Centers & Labs

RIKEN Center for Life Science Technologies

Genomics Miniaturization Technology Unit

Unit Leader: Charles Plessy (Ph.D.)
Charles  Plessy(Ph.D.)

We develop methods for "population transcriptomics", to describe a biological sample as a population of single cells, classified by the RNAs that they contain. We use new methods to prepare sequence libraries from tens of thousands of individual cells. We expect population transcriptomics to contribute to the discovery and monitoring of biomarkers, and to provide a high resolution to all the studies of the effect of drug treatments in therapies and cellular reprogramming.

Research Subjects

  • Single-cell population transcriptomics
  • Quantitative sequencing
  • High-throughput sequencing of antibodies and T cell receptors.

Selected Publications

  1. Kratz A., Beguin P., Kaneko M., Chimura T., Suzuki AM., Matsunaga A., Kato S., Bertin N., Lassmann T., Vigot R., Carninci P., Plessy C., Launey T.:
    "Digital expression profiling of the compartmentalized translatome of Purkinje neurons"
    Genome Res. 2014 Aug;24(8):1396-410. PMID: 24904046
  2. Abdelhamid RF., Plessy C., Yamauchi Y., Taoka M., de Hoon M., Gingeras TR., Isobe T., Carninci P.:
    "Multiplicity of 5' Cap Structures Present on Short RNAs"
    PLoS One. 2014 Jul 31;9(7):e102895. PMID: 25079783
  3. Haberle V., Li N., Hadzhiev Y., Plessy C., Previti C., Nepal C., Gehrig J., Dong X., Akalin A., Suzuki AM., van IJcken WF., Armant O., Ferg M., Strähle U., Carninci P., Müller F., Lenhard B.:
    "Two independent transcription initiation codes overlap on vertebrate core promoters"
    Nature. 2014 Mar 20;507(7492):381-5. PMID: 24531765
  4. Harbers M., Kato S., de Hoon M., Hayashizaki Y., Carninci P., Plessy C.:
    "Comparison of RNA- or LNA-hybrid oligonucleotides in template-switching reactions for high-speed sequencing library preparation"
    BMC Genomics. 2013 Sep 30 14(1):665. PMID: 24079827
  5. Plessy C., Desbois L., Fujii T., Carninci P.:
    "Population transcriptomics with single-cell resolution: a new field made possible by microfluidics: a technology for high throughput transcript counting and data-driven definition of cell types"
    Bioessays. 2013 Feb;35(2):131-40. Epub 2012 Dec 27. PMID: 23281054 (review article)
  6. Tang DT., Plessy C., Salimullah M., Suzuki AM., Calligaris R., Gustincich S., Carninci P.:
    "Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching"
    Nucleic Acids Res. 2013 Feb 1;41(3):e44. Epub 2012 Nov 24. PMID: 23180801
  7. Plessy C., Pascarella G., Bertin N., Akalin A., Carrieri C., Vassalli A., Lazarevic D., Severin J., Vlachouli C., Simone R., Faulkner GJ., Kawai J., Daub CO., Zucchelli S., Hayashizaki Y., Mombaerts P., Lenhard B., Gustincich S., Carninci P.:
    "Promoter architecture of mouse olfactory receptor genes"
    Genome Res. 2012 Mar;22(3):486-97. Epub 2011 Dec 22. PMID: 22194471
  8. Plessy C., Bertin N., Takahashi H., Simone R., Salimullah M., Lassmann T., Vitezic M., Severin J., Olivarius S., Lazarevic D., Hornig N., Orlando V., Bell I., Gao H., Dumais J., Kapranov P., Wang H., Davis CA., Gingeras TR., Kawai J., Daub CO., Hayashizaki Y., Gustincich S., Carninci P.:
    "Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan"
    Nat Methods. 2010 Jul;7(7):528-34. Epub 2010 Jun 13. PMID: 20543846
  9. Salimullah M., Kato S., Murata M., Kawazu C., Plessy C., Carninci P.:
    "Tunable fractionation of nucleic acids"
    Biotechniques. 2009 Dec;47(6):1041-3. PMID: 20041857
  10. Olivarius S., Plessy C., Carninci P.:
    "High-throughput verification of transcriptional starting sites by Deep-RACE"
    Biotechniques. 2009 Feb;46(2):130-2. PMID: 19317658