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@MISC{Lee:279508,
      author       = {Lee, Jaehyun and Danzer, Karin},
      title        = {{D}ataset: sn{RNA} data of {B}rain section from {P}arkinson
                      {M}ouse {M}odel based on inducible expression of human a-syn
                      constructs, v1},
      publisher    = {Zenodo},
      reportid     = {DZNE-2025-00835},
      year         = {2025},
      abstract     = {Using 6-months, 16-months, and 24-months old mice of a
                      inducible expression of human a-syn constructs based
                      Parkinson mouse model, we produced a single nucleus RNA
                      dataset by cutting 0mm Bregma to -5mm Bregma. The Chromium
                      3’ Single Cell Library Kit (10x Genomics) was used and
                      Sequencing was performed on a NovaSeq 6000. Paired 150bp
                      snRNA-seq was performed using the 10X Genomics Gene
                      Expression (GEX) 3´protocol with an NovaSeq 6000 sequencer.
                      For the alignment of reads, a custom reference was created
                      by adding the sequences of the S1/S2 transgene and the
                      CamkIIa promoter to the mm10 mouse reference genome. Count
                      matrices were obtained using the cellranger count 7.1
                      pipeline, including introns. Six samples were mapped using
                      the bwUni2.0 High-Performance Computing infrastructure. The
                      unfiltered count matrices were loaded into R and corrected
                      for ambient mRNA using SoupX 1.6.0 with default settings,
                      adjusting “tfidfMin” settings between 0.9 and 1.3
                      depending on the sample. Seurat objects were created for
                      each sample and subsequently merged. Cells were filtered out
                      based on the following criteria: number of unique molecular
                      identifiers (nUMI) $3\%,$ ribosomal gene percentage >
                      $1.5\%,$ or log10(Genes/nUMI)},
      cin          = {AG Danzer},
      cid          = {I:(DE-2719)5000072},
      pnm          = {352 - Disease Mechanisms (POF4-352)},
      pid          = {G:(DE-HGF)POF4-352},
      typ          = {PUB:(DE-HGF)32},
      doi          = {10.5281/zenodo.14893737},
      url          = {https://pub.dzne.de/record/279508},
}