Genomics Miniaturization Technology Unit

We propose "population transcriptomics", to describe a biological sample as a population of single cells, classified by their transcriptomes. This unit develops methods to prepare individual reactions and 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 trans-differentiation.

Research Fields

Molecular Biology & Genetics / Immunology / Neuroscience & Behavior

Research Subjects

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

Publications

1. 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.
   Plessy C, Desbois L, Fujii T, Carninci P.
   Bioessays. 2013 Feb;35(2):131-40. Epub 2012 Dec 27.
   PMID: 23281054 (review article)
2. Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching.
   Tang DT, Plessy C, Salimullah M, Suzuki AM, Calligaris R, Gustincich S, Carninci P.
   Nucleic Acids Res. 2013 Feb 1;41(3):e44. Epub 2012 Nov 24.
   PMID: 23180801
3. Promoter architecture of mouse olfactory receptor genes.
   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.
   Genome Res. 2012 Mar;22(3):486-97. Epub 2011 Dec 22.
   PMID: 22194471
4. Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan.
   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.
   Nat Methods. 2010 Jul;7(7):528-34. Epub 2010 Jun 13.
   PMID: 20543846
5. Tunable fractionation of nucleic acids.
   Salimullah M, Kato S, Murata M, Kawazu C, Plessy C, Carninci P.
   Biotechniques. 2009 Dec;47(6):1041-3.
   PMID: 20041857
6. High-throughput verification of transcriptional starting sites by Deep-RACE.
   Olivarius S, Plessy C, Carninci P.
   Biotechniques. 2009 Feb;46(2):130-2.
   PMID: 19317658