Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
Biology Department, Brandeis University, Waltham, MA, 02454, USA.
Genome Biol. 2021 Sep 23;22(1):277. doi: 10.1186/s13059-021-02497-7.
Here we describe a new integrative approach for accurate annotation and quantification of circRNAs named Short Read circRNA Pipeline (SRCP). Our strategy involves two steps: annotation of validated circRNAs followed by a quantification step. We show that SRCP is more sensitive than other individual pipelines and allows for more comprehensive quantification of a larger number of differentially expressed circRNAs. To facilitate the use of SRCP, we generate a comprehensive collection of validated circRNAs in five different organisms, including humans. We then utilize our approach and identify a subset of circRNAs bound to the miRNA-effector protein AGO2 in human brain samples.
在这里，我们描述了一种新的综合方法，用于准确注释和定量 circRNAs，名为短读 circRNA 分析流程 (Short Read circRNA Pipeline, SRCP)。我们的策略包括两个步骤：已验证的 circRNAs 的注释，然后是定量步骤。我们表明，SRCP 比其他单个管道更敏感，并允许更全面地定量更多数量的差异表达 circRNAs。为了方便使用 SRCP，我们在五个不同的生物体中（包括人类）生成了一套全面的已验证 circRNAs 集合。然后，我们利用我们的方法在人脑样本中鉴定出一组与 miRNA 效应蛋白 AGO2 结合的 circRNAs。
