Protocol for direct cDNA cap analysis of gene expression for paired-end patterned flow cell sequencing
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.
Authors
- Hiromi Nishiyori-Sueki (ORCID: https://orcid.org/0000-0002-7370-3909)
- Pauline Robbe (ORCID: https://orcid.org/0000-0002-0691-1126)
- Hazuki Takahashi (ORCID: https://orcid.org/0000-0001-7315-7349)
- Diane Delobel (ORCID: https://orcid.org/0000-0002-1644-1228)
- Hideya Kawaji (ORCID: https://orcid.org/0000-0002-0575-0308)
- Ilaria Nisoli
- Piero Carninci (ORCID: https://orcid.org/0000-0001-7202-7243)
Institutions
- Tokyo Metropolitan Institute of Medical Science (JP)
- Human Technopole (IT)
- RIKEN Center for Integrative Medical Sciences (JP)
Publication Details
- Journal
- STAR Protocols
- Published
- 2025-02-06
- DOI
- https://doi.org/10.1016/j.xpro.2024.103594
- Citations
- 1
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 0.81
Funders
- Japan Science and Technology Corporation
- Ministry of Education, Culture, Sports, Science and Technology
- RIKEN