扩展和运行蚊子小 RNA 基因组学资源管道。
Extending and Running the Mosquito Small RNA Genomics Resource Pipeline.
机构信息
Boston University School of Medicine, Department of Biochemistry, Boston University Bioinformatics Program, Boston, MA, USA.
Boston University Research Computing Services, Information Services and Technology, Boston, MA, USA.
出版信息
Methods Mol Biol. 2022;2509:341-352. doi: 10.1007/978-1-0716-2380-0_20.
The Mosquito Small RNA Genomics (MSRG) resource is a repository of analyses on the small RNA transcriptomes of mosquito cell cultures and somatic and gonadal tissues. This resource allows for comparing the regulation dynamics of small RNAs generated from transposons and viruses across mosquito species. This chapter covers the procedures to set up the MSRG resource pipeline as a new installation by detailing the necessary collection of genome reference and annotation files and lists of microRNAs (miRNAs) hairpin sequences, transposon repeats consensus sequences, and virus genome sequences. Proper execution of the MSRG resource pipeline yields outputs amenable to biologists to further analyze with desktop and spreadsheet software to gain insights into the balance between arthropod endogenous small RNA populations and the proportions of virus-derived small RNAs that include Piwi-interacting RNAs (piRNAs) and endogenous small interfering RNAs (siRNAs).
蚊子小 RNA 基因组学（MSRG）资源是一个对蚊子细胞培养物以及体节和生殖组织的小 RNA 转录组进行分析的存储库。该资源允许比较来自转座子和病毒的小 RNA 产生的调控动态，跨越不同的蚊子物种。本章涵盖了作为新安装设置 MSRG 资源管道的过程，详细说明了必要的基因组参考和注释文件的收集，以及 microRNAs（miRNAs）发夹序列、转座子重复序列共识序列和病毒基因组序列的列表。正确执行 MSRG 资源管道的输出可用于生物学家进一步使用桌面和电子表格软件进行分析，以深入了解节肢动物内源性小 RNA 群体与病毒衍生小 RNA（包括 Piwi 相互作用 RNA（piRNAs）和内源性小干扰 RNA（siRNAs））的比例之间的平衡。
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