Protocol for direct cDNA cap analysis of gene expression for paired-end patterned flow cell sequencing

Protocol for direct cDNA cap analysis of gene expression for paired-end patterned flow cell sequencing

Summary: Cap analysis of gene expression (CAGE) is a technique that facilitates the assessment of the 5′-end of RNA transcript starting site (TSS) of both coding and non-coding genes. Here, we present a protocol for using CAGE on Illumina patterned flow cell technology with dual indexes on mouse and...

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Bibliographic Details
Main Authors: Diane Delobel, Hiromi Nishiyori-Sueki, Ilaria Nisoli, Hideya Kawaji, Pauline Robbe, Piero Carninci, Hazuki Takahashi
Format: Article
Language:English
Published: Elsevier 2025-03-01
Series:STAR Protocols
Subjects:
sequencing
RNA-seq
gene expression
Online Access:http://www.sciencedirect.com/science/article/pii/S2666166724007597
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Summary:Summary: Cap analysis of gene expression (CAGE) is a technique that facilitates the assessment of the 5′-end of RNA transcript starting site (TSS) of both coding and non-coding genes. Here, we present a protocol for using CAGE on Illumina patterned flow cell technology with dual indexes on mouse and human samples. We describe steps for sequencing, automated data processing, and complete analytical framework ensuring CAGE operability for the determination of TSS and enhancers on the ever-evolving Illumina sequencing platforms. : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
ISSN:2666-1667

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