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<p>Current single-cell RNA sequencing (scRNA-seq) methods suffer from biases that restrict the detection of cellular transcripts to 10–40% of total RNAs. This hinders the identification of transcripts of interest. Additionally, information retrieved from most high-throughput scRNA-seq methods is confined to untranslated regions toward transcript ends, resulting in loss of detail in internal regions. In this review, we outline biases in scRNA-seq protocol steps that limit transcript and region detection. We then discuss the advantages and disadvantages of targeted sequencing solutions, grouped into five categories according to the protocol step they target. Finally, we present a decision tree that guides researchers in selecting the most suitable targeted method for their experiment.</p>

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A practical guide to targeted single-cell RNA sequencing technologies

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年2月14日

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  • Giulia Moro,
  • Erich Brunner,
  • Konrad Basler

摘要

Current single-cell RNA sequencing (scRNA-seq) methods suffer from biases that restrict the detection of cellular transcripts to 10–40% of total RNAs. This hinders the identification of transcripts of interest. Additionally, information retrieved from most high-throughput scRNA-seq methods is confined to untranslated regions toward transcript ends, resulting in loss of detail in internal regions. In this review, we outline biases in scRNA-seq protocol steps that limit transcript and region detection. We then discuss the advantages and disadvantages of targeted sequencing solutions, grouped into five categories according to the protocol step they target. Finally, we present a decision tree that guides researchers in selecting the most suitable targeted method for their experiment.