Protocol for evaluating RNA-protein associations in mammalian cells with RIP-seq and RIP-qPCR
Jackson B Trotman1, Shuang Li1, Quinn E Eberhard2
1Department of Pharmacology, RNA Discovery Center, and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
None:
RNA-protein interactions drive gene regulation, subcellular organization, and noncoding RNA function. Here, we present a protocol for measuring RNA-protein associations in formaldehyde-crosslinked mammalian cells using RNA immunoprecipitation followed by sequencing (RIP-seq) and quantitative PCR (RIP-qPCR). We include steps and best practices for qualifying reagents, preparing cells, and processing and analyzing data, including a standardized set of steps to quantify signal over noise. This protocol is broadly applicable for the study of RNA-protein interactions in cells. For complete details on the use and execution of this protocol, please refer to Trotman et al.1.
More Related Videos
Related Concept Videos
RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Ribosome Profiling
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...


