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Rapid functional annotation of native enhancers in embryonic stem cells with a Neisseria meningitidis CRISPR-Cas9 system (BeadChip)

ABSTRACT: Gene regulatory elements such as enhancers have profound effects on cellular function, health, and disease. Our understanding of mammalian enhancer function is limited by the lack of a technology that would allow for a rapid and thorough test of their cell type-specific function. Here, we describe a novel Cas9-effector system that enables rapid testing and functional annotation of native enhancers in embryonic stem cells.

ORGANISM(S): Mus musculus

PROVIDER: GSE64057 | GEO | 2015/03/03

SECONDARY ACCESSION(S): PRJNA269981

REPOSITORIES: GEO

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Rapid functional annotation of native enhancers in embryonic stem cells with a Neisseria meningitidis CRISPR-Cas9 system (BeadChip)

Project description:Gene regulatory elements such as enhancers have profound effects on cellular function, health, and disease. Our understanding of mammalian enhancer function is limited by the lack of a technology that would allow for a rapid and thorough test of their cell type-specific function. Here, we describe a novel Cas9-effector system that enables rapid testing and functional annotation of native enhancers in embryonic stem cells. Total RNA obtained from R26 dCas9-effector mESC lines after viral delivery of sgRNAs directed against proximal promoter or enhancer regions

2015-03-03 | E-GEOD-64057 | biostudies-arrayexpress

Rapid functional annotation of native enhancers in embryonic stem cells with a Neisseria meningitidis CRISPR-Cas9 system (ATAC-Seq)

Project description:Gene regulatory elements such as enhancers have profound effects on cellular function, health and disease. Our understanding of mammalian enhancer function is limited by the lack of technology that would allow for a rapid and thorough test of their cell type-specific function. Here we describe a novel Cas9-effector system that enables rapid testing and functional annotation of native enhancers in embryonic stem cells. V6.5 mouse ES cells according to the protocol as described

2015-03-03 | E-GEOD-64058 | biostudies-arrayexpress

Rapid functional annotation of native enhancers in embryonic stem cells with a Neisseria meningitidis CRISPR-Cas9 system (ATAC-Seq)

2015-03-03 | GSE64058 | GEO

Rapid functional annotation of native enhancers in embryonic stem cells with a Neisseria meningitidis CRISPR-Cas9 system

Project description:This SuperSeries is composed of the SubSeries listed below.

2015-03-03 | GSE64059 | GEO

Rapid functional annotation of native enhancers in embryonic stem cells with a Neisseria meningitidis CRISPR-Cas9 system

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-03-03 | E-GEOD-64059 | biostudies-arrayexpress

Rapid functional annotation of native enhancers in embryonic stem cells with a Neisseria meningitidis CRISPR-Cas9 system

Project description:Rapid functional annotation of native enhancers in embryonic stem cells with a Neisseria meningitidis CRISPR-Cas9 system

| PRJNA269978 | ENA

Improved production process for native outer membrane vesicle vaccine against Neisseria meningitidis.

Project description:An improved detergent-free process has been developed to produce vaccine based on native outer membrane vesicles (NOMV) against Neisseria meningitidis serogroup B. Performance was evaluated with the NonaMen vaccine concept, which provides broad coverage based on nine distinct PorA antigens. Scalable aseptic equipment was implemented, replacing undesirable steps like ultracentrifugation, inactivation with phenol, and the use of preservatives. The resulting process is more consistent and gives a higher yield than published reference processes, enabling NOMV production at commercial scale. Product quality met preliminary specifications for 9 consecutive batches, and an ongoing study confirmed real-time stability up to 12 months after production. As the NOMV had low endotoxic activity and induced high bactericidal titres in mice, they are expected to be safe and effective in humans. The production process is not limited to NonaMen and may be applicable for other N. meningitidis serogroups and other gram-negative pathogens. The current results therefore facilitate the late-stage development and clinical evaluation of NOMV vaccines.

| S-EPMC3669287 | biostudies-literature

Zur regulon of Neisseria meningitidis

Project description:The zur regulon in Neisseria meningitidis was elucidated in the strain MC58 using a zur knockout strain and conditions which activate Zur ( zinc supplementation in the medium)

2012-10-05 | GSE38033 | GEO

New rapid diagnostic tests for Neisseria meningitidis serogroups A, W135, C, and Y.

