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. 2021 Mar 18;2(1):100366.
doi: 10.1016/j.xpro.2021.100366. eCollection 2021 Mar 19.

Transcriptome-wide quantification of double-stranded RNAs in live mouse tissues by dsRIP-Seq

Yimeng Gao  1   2 , Shirui Chen  3 , Stephanie Halene  1   2 , Toma Tebaldi  1   2   4
Affiliations

Transcriptome-wide quantification of double-stranded RNAs in live mouse tissues by dsRIP-Seq

Yimeng Gao et al. STAR Protoc. .

Abstract

Double-stranded RNAs (dsRNAs) are abundantly present in cells, playing multiple regulatory functions. dsRNAs of viral origin activate innate immune responses. Since RNA editing and modifications affect the structure and recognition of RNAs, their alteration can result in the accumulation of aberrant endogenous dsRNAs inducing a deleterious innate immune response. Here, we present a complete protocol for the measurement of dsRNAs in a live mouse tissue using dsRNA immunoprecipitation and sequencing (dsRIP-Seq). This protocol focuses on tissue isolation, dsRNA immunoprecipitation and downstream computational analysis. For complete details on the use and execution of this protocol, please refer to Gao et al. (2020).

Keywords: Cell Biology; Immunology; Model Organisms; RNA-seq; Sequencing.

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Conflict of interest statement

The authors declare no competing interests.

Figures

None
Graphical abstract
Figure 1
Figure 1
Morphology of murine E14.5 embryos and fetal livers
Figure 2
Figure 2
Examples of RNA profiles obtained by dsRIP on the TapeStation System
Figure 3
Figure 3
Computational analysis to identify and compare dsRNAs, with examples
Figure 4
Figure 4
Examples of downstream analysis of the identified dsRNAs
Figure 5
Figure 5
Example of analysis and dsRNA quantification of transposable elements
See this image and copyright information in PMC

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