Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer
CAGE (cap analysis of gene expression) is a method for identifying transcription start sites by sequencing the first 20 or 21 nucleotides from the 5′ end of capped transcripts, allowing genome-wide promoter analyses to be performed. The potential of the CAGE as a form of expression profiling was lim...
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| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2008-07-01
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| Series: | BioTechniques |
| Online Access: | https://www.future-science.com/doi/10.2144/000112814 |
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| author | Norihiro Maeda Hiromi Nishiyori Mari Nakamura Chika Kawazu Mitsuyoshi Murata Hiromi Sano Kengo Hayashida Shiro Fukuda Michihira Tagami Akira Hasegawa Kayoko Murakami Kate Schroder Katharine Irvine David A. Hume Yoshihide Hayashizaki Piero Carninci Harukazu Suzuki |
| author_facet | Norihiro Maeda Hiromi Nishiyori Mari Nakamura Chika Kawazu Mitsuyoshi Murata Hiromi Sano Kengo Hayashida Shiro Fukuda Michihira Tagami Akira Hasegawa Kayoko Murakami Kate Schroder Katharine Irvine David A. Hume Yoshihide Hayashizaki Piero Carninci Harukazu Suzuki |
| author_sort | Norihiro Maeda |
| collection | DOAJ |
| description | CAGE (cap analysis of gene expression) is a method for identifying transcription start sites by sequencing the first 20 or 21 nucleotides from the 5′ end of capped transcripts, allowing genome-wide promoter analyses to be performed. The potential of the CAGE as a form of expression profiling was limited previously by sequencing technology and the labor-intensive protocol. Here we describe an improved CAGE method for use with a next generation sequencer. This modified method allows the identification of the RNA source of each CAGE tag within a pooled library by introducing DNA tags (barcodes). The method not only drastically improves the sequencing capacity, but also contributes to savings in both time and budget. Additionally, this pooled CAGE tag method enables the dynamic changes in promoter usage and gene expression to be monitored. |
| format | Article |
| id | doaj-art-ade8da03359e4b5f8b2e86b21c54107a |
| institution | OA Journals |
| issn | 0736-6205 1940-9818 |
| language | English |
| publishDate | 2008-07-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | BioTechniques |
| spelling | doaj-art-ade8da03359e4b5f8b2e86b21c54107a2025-08-20T02:25:59ZengTaylor & Francis GroupBioTechniques0736-62051940-98182008-07-01451959710.2144/000112814Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencerNorihiro Maeda0Hiromi Nishiyori1Mari Nakamura2Chika Kawazu3Mitsuyoshi Murata4Hiromi Sano5Kengo Hayashida6Shiro Fukuda7Michihira Tagami8Akira Hasegawa9Kayoko Murakami10Kate Schroder11Katharine Irvine12David A. Hume13Yoshihide Hayashizaki14Piero Carninci15Harukazu Suzuki161Advanced Science Institute, RIKEN Wako Main Campus, Saitama2RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Kanagawa, Japan2RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Kanagawa, Japan2RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Kanagawa, Japan2RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Kanagawa, Japan2RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Kanagawa, Japan2RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Kanagawa, Japan2RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Kanagawa, Japan2RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Kanagawa, Japan2RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Kanagawa, Japan2RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Kanagawa, Japan3Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia3Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia4The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Scotland, UK1Advanced Science Institute, RIKEN Wako Main Campus, Saitama1Advanced Science Institute, RIKEN Wako Main Campus, Saitama2RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Kanagawa, JapanCAGE (cap analysis of gene expression) is a method for identifying transcription start sites by sequencing the first 20 or 21 nucleotides from the 5′ end of capped transcripts, allowing genome-wide promoter analyses to be performed. The potential of the CAGE as a form of expression profiling was limited previously by sequencing technology and the labor-intensive protocol. Here we describe an improved CAGE method for use with a next generation sequencer. This modified method allows the identification of the RNA source of each CAGE tag within a pooled library by introducing DNA tags (barcodes). The method not only drastically improves the sequencing capacity, but also contributes to savings in both time and budget. Additionally, this pooled CAGE tag method enables the dynamic changes in promoter usage and gene expression to be monitored.https://www.future-science.com/doi/10.2144/000112814 |
| spellingShingle | Norihiro Maeda Hiromi Nishiyori Mari Nakamura Chika Kawazu Mitsuyoshi Murata Hiromi Sano Kengo Hayashida Shiro Fukuda Michihira Tagami Akira Hasegawa Kayoko Murakami Kate Schroder Katharine Irvine David A. Hume Yoshihide Hayashizaki Piero Carninci Harukazu Suzuki Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer BioTechniques |
| title | Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer |
| title_full | Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer |
| title_fullStr | Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer |
| title_full_unstemmed | Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer |
| title_short | Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer |
| title_sort | development of a dna barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high throughput sequencer |
| url | https://www.future-science.com/doi/10.2144/000112814 |
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