. Meanwhile, inflammatory oral environment alters P.gingivalis W83 gene expression profile. These changes in gene expression may limit the proliferation and weaken the pathogenicity of P.gingivalis W83, and favor themselves to adapt local environment for survival.

2015-04-07 | GSE67608 | GEO

Acetylome of Acinetobacter baumannii SK17 reveals a highly-conserved modification of histone-like protein HU

Project description:Lysine acetylation is a prevalent post-translational modification in both eukaryotes and prokaryotes. Whereas this modification is known to play pivotal roles in eukaryotes, the function and extent of this modification in prokaryotic cells remain largely unexplored. Here we report the acetylome of a pair of antibiotic-sensitive and -resistant nosocomial pathogen Acinetobacter baumannii SK17-S and SK17-R. A total of 145 lysine acetylation sites on 125 proteins was identified, and there are 23 acetylated proteins found in both strains, including histone-like protein HU which was found to be acetylated at Lys13. HU is a dimeric DNA-binding protein critical for maintaining chromosomal architecture and other DNA-dependent functions. To analyze the effects of site-specific acetylation, homogenously Lys13-acetylated HU protein, HU(K13ac) was prepared by genetic code expansion. Whilst not exerting an obvious effect on the oligomeric state, Lys13 acetylation alters both the thermal stability and DNA binding kinetics of HU. Accordingly, this modification likely destabilizes the chromosome structure and regulates bacterial gene transcription. By preparing and characterizing site-specifically acetylated bacterial protein for the first time, this work indicates that acetyllysine plays an important role in bacterial epigenetics and presents a promising target against bacterial infections.

2018-10-24 | PXD007289 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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