Unknown,Transcriptomics,Genomics,Proteomics

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Cell-type and subcellular compartment specific isolation of miRNAs directly from the mouse brain by in vivo AGO-APP

ABSTRACT: We derived two transgenic mouse lines expressing a T6B peptide either in the whole cytoplasm or targeted at the post-synapse, in order to perform AGO-APP directly from mouse tissues. We used these mice first to compare the expression of AGO-bound micro-RNAs in 2 types of neuron, the olfactory bulb inhibitory interneurons and the cortical excitatory neurons, and second to analyze the post-synaptic targeting of micro-RNAs in these 2 neuron types.

INSTRUMENT(S): Illumina MiniSeq

ORGANISM(S): Mus musculus

SUBMITTER: christophe beclin

PROVIDER: E-MTAB-15124 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Specific Lactobacillus strains are marketed as probiotics i.e. health promoting organisms. As previously shown in vivo, L. plantarum WCFS1 modulates immune responses via nuclear factor (NF)kB in a growth phase dependent manner, likely caused by changed microbial cell surface characteristics. Here, we identified the differential cell-surface proteome composition of L. plantarum WCFS1 cells derived from the mid-logarithmic and late stationary growth phase by surface trypsination of intact bacterial cells, followed by a combined 1D- and 2D-LC-MS shotgun proteomics strategy, and growth phase dependent transcriptome analysis. Overall, these analyses led to the identification of 31 surface proteins differentially present in the logarithmic and stationary phase, whereas additional 17 and 33 proteins appeared solely present in stationary and logarithmic phase of growth, respectively. From 75% of predicted surface related genes displaying relatively high expression levels, the corresponding proteins were detected, demonstrating a high correlation between transcriptome and proteome profiles. The impact of cell-surface peptide fractions on cellular host responses was evaluated using NFkB promoter activation assays in intestinal epithelial cells, revealing that only late stationary phase derived peptides are capable of attenuating flagellin and cell envelope induced NFkB activation. Overall our data mechanistically expand earlier observations that revealed growth-phase dependent immunomodulation by L. plantarum WCFS1, leading to a typical adjuvant- or tolerance-like response after exposure to stationary phase harvested bacterial cells. Sub-fractionation of the late stationary phase peptide fraction revealed a sub-set of strong attenuator peptides able to manipulate NFkB related pathways to hereby attenuate pro-inflammatory signaling. Samples were hybridizedin a loop design linking each timepoint to the next as well as the previous timepoint. Additional hybridizations were introduced linking each sample three timepoints forward and three timepoints back. All samples were hybridized unsing at least each of the two dyes once.

Dataset Information

Cell-type and subcellular compartment specific isolation of miRNAs directly from the mouse brain by in vivo AGO-APP

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