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@ARTICLE{Braband:285097,
      author       = {K. L. Braband and A. S. Nedwed and S. S. Helbich and M.
                      Simon$^*$ and N. Beumer$^*$ and B. Brors$^*$ and F. Marini
                      and M. Delacher},
      title        = {{U}sing single-cell chromatin accessibility sequencing to
                      characterize {CD}4+ {T} cells from murine tissues.},
      journal      = {Frontiers in immunology},
      volume       = {14},
      issn         = {1664-3224},
      address      = {Lausanne},
      publisher    = {Frontiers Media},
      reportid     = {DKFZ-2023-02221},
      pages        = {1232511},
      year         = {2023},
      abstract     = {The Assay for Transposase-Accessible Chromatin using
                      sequencing (ATAC-seq) is a cutting-edge technology that
                      enables researchers to assess genome-wide chromatin
                      accessibility and to characterize cell type specific
                      gene-regulatory programs. Recent technological progress
                      allows for using this technology also on the single-cell
                      level. In this article, we describe the whole value chain
                      from the isolation of T cells from murine tissues to a
                      complete bioinformatic analysis workflow. We start with
                      methods for isolating scATAC-seq-ready CD4+ T cells from
                      murine tissues such as visceral adipose tissue, skin, colon,
                      and secondary lymphoid tissues such as the spleen. We
                      describe the preparation of nuclei and quality control
                      parameters during library preparation. Based on publicly
                      available sequencing data that was generated using these
                      protocols, we describe a step-by-step bioinformatic analysis
                      pipeline for data pre-processing and downstream analysis.
                      Our analysis workflow will follow the R-based bioinformatics
                      framework ArchR, which is currently well established for
                      scATAC-seq datasets. All in all, this work serves as a
                      one-stop shop for generating and analyzing chromatin
                      accessibility landscapes in T cells.},
      keywords     = {ArchR (Other) / Signac (Other) / T cell isolation (Other) /
                      scATAC-seq (Other) / tissue digestion (Other)},
      cin          = {B330 / A420 / HD01},
      ddc          = {610},
      cid          = {I:(DE-He78)B330-20160331 / I:(DE-He78)A420-20160331 /
                      I:(DE-He78)HD01-20160331},
      pnm          = {312 - Funktionelle und strukturelle Genomforschung
                      (POF4-312)},
      pid          = {G:(DE-HGF)POF4-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:37908367},
      pmc          = {pmc:PMC10613658},
      doi          = {10.3389/fimmu.2023.1232511},
      url          = {https://inrepo02.dkfz.de/record/285097},
}