Centers & Labs

RIKEN Center for Integrative Medical Sciences

Laboratory for Single Cell Technologies

Team Leader: Piero Carninci (Ph.D.)
Piero  Carninci(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.

Main Research Field

Biological Sciences

Keywords

  • transcriptome
  • single-cell
  • open source

Selected Publications

  1. Arnaud O., Kato S., Poulain S., Plessy C.:
    "Targeted reduction of highly abundant transcripts using pseudo-random primers"
    Biotechniques. 2016 Apr 1;60(4):169-74. PMID: 27071605.
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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)
  7. 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
  8. 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
  9. 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
  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

Contact information

1-7-22 Suehiro-cho, Tsurumi-ku
Yokohama, Kanagawa
230-0045, Japan

Email: carninci [at] riken.jp

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