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@ARTICLE{Ernst:300359,
      author       = {K. Ernst$^*$ and K. Okonechnikov$^*$ and J. Bageritz$^*$
                      and A. A. Perera$^*$ and J.-P. Mallm$^*$ and A. Wittmann$^*$
                      and K. K. Maaß$^*$ and S. Leible$^*$ and M. Boutros$^*$ and
                      S. M. Pfister$^*$ and M. Zuckermann$^*$ and D. Jones$^*$},
      title        = {{A} simplified preparation method for single-nucleus
                      {RNA}-sequencing using long-term frozen brain tumor
                      tissues.},
      journal      = {Scientific reports},
      volume       = {15},
      number       = {1},
      issn         = {2045-2322},
      address      = {[London]},
      publisher    = {Springer Nature},
      reportid     = {DKFZ-2025-00793},
      pages        = {12849},
      year         = {2025},
      note         = {#EA:B360#EA:B062#LA:B360#LA:B062#},
      abstract     = {Single-cell RNA-sequencing has provided intriguing new
                      insights into research areas such as developmental processes
                      and tumor heterogeneity. Most approaches, however, rely on
                      the availability of fresh surgical specimens, thereby
                      dramatically reducing the ability to profile particularly
                      rare tissue types. Here, we optimized a method to isolate
                      intact nuclei from long-term frozen pediatric glioma
                      tissues. We performed a technical comparison between
                      different single-nucleus RNA-sequencing (snRNA-seq) systems
                      and applied the established nucleus isolation method to
                      analyze frozen primary glioma tissues. The results show that
                      our fast, simple and low-cost nuclear isolation protocol
                      provides intact nuclei, which can be used in both droplet-
                      and plate-based single-cell sequencing platforms - allowing
                      the identification of distinct tumor cell populations and
                      infiltrating microglia. Additional optimization to include
                      shorter RNA fragments in the 3' sequencing library improved
                      gene detection and cell type annotation. Taken together, the
                      method dramatically increases the potential of studying rare
                      tumor entities and is specifically tailored for using frozen
                      brain tumor tissue.},
      keywords     = {Humans / Brain Neoplasms: genetics / Brain Neoplasms:
                      pathology / Single-Cell Analysis: methods / Sequence
                      Analysis, RNA: methods / Glioma: genetics / Glioma:
                      pathology / Cell Nucleus: genetics / Child / Freezing},
      cin          = {B360 / B062 / B110 / W192},
      ddc          = {600},
      cid          = {I:(DE-He78)B360-20160331 / I:(DE-He78)B062-20160331 /
                      I:(DE-He78)B110-20160331 / I:(DE-He78)W192-20160331},
      pnm          = {312 - Funktionelle und strukturelle Genomforschung
                      (POF4-312)},
      pid          = {G:(DE-HGF)POF4-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:40229354},
      doi          = {10.1038/s41598-025-97053-9},
      url          = {https://inrepo02.dkfz.de/record/300359},
}