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协议组装，优先排序，并表征piRNA集群使用piRNA集群构建器。

IF 1.3 Q4 BIOCHEMICAL RESEARCH METHODS

STAR Protocols Pub Date : 2025-04-10 DOI:10.1016/j.xpro.2025.103759

Franziska Ahrend, Parthena Konstantinidou, Zuzana Loubalova, Yuejun Wang, Hernan Lorenzi, Gunter Meister, Astrid D Haase

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引用次数: 0

摘要

piwi相互作用rna （piRNAs）在保护生殖细胞基因组完整性、确保生殖能力方面发挥着关键作用。在这里，我们提供了一种处理piRNA测序数据的方案，将富含piRNA的基因组区域识别为piRNA簇，并为下游分析准备这些簇。我们描述了使用基于r的工具组装piRNA集群区域的步骤，piRNA集群构建器（PICB），它逐步集成了唯一和多映射的piRNA读取。该协议允许参数优化，并为piRNA集群的优先级生成规范化输出。有关本协议使用和执行的完整细节，请参阅Konstantinidou等人。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Protocol for assembling, prioritizing, and characterizing piRNA clusters using the piRNA Cluster Builder.

PIWI-interacting RNAs (piRNAs) play a critical role in safeguarding genome integrity in germ cells, ensuring fertility. Here, we provide a protocol for processing piRNA sequencing data, identifying piRNA-rich genomic regions as piRNA clusters, and preparing these clusters for downstream analyses. We describe steps for assembling piRNA cluster regions using an R-based tool, the piRNA Cluster Builder (PICB), which integrates unique and multimapping piRNA reads stepwise. The protocol allows for parameter optimizations and generates normalized outputs for prioritization of piRNA clusters. For complete details on the use and execution of this protocol, please refer to Konstantinidou et al.¹.

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来源期刊

STAR Protocols Biochemistry, Genetics and Molecular Biology-General Biochemistry, Genetics and Molecular Biology

CiteScore

2.00

自引率

0.00%

发文量

789

审稿时长

10 weeks

期刊介绍：

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