Project description:BackgroundOutbreaks of meningococcal meningitis (meningitis caused by Neisseria meningitidis) are a major public health concern in the African "meningitis belt," which includes 21 countries from Senegal to Ethiopia. Of the several species that can cause meningitis, N. meningitidis is the most important cause of epidemics in this region. In choosing the appropriate vaccine, accurate N. meningitidis serogroup determination is key. To this end, we developed and evaluated two duplex rapid diagnostic tests (RDTs) for detecting N. meningitidis polysaccharide (PS) antigens of several important serogroups.Methods and findingsMouse monoclonal IgG antibodies against N. meningitidis PS A, W135/Y, Y, and C were used to develop two immunochromatography duplex RDTs, RDT1 (to detect serogroups A and W135/Y) and RDT2 (to detect serogroups C and Y). Standards for Reporting of Diagnostic Accuracy criteria were used to determine diagnostic accuracy of RDTs on reference strains and cerebrospinal fluid (CSF) samples using culture and PCR, respectively, as reference tests. The cutoffs were 10(5) cfu/ml for reference strains and 1 ng/ml for PS. Sensitivities and specificities were 100% for reference strains, and 93.8%-100% for CSF serogroups A, W135, and Y in CSF. For CSF serogroup A, the positive and negative likelihood ratios (+/- 95% confidence intervals [CIs]) were 31.867 (16.1-63.1) and 0.065 (0.04-0.104), respectively, and the diagnostic odds ratio (+/- 95% CI) was 492.9 (207.2-1,172.5). For CSF serogroups W135 and Y, the positive likelihood ratio was 159.6 (51.7-493.3) Both RDTs were equally reliable at 25 degrees C and 45 degrees C.ConclusionsThese RDTs are important new bedside diagnostic tools for surveillance of meningococcus serogroups A and W135, the two serogroups that are responsible for major epidemics in Africa.

| S-EPMC1563501 | biostudies-literature

Expression of phosphofructokinase in Neisseria meningitidis

Project description:Neisseria meningitidis serogroup B is a pathogen that can infect diverse sites within the human host. According to the N. meningitidis genomic information and experimental observations glucose can be completely catabolized through the Entner-Doudoroff pathway and the pentose phosphate pathway. The Embden-Meyerhof-Parnas pathway is not functional, because the gene for phosphofructokinase is not present. The phylogenetic distribution of phosphofructokinase indicates that in most obligate aerobic organisms PFK is lacking. We conclude that this is because of the limited contribution of PFK to the energy supply in aerobically grown organisms in comparison with the energy generated through oxidative phosphorylation. Under anaerobic or microaerobic conditions the available energy is limiting and PFK provides an advantage, which explains the presence of PFK in many (facultative) anaerobic organisms. In accordance with this, in silico flux balance analysis predicted an increase of biomass yield as a result of PFK expression. However, analysis of a genetically engineered N. meningitidis strain that expresses a heterologous phosphofructokinase showed that the yield of biomass on substrate decreased in comparison with a pfkA deficient control strain, which was associated mainly with an increase in CO2 production, whereas production of by-products was comparable between the two strains. This might explain why the pfkA gene has not been obtained by horizontal gene transfer, since it is initially unfavourable for biomass yield. No large effects related to heterologous expression of pfkA were observed in the transcriptome. Although our results suggest that introduction of PFK does not contribute to a more efficient strain in terms of biomass yield, achievement of a robust, optimal metabolic network that enables a higher growth rate or a higher biomass yield, might be possible after adaptive evolution of the strain, which remains to be investigated.

2009-11-11 | GSE18951 | GEO

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