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Next Generation Sequencing Facilitates Quantitative Analysis of wild type and Rbm25-deficient Bone Marrow Derived macrophage Transcriptomes

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of wild type and Rbm25-deficient Bone Marrow Derived macrophage Transcriptomes

PROVIDER: PRJNA1002385 | ENA |

REPOSITORIES: ENA

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Next Generation Sequencing Facilitates Quantitative Analysis of wild type and Rbm25-deficient Bone Marrow Derived macrophage Transcriptomes

Project description:Purpose: The purpose of this study is to detect activated or silenced genes during wild type (WT) and Rbm25-deficient bone marrow derived macrophages (BMDMs). Gene expression differences between two samples could be found using transcriptome profiling (RNA-seq) analysis. Methods: Mouse BMDMs were generated from bone marrow cells in RPMI-1640 medium with recombinant mouse M-CSF (20ng/ml). BMDMs were stained to confirm the surface expression of CD11b and F4/80. Cells with purity >97.5% were used for subsequent experiments. WT and Rbm25 deficient BMDMs were stimulated with LPS (100ng/ml) for 0, 2 or 8 hours, of which RNA profiles were generated by deep sequencing, using Illumina. Results: We mapped about 10 million sequence reads per sample to the mouse genome, identified hundreds of genes with significant mRNA variation between WT and Rbm25 deficient BMDMs.

2024-11-06 | GSE240157 | GEO

H3K9ac and H3K27ac Cut&Tag profiling of wild type and Rbm25-deficient Bone Marrow Derived macrophage

Project description:Purpose: To transcriptome widely reveal histone acetylation modification H3K9ac and H3K27ac regulation by Rbm25, we performed Cleavage Under Targets and Tagmentation (CUT&Tag) analysis of wild-type (WT) and Rbm25-deficiency BMDMs. Methods: Mouse BMDMs were generated from bone marrow cells in RPMI-1640 medium with recombinant mouse M-CSF (20ng/ml). BMDMs were stained to confirm the surface expression of CD11b and F4/80. Cells with purity >97.5% were used for subsequent experiments. WT and Rbm25 deficient BMDMs were stimulated with LPS (100ng/ml) for 4 hours. Results: We carried out CUT&Tag assays using antibody against H3K9ac or H3K27ac, and found the global influence of Rbm25 in regulating H3K9ac and H3K27ac of transcription regulatory regions of key genes for inflammatory macrophage effector function.

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Next Generation Sequencing Facilitates Quantitative Analysis of wild type and Rbm25-deficient Bone Marrow Derived macrophages

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of wild type and Rbm25-deficient Bone Marrow Derived macrophages

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Identification of Rbm25-binding RNAs in bone-marrow-derived macrophages by RIP-seq

Project description:To identify the potential mRNAs that bound by Rbm25, which might be the direct target of Rbm25 for alternative splicing in murine macrophages.

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H3K9ac and H3K27ac Cut&Tag profiling of wild type and Rbm25-deficient Bone Marrow Derived macrophage

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Next Generation Sequencing Facilitates Quantitative Analysis of wild type and Rbm25-deficient Bone Marrow Derived macrophages

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

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Tet2 Mutant Macrophage Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Tet2 Mutant Macrophage Transcriptomes