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Gene expression profiles of whole blood incubated with live meningococci

ABSTRACT: Blood from two donors was incubated for timepoints up to 24 hours in the presence and absence of live meningococci. The donors are labelled NP and SW. 'SWB' refers to blood that was incubated with meningococci; 'Unstim' refers to control blood incubated in the absence of meningococci. Duplicate arrays were prepared for the majority of timepoints ('a' and 'b'), except where the array of of poor quality and not used in the analysis. We infected heparinised whole blood from two healthy donors (adult volunteers) with 108 live meningococci, serogroup B, type MC58, as previously described.8 Blood was incubated at 37°C for 0, 1, 3, 6, 12, and 24 h. At every timepoint we removed a sample and harvested the plasma by centrifugation (1200 g, 10 min). We gathered the remaining blood into RNA stabilisation fluid. Uninfected control blood was obtained for every timepoint. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. Keywords: all_pairs

ORGANISM(S): Homo sapiens

PROVIDER: GSE3934 | GEO | 2005/12/30

SECONDARY ACCESSION(S): PRJNA94195

REPOSITORIES: GEO

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Gene expression profiles of whole blood incubated with live meningococci

Project description:Blood from two donors was incubated for timepoints up to 24 hours in the presence and absence of live meningococci. The donors are labelled NP and SW. 'SWB' refers to blood that was incubated with meningococci; 'Unstim' refers to control blood incubated in the absence of meningococci. Duplicate arrays were prepared for the majority of timepoints ('a' and 'b'), except where the array of of poor quality and not used in the analysis. We infected heparinised whole blood from two healthy donors (adult volunteers) with 108 live meningococci, serogroup B, type MC58, as previously described.8 Blood was incubated at 37°C for 0, 1, 3, 6, 12, and 24 h. At every timepoint we removed a sample and harvested the plasma by centrifugation (1200 g, 10 min). We gathered the remaining blood into RNA stabilisation fluid. Uninfected control blood was obtained for every timepoint. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. Using regression correlation

2005-12-29 | E-GEOD-3934 | biostudies-arrayexpress

Transcription profiling of blood from two human donors was incubated for timepoints up to 24 hours in the presence and absence of live meningococci

2005-10-14 | E-SMDB-2328 | biostudies-arrayexpress

Homo sapiens

Project description:Gene expression profiles of whole blood incubated with live meningococci

| PRJNA94195 | ENA

Zika infection disrupts proteins involved in the neurosensory system

Project description:Vero cells were infected with Zika virus in three biological replicates and sampled at three post-infection timepoints (12 hrs, 24 hrs, 48 hrs). Biological replicate mock uninfected cells were also done for each timepoint. We used TMT6 labeled quantitation at each timepoint to examine proteome changes in response to infection.

2020-03-05 | MSV000085057 | MassIVE

Transcription profiling by array of Transcriptional profiling of serogroup B Neisseria meningitidis growing in human blood: an approach to vaccine antigen discovery.

Project description:Neisseria meningitidis is a nasopharyngeal commensal of humans which occasionally invades the blood to cause septicaemia. The transcriptome of N. meningitidis strain MC58 grown in human blood for up to 4 hours was determined and around 10% of the genome was found to be differentially regulated. The nuo, pet and atp operons, involved in energy metabolism, were up-regulated, while many house-keeping genes were down-regulated. Genes encoding protein chaperones and proteases, involved in the stress response; complement resistant genes encoding enzymes for LOS sialylation and biosynthesis; and fHbp (NMB1870) and nspA (NMB0663), encoding vaccine candidates, were all up-regulated. Genes for glutamate uptake and metabolism, and biosynthesis of purine and pyrimidine were also up-regulated. Blood grown meningococci are under stress and undergo a metabolic adaptation and energy conservation strategy. The localisation of four putative outer membrane proteins encoded by genes found to be up-regulated in blood was assessed by FACS using polyclonal mouse antisera, and one (NMB0390) showed evidence of surface expression, supporting its vaccine candidacy. [Data is also available from http://bugs.sgul.ac.uk/E-BUGS-121]

