Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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SRNAs from Neisseria extracellular vesicles

ABSTRACT: Similar to bacterial proteins that are targeted to distinct macrophages organelles via extracellular vesicles, we propose that these vesicles also traffic small RNAs to modulate specific host factors. To test this, we aim to sequence extracellular vesicle derived sRNA, and whole bacterial small RNAs to determine selectivity, and to identify their bacterial and mammalian targets (Experimental Plan in Table-1). For this we will collect highly purified vesicles from N. gonorrhoeae (strain MS11A). We will also treat mouse derived primary macrophages with extracellular vesicles and compare their RNA response to untreated macrophages (Table-2). This will provide novel insights into how macrophages respond to N. gonorrhoeae infections. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Neisseria Gonorrhoeae

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PROVIDER: E-ERAD-439 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:This series represent several subgroups of experiments designed to investigate the role of basal immunoglobulin signaling in immature B cell development. The first subgroup of arrays (Ctrl Mhi, Cre Mhi, Cre Mlo) was done to identify the changes in gene expression in immature B cells as a consequence of inducible deletion of surface IgM expression via Cre-LoxP mediated excision of Ig heavy chain. The second subgroup of arrays (GFPneg, GFPpos, FxE Ctrl, FxE HA) was done to identify the changes in gene expression in immature B cells as a consequence of blockade of tyrosine kinase signaling with herbimycin A treatment. The third subgroup of arrays (FxD, FxE, B6 Mneg, HEL Mhi) was done to establish gene expression profiles of immature B, pre B and pro B cells as reference platforms for the other two subgroups. (Tze etal. Public Library of Science Biology, 2005) The appended supplementary tables are described as follows: TABLE 1: Transformed array signal intensities used for statistical analysis. Listed are all probe sets excluding masked probe sets and Affymetrix hybridization control probe sets. Results are based on the following definitions: - Values with detection p values <0.1 were considered present. - Signal intensities with detection = "A" or with values < 20 were set to "20". TABLE 2: Genes differentially expressed between Ctrl Mhi and Cre Mlo cell populations and associated signal values. Results are based on the following definitions: - 2-fold or greater difference in means - difference in mean expression values > 200 - P < 0.01 (by Student's T test) TABLE 3: Probesets used for clustering in Figures 2 and 3 of publication TABLE 4: Probesets used for clustering in Figure 7 of publication TABLE 5: Correlation coefficients between all cell populations. Correlation coefficients were calculated as an additional method to demonstrate the relationship of the various cell populations to each other. Shown are the correlation coefficients generated using the mean expression values for each of the 101 transcripts from Figure 7 of publication. Keywords = bone marrow B cells

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SRNAs from Neisseria extracellular vesicles

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