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<p>The 10 × Genomics Flex Gene Expression protocol is a probe-based method that profiles fixed or frozen material, simplifying sample handling before scRNA-seq. Although probes exist only for human and mouse, we show that xenograft samples containing mixed human–mouse cells can be profiled by combining both probe sets in a single reaction. Cellranger generates species-specific count tables in which specific probes strongly outperform cross-reactive ones. We implement an approach to remove cross-reactive signals, yielding clean species-specific matrices. This solution enables scRNA-seq of xenografts without flow sorting and supports analysis of both the graft and its microenvironment.</p>

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10 × Genomics Flex Gene Expression is a powerful tool for single-cell transcriptomics of xenografts models

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年5月8日

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  • Oriol Llorà-Batlle,
  • Anca Farcas,
  • Doreth Fransen,
  • Nicolas Floc’h,
  • Sara Talbot,
  • Alix Schwiening,
  • Laura Bojko,
  • John Calver,
  • Natasa Josipovic,
  • Kanstantsin Lashuk,
  • Julia Schueler,
  • Andrei Prodan,
  • Dylan Mooijman,
  • Ultan McDermott

摘要

The 10 × Genomics Flex Gene Expression protocol is a probe-based method that profiles fixed or frozen material, simplifying sample handling before scRNA-seq. Although probes exist only for human and mouse, we show that xenograft samples containing mixed human–mouse cells can be profiled by combining both probe sets in a single reaction. Cellranger generates species-specific count tables in which specific probes strongly outperform cross-reactive ones. We implement an approach to remove cross-reactive signals, yielding clean species-specific matrices. This solution enables scRNA-seq of xenografts without flow sorting and supports analysis of both the graft and its microenvironment.