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Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

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GRO-seq, A Tool for Identification of Transcripts Regulating Gene Expression.

Rui Lopes¹, Reuven Agami^2,3, Gozde Korkmaz⁴

¹Division of Biological Stress Response, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands.

Methods in Molecular Biology (Clifton, N.J.)

|March 29, 2017

Summary

This summary is machine-generated.

Global run-on sequencing (GRO-seq) measures nascent RNA to reveal transcription dynamics. This protocol details GRO-seq for investigating RNA biology and noncoding RNA functions in human cells.

Keywords:

Enhancer GRO-seq Nascent transcription Noncoding RNA Running Head: GRO-seq Sequencing

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Area of Science:

Molecular Biology
Genomics
Transcriptomics

Background:

Next-generation sequencing (NGS) revolutionized gene expression research.
RNA sequencing (RNA-seq) advanced genome knowledge but measures steady-state RNA levels.
Dedicated methods are needed to specifically measure transcription events.

Purpose of the Study:

To present a detailed protocol for Global run-on sequencing (GRO-seq).
To enable investigation of RNA biology and noncoding RNA functions.
To facilitate the study of nascent RNA transcription in human cells.

Main Methods:

Global run-on sequencing (GRO-seq) protocol.
Focus on measuring nascent RNA.
Application in human cell studies.

Main Results:

The described GRO-seq protocol is readily applicable.
Enables detailed investigation of RNA biology.
Facilitates study of noncoding RNA mechanisms.

Conclusions:

GRO-seq is a powerful tool for studying transcription.
This protocol provides a standardized method for RNA biology research.
Advances understanding of nascent RNA and noncoding RNA functions.