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Combined Analysis of mRNA Expression and Open Chromatin in Microglia

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Tissue-Resident Macrophages

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2713))

Abstract

The advance of single-cell RNA-sequencing technologies in the past years has enabled unprecedented insights into the complexity and heterogeneity of microglial cell states in the homeostatic and diseased brain. This includes rather complex proteomic, metabolomic, morphological, transcriptomic, and epigenetic adaptations to external stimuli and challenges resulting in a novel concept of core microglia properties and functions. To uncover the regulatory programs facilitating the rapid transcriptomic adaptation in response to changes in the local microenvironment, the accessibility of gene bodies and gene regulatory elements can be assessed. Here, we describe the application of a previously published method for simultaneous high-throughput ATAC and RNA expression with sequencing (SHARE-seq) on microglia nuclei isolated from frozen mouse brain tissue.

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Author information

Authors and Affiliations

  1. Immunogenomics & Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany

    Rebekka Scholz & Marc Beyer

  2. Neuroimmunology and Neurodegenerative Disease, German Center for Neurodegenerative Diseases (DZNE), Tuebingen, Germany

    Desirée Brösamle, Xidi Yuan & Jonas J. Neher

  3. Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tuebingen, Germany

    Desirée Brösamle, Xidi Yuan & Jonas J. Neher

  4. Platform for Single Cell Genomics and Epigenomics at the University of Bonn and the German Center for Neurodegenerative Diseases, Bonn, Germany

    Marc Beyer

Authors
  1. Rebekka Scholz
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  2. Desirée Brösamle
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  3. Xidi Yuan
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  4. Jonas J. Neher
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  5. Marc Beyer
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Corresponding author

Correspondence to Marc Beyer .

Editor information

Editors and Affiliations

  1. Life & Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany

    Elvira Mass

1 Electronic Supplementary Material

Supplementary Table 1

Overview of all necessary oligonucleotides and primers as published by Ma and colleagues in 2020 [27] (XLSX 9 kb)

Supplementary Table 2

Sequences for barcoding oligonucleotides as published by Ma and colleagues in 2020 [27] (XLSX 17 kb)

Supplementary Table 3

Sequences for the library-specific Ad1 primer as published by Ma and colleagues in 2020 [27] (XLSX 10 kb)

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© 2024 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Scholz, R., Brösamle, D., Yuan, X., Neher, J.J., Beyer, M. (2024). Combined Analysis of mRNA Expression and Open Chromatin in Microglia. In: Mass, E. (eds) Tissue-Resident Macrophages. Methods in Molecular Biology, vol 2713. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3437-0_35

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  • DOI: https://doi.org/10.1007/978-1-0716-3437-0_35

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3436-3

  • Online ISBN: 978-1-0716-3437-0

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