Maragkakis Manolis, Alexiou Panagiotis, Nakaya Tadashi, Mourelatos Zissimos
Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
Laboratory of Neuroscience, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan.
RNA. 2016 Jan;22(1):1-9. doi: 10.1261/rna.052167.115. Epub 2015 Nov 17.
Immunoprecipitation of RNA binding proteins (RBPs) after in vivo crosslinking, coupled with sequencing of associated RNA footprints (HITS-CLIP, CLIP-seq), is a method of choice for the identification of RNA targets and binding sites for RBPs. Compared with RNA-seq, CLIP-seq analysis is widely diverse and depending on the RBPs that are analyzed, the approaches vary significantly, necessitating the development of flexible and efficient informatics tools. In this study, we present CLIPSeqTools, a novel, highly flexible computational suite that can perform analysis from raw sequencing data with minimal user input. It contains a wide array of tools to provide an in-depth view of CLIP-seq data sets. It supports extensive customization and promotes improvization, a critical virtue, since CLIP-seq analysis is rarely well defined a priori. To highlight CLIPSeqTools capabilities, we used the suite to analyze Ago-miRNA HITS-CLIP data sets that we prepared from human brains.
体内交联后对RNA结合蛋白（RBP）进行免疫沉淀，再结合相关RNA足迹测序（HITS-CLIP、CLIP-seq），是鉴定RBP的RNA靶标和结合位点的首选方法。与RNA测序相比，CLIP-seq分析具有广泛的多样性，并且根据所分析的RBP不同，方法差异很大，因此需要开发灵活高效的信息学工具。在本研究中，我们展示了CLIPSeqTools，这是一种新颖、高度灵活的计算套件，只需最少的用户输入即可从原始测序数据进行分析。它包含大量工具，可深入查看CLIP-seq数据集。它支持广泛的定制并促进改进，这是一个关键优点，因为CLIP-seq分析很少能先验地明确界定。为了突出CLIPSeqTools的功能，我们使用该套件分析了我们从人脑中制备的Ago-miRNA HITS-CLIP数据集。
