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Genome wide expression analysis of bone marrow derived macrophage cells (BMDMs) stimulated with IFNg and effect of Batf2 knockdown in BMDMs stimulated with IFNg

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE59210 | GEO | 2015/04/30

SECONDARY ACCESSION(S): PRJNA254728

REPOSITORIES: GEO

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Genome wide expression analysis of bone marrow derived macrophage cells (BMDMs) stimulated with IFNg and effect of Batf2 knockdown in BMDMs stimulated with IFNg

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

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Genome wide expession analysis of effect of Batf2 knock down in bone marrow derived macrophage cells stimulated with IFNg

Project description:Bmdm cells were differentiated for 10 days and harvested and culture in six well plate followed by transfection with Batf2 ShRNA. Media was replanished in every two days and on 10th day cells were stimulated with IFNg for 4 hrs. Total RNA was obtain after 4 hrs of stimulation. Total RNA was colloected from control ShRNA transfected Bmdm cells and Batf2 shRNA transfected Bmdm cells stimulated with/with out IFNg

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Genome wide expession analysis of mouse bone marrow derive macrophage (Bmdm) cell stimulated with IFNg

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Identification of the long, edited dsRNAome in LPS-stimulated bone marrow-derived macrophages (BMDMs)

Project description:Endogenous double-stranded RNA (dsRNA) is intricately regulated in mammals to prevent aberrant activation of host inflammatory pathways by cytosolic dsRNA binding proteins. We define the endogenous dsRNA repertoire in mouse BMDMs during the inflammatory response to bacterial lipopolysaccharide. Editing by adenosine deaminases that act of RNA (ADAR) enzymes was quantified temporally using RNA-Seq data from activated mouse macrophages to identify 342 Editing Enriched Regions (EERs), indicative of highly structured dsRNA. Nearly all mouse EERs were present in 3’UTRs. A comparison of EERs from mouse and human revealed significant conservation of EERs between mouse EER- associated genes and homologous human genes. In addition, using publicly available data and experimental validation, a significant proportion of EERs were shown to accumulate in the nucleus, a strategy that is thought to prevent aberrant activation of proinflammatory cascades in the cytoplasm. Finally, the significant conservation of EERs and the enhancement of structured regions in human suggests an increasingly important role for these regions in human biology.

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