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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| Format: | Article |
| Language: | English |
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Elsevier
2025-03-01
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| Series: | STAR Protocols |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166724007597 |
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| author | Diane Delobel Hiromi Nishiyori-Sueki Ilaria Nisoli Hideya Kawaji Pauline Robbe Piero Carninci Hazuki Takahashi |
| author_facet | Diane Delobel Hiromi Nishiyori-Sueki Ilaria Nisoli Hideya Kawaji Pauline Robbe Piero Carninci Hazuki Takahashi |
| author_sort | Diane Delobel |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-fdd6d1f9b34140ee91207184e500f5ef |
| institution | Kabale University |
| issn | 2666-1667 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj-art-fdd6d1f9b34140ee91207184e500f5ef2025-02-08T05:01:16ZengElsevierSTAR Protocols2666-16672025-03-0161103594Protocol for direct cDNA cap analysis of gene expression for paired-end patterned flow cell sequencingDiane Delobel0Hiromi Nishiyori-Sueki1Ilaria Nisoli2Hideya Kawaji3Pauline Robbe4Piero Carninci5Hazuki Takahashi6RIKEN Center for Integrative Medical Sciences (IMS), Yokohama 230-0045, JapanRIKEN Center for Integrative Medical Sciences (IMS), Yokohama 230-0045, JapanHuman Technopole Research Center for Genomics, 20157 Milan, ItalyTokyo Metropolitan Institute of Medical Science, Research Center for Genome & Medical Sciences, Tokyo 156-8506, JapanRIKEN Center for Integrative Medical Sciences (IMS), Yokohama 230-0045, JapanRIKEN Center for Integrative Medical Sciences (IMS), Yokohama 230-0045, Japan; Human Technopole Research Center for Genomics, 20157 Milan, Italy; Corresponding authorRIKEN Center for Integrative Medical Sciences (IMS), Yokohama 230-0045, Japan; Corresponding authorSummary: 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.http://www.sciencedirect.com/science/article/pii/S2666166724007597sequencingRNA-seqgene expression |
| spellingShingle | Diane Delobel Hiromi Nishiyori-Sueki Ilaria Nisoli Hideya Kawaji Pauline Robbe Piero Carninci Hazuki Takahashi Protocol for direct cDNA cap analysis of gene expression for paired-end patterned flow cell sequencing STAR Protocols sequencing RNA-seq gene expression |
| title | Protocol for direct cDNA cap analysis of gene expression for paired-end patterned flow cell sequencing |
| title_full | Protocol for direct cDNA cap analysis of gene expression for paired-end patterned flow cell sequencing |
| title_fullStr | Protocol for direct cDNA cap analysis of gene expression for paired-end patterned flow cell sequencing |
| title_full_unstemmed | Protocol for direct cDNA cap analysis of gene expression for paired-end patterned flow cell sequencing |
| title_short | Protocol for direct cDNA cap analysis of gene expression for paired-end patterned flow cell sequencing |
| title_sort | protocol for direct cdna cap analysis of gene expression for paired end patterned flow cell sequencing |
| topic | sequencing RNA-seq gene expression |
| url | http://www.sciencedirect.com/science/article/pii/S2666166724007597 |
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