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

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Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms

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Published on: September 13, 2018

Diane Delobel¹, Hiromi Nishiyori-Sueki¹, Ilaria Nisoli²

¹RIKEN Center for Integrative Medical Sciences (IMS), Yokohama 230-0045, Japan.

|February 8, 2025

Abstract:

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.

Keywords:

RNA-seq gene expression sequencing

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