2012-11-06 | E-BUGS-121 | biostudies-arrayexpress

Timepoints Control strain

Project description:6 Timepoint microarray from control strain Keywords: Timepoints yw

2007-07-09 | GSE7652 | GEO

Early gene expression changes in peripheral blood leukocytes with rush immunotherapy

Project description:Peripheral blood mononuclear cells (PBMC) were collected from ficoll gradients of whole blood and immediately processed for total RNA and stored at -80oC until use. Blood was from allergic patients at different timepoints pre or post immunotherapy (RIT). Gene expression was compared for the different timepoints. Blood samples were collected from allergic patients before or after rush immunotherapy (RIT), total RNA was prepared and gene expression assessed by Illumina. Samples were collected pre-rush or at 1 week, 7 weeks, 4 months (and for one patient 5 months) after beginning rush immunotherapy. Blood was taken at each timepoint prior to the patient receiving immunotherapy at each timepoint.

2011-12-30 | E-GEOD-29521 | biostudies-arrayexpress

Whole blood expression profiling of obese diet-sensitive, obese diet-resistant and lean human subjects

Project description:We have carried out whole-genome expression profiling of whole blood from obese subjects, defined as obese diet-sensitive and obese diet-resistant, and well matched lean individuals. The diet-sensitive or diet-resistant status refers to the different rates of weight loss observed in the two groups on a low-calorie diet regimen. Bioinformatic analysis revealed alterations in transcription in key pathways that are consistent with impaired capacity for fatty acid oxidation driven mitochondrial ATP synthesis in obese subjects who are resistant to weight loss. A total of 80 samples are analyzed. This consists of 20 lean subjects studied at one timepoint and 20 obese subjects (10 diet-sensitive and 10 diet-resistant) studied at 3 timepoints during caloric restriction (day of entry into program, week 3 into the program and week 6 into the program)

2009-11-04 | E-GEOD-18897 | biostudies-arrayexpress

Signaling of Neisseria meningitidis MC58 mutants to primary human umbilical vein endothelial cells (HUVEC)

Project description:We examined the adherence-mediated signaling of meningococci to human cells by comparing gene expression profiles of primary human umbilical vein endothelial cells (HUVEC) infected by piliated and adherent wild-type (WT), frpC/frpA-deficient mutant, or the non-adherent (ΔpilD) N. meningitidis MC58 bacteria defective in production of the type IV pilus, respectively. Surprisingly, no significant difference was found between the transcriptomes of HUVECs infected by bacteria producing, or not the RTX FrpC and FrpA proteins, thus failing to provide any hints on their biological activity. In contrast, pili-mediated adhesion of meningococci resulted in alterations of expression levels of human genes known to regulate apoptosis, cell proliferation, inflammatory response or adhesion. In particular, genes for signaling pathway proteins involved in early embryonic development, such as transforming growth factor-β (TGF-β)/Smad, Wnt/β-catenin, and Notch/Jagged were found to be upregulated upon adhesion of N. meningitidis together with genes for a number of transcription factors. This reveals that adhering piliated meningocci manipulate signaling pathways controlling human cell proliferation, survival and defense mechanisms, while establishing a commensal relationship with the host. Keywords: time course, infection response, genetic modification

2006-09-01 | GSE4646 | GEO

Temporal Analysis of the Honey Bee Microbiome Reveals Four Novel Viruses and Seasonal Prevalence of Known Viruses, Nosema, and Crithidia

Project description:Pathogen detection microarrays analyzing honeybee samples taken from the same hives over the course of a year, oligos correspond to specific pathogens or pathogen families of viruses, bacteria, fungi, protists, and other parasites Samples were analyzed with the E-Predict analysis package Twenty hives samples biweekly, Timepoint refers to sample collection week after start, where T01 refers to April 15, 2009. Hive refers to the specific hive sampled.

2011-06-06 | E-GEOD-28235 | biostudies-arrayexpress

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