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<p>Single-cell transcriptomics is valuable for uncovering individual cell properties, particularly in heterogeneous systems. However, this technique often results in the reanalysis of many well-characterized cells, increasing costs and diluting rare cell populations. To address this, we develop PIP-seq for Rare-cell Enrichment and Sequencing (PURE-seq). PURE-seq allows direct FACS sorting of cells into PIP-seq reactions, minimizing handling and reducing cell loss. PURE-seq reliably sequences ultrarare cells, with 1 hour of sorting capturing tens of target cells at a rarity of 1 in 1,000,000. Leveraging this extreme sensitivity, we use PURE-seq to isolate and single-cell sequence circulating tumor cells from metastatic melanoma patient blood, obtaining detailed single cancer cell gene expression profiles. Additionally, we use PURE-seq to examine hematopoietic stem and progenitor cells from young, old and middle-aged mice. Transcriptomic analysis identifies <i>Egr1</i> as a putative master regulator of murine hematopoietic stem and progenitor cell aging, demonstrating PURE-seq’s utility as a discovery platform for basic science applications. PURE-seq offers a simple and highly sensitive method for single-cell sequencing ultra-rare cells.</p>

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PURE-seq integrates FACS and PIP-seq for single-cell genomics of ultra-rare cells

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年1月21日

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  • Sixuan Pan,
  • Inés Fernández-Maestre,
  • Kai-Chun Chang,
  • Stéphane Van Haver,
  • Matthew G. Wereski,
  • Alexandra M. Haugh,
  • Katy K. Tsai,
  • Adil I. Daud,
  • Robert L. Bowman,
  • Harish N. Vasudevan,
  • Ross L. Levine,
  • Adam R. Abate

摘要

Single-cell transcriptomics is valuable for uncovering individual cell properties, particularly in heterogeneous systems. However, this technique often results in the reanalysis of many well-characterized cells, increasing costs and diluting rare cell populations. To address this, we develop PIP-seq for Rare-cell Enrichment and Sequencing (PURE-seq). PURE-seq allows direct FACS sorting of cells into PIP-seq reactions, minimizing handling and reducing cell loss. PURE-seq reliably sequences ultrarare cells, with 1 hour of sorting capturing tens of target cells at a rarity of 1 in 1,000,000. Leveraging this extreme sensitivity, we use PURE-seq to isolate and single-cell sequence circulating tumor cells from metastatic melanoma patient blood, obtaining detailed single cancer cell gene expression profiles. Additionally, we use PURE-seq to examine hematopoietic stem and progenitor cells from young, old and middle-aged mice. Transcriptomic analysis identifies Egr1 as a putative master regulator of murine hematopoietic stem and progenitor cell aging, demonstrating PURE-seq’s utility as a discovery platform for basic science applications. PURE-seq offers a simple and highly sensitive method for single-cell sequencing ultra-rare cells.