The majority of clinical cancer specimens are preserved as formalin-fixed paraffin-embedded (FFPE) samples. For clinical molecular tests to have wide-reaching impact, they must be applicable to FFPE material. Accurate quantitative measurements of RNA derived from FFPE specimens is challenging because of low yields and high amounts of degradation. Here, we present FFPEcap-seq, a method specifically designed for sequencing capped 5' ends of RNA derived from FFPE samples. FFPEcap-seq combines enzymatic enrichment of 5' capped RNAs with template switching to create sequencing libraries. We find that FFPEcap-seq can faithfully capture mRNA expression levels in FFPE specimens while also detecting enhancer RNAs that arise from distal regulatory regions. FFPEcap-seq is a fast and straightforward method for making high-quality 5' end RNA-seq libraries from FFPE-derived RNA.

中文翻译：

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FFPEcap-seq：一种对福尔马林固定的石蜡包埋样品中的加帽 RNA 进行测序的方法。

大多数临床癌症标本保存为福尔马林固定石蜡包埋 (FFPE) 样品。要使临床分子测试产生广泛影响，它们必须适用于 FFPE 材料。由于低产量和大量降解，对源自 FFPE 样本的 RNA 进行准确定量测量具有挑战性。在这里，我们介绍了 FFPEcap-seq，这是一种专门设计用于对来自 FFPE 样本的 RNA 的加帽 5' 末端进行测序的方法。FFPEcap-seq 将 5' 加帽 RNA 的酶促富集与模板切换相结合，以创建测序文库。我们发现 FFPEcap-seq 可以忠实地捕获 FFPE 标本中的 mRNA 表达水平，同时还可以检测来自远端调节区的增强子 RNA。FFPEcap-seq 是一种快速而直接的方法，可用于制作高质量的 5'