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Updated: May 12, 2026

Method for the Isolation and Identification of mRNAs, microRNAs and Protein Components of Ribonucleoprotein Complexes from Cell Extracts using RIP-Chip

Method for the Isolation and Identification of mRNAs, microRNAs and Protein Components of Ribonucleoprotein Complexes from Cell Extracts using RIP-Chip

Published on: September 29, 2012

Protocolo para la evaluación de asociaciones ARN-proteína en células de mamífero con RIP-seq y 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.

|December 27, 2025

Abstract:

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.

Palabras clave:

Anticuerpo Bioinformática ChIP-seq Expresión génica RNA-seq Análisis de secuencias Secuenciación

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