2015 Fiscal Year Annual Research Report
Single cell transcriptome analysis
| Project/Area Number |
25710018
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| Research Institution | Institute of Physical and Chemical Research |
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Principal Investigator |
PLESSY Charles 国立研究開発法人理化学研究所, ライフサイエンス技術基盤研究センター, ユニットリーダー (60391984)
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| Project Period (FY) |
2013-04-01 – 2016-03-31
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| Keywords | Transcriptome / CAGE / HPV / Human Papillomavirus / Single-cell |
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| Outline of Annual Research Achievements |
* Taking the opportunity of an invitation to write a chapter in a book on non-coding transcriptome analysis, we wrote an extensively detailed protocol of our latest nanoCAGE method, including the developments done as part of this granted project. The book chapter, which will be indexed in Medline, has been received by the editor and its publication is pending.
* The availability of a machine for high-throughput liquid transfers in the nanoliter range ("Labcyte Echo") was final breaktrough that led us to the production of a data set where more than 6,000 single-cell transcriptomes were prepared. In order to make this possible, we did final adjustments on the nanoCAGE protocol, in particular to perform it with 1 microliter reverse-transcriptions per single cell. The cells were flow-sorted in 384-well plates, and all the reverse-transcriptions are completed now. High-throughput sequencing is pending.
* The subproject on pseudo-random primers was completed by the publication of a research article in BioTechniques. The data was analysed following the principles of "reproducible research", and our bioinformatics scripts are deposited on the "GitHub" source code platform, for anybody to verify or extend or work.
* The bioinformatics detection of cell cycle phases using a RNA-seq dataset of singl "Fucci" HeLa cells (indicating their phase with fluorescent indicators) is ongoing, and we could produce a list of markers which were efficient on control third-party human ES cells. Consolidation of this work as a tool and as a research article are under way.
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| Research Progress Status |
27年度が最終年度であるため、記入しない。
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| Strategy for Future Research Activity |
27年度が最終年度であるため、記入しない。
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