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@ARTICLE{Otonicar:295958,
      author       = {J. Otonicar$^*$ and O. Lazareva$^*$ and J.-P. Mallm$^*$ and
                      M. Simovic-Lorenz$^*$ and G. Philippos$^*$ and P. Sant$^*$
                      and U. Parekh$^*$ and L. Hammann$^*$ and A. Li$^*$ and U.
                      Yildiz and M. Marttinen and J. Zaugg and K. M. Noh and O.
                      Stegle$^*$ and A. Ernst$^*$},
      title        = {${HIPSD}\&{R}-seq$ enables scalable genomic copy number and
                      transcriptome profiling.},
      journal      = {Genome biology},
      volume       = {25},
      number       = {1},
      issn         = {1465-6906},
      address      = {London},
      publisher    = {BioMed Central},
      reportid     = {DKFZ-2024-02739},
      pages        = {316},
      year         = {2024},
      note         = {#EA:B420#EA:B260#EA:W192#EA:E250#LA:B420#LA:B260#},
      abstract     = {Single-cell DNA sequencing (scDNA-seq) enables decoding
                      somatic cancer variation. Existing methods are hampered by
                      low throughput or cannot be combined with transcriptome
                      sequencing in the same cell. We propose $HIPSD\&R-seq$
                      (HIgh-throughPut Single-cell Dna and Rna-seq), a scalable
                      yet simple and accessible assay to profile low-coverage DNA
                      and RNA in thousands of cells in parallel. Our approach
                      builds on a modification of the 10X Genomics platform for
                      scATAC and multiome profiling. In applications to human cell
                      models and primary tissue, we demonstrate the feasibility to
                      detect rare clones and we combine the assay with
                      combinatorial indexing to profile over 17,000 cells.},
      keywords     = {Humans / Single-Cell Analysis: methods / Gene Expression
                      Profiling: methods / High-Throughput Nucleotide Sequencing:
                      methods / Genomics: methods / Transcriptome / Sequence
                      Analysis, DNA: methods / Sequence Analysis, RNA: methods /
                      DNA Copy Number Variations / Single Cell DNA sequencing
                      (Other) / Single Cell copy Number profiling (Other) / Single
                      Cell multiome (Other)},
      cin          = {B420 / HD01 / B260 / W192 / E250},
      ddc          = {570},
      cid          = {I:(DE-He78)B420-20160331 / I:(DE-He78)HD01-20160331 /
                      I:(DE-He78)B260-20160331 / I:(DE-He78)W192-20160331 /
                      I:(DE-He78)E250-20160331},
      pnm          = {312 - Funktionelle und strukturelle Genomforschung
                      (POF4-312)},
      pid          = {G:(DE-HGF)POF4-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:39696535},
      pmc          = {pmc:PMC11657747},
      doi          = {10.1186/s13059-024-03450-0},
      url          = {https://inrepo02.dkfz.de/record/295958},
}