Labs & Technologies

Genomics Miniaturization Technology Unit

Population transcriptomics

* Due to the reorganization starting as new centers in April 2018, this laboratory is now belong to the Center for Integrative Medical Sciences. As for the latest information, please see the following URL below.
> The webpage of Labs Index, Center for Integrative Medical Sciences

Unit Leader
Charles Plessy Ph.D.

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

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Research Area

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 Topics

Cutting edge methods reveal what makes Purkinje neurons unique (A collaborative study)
2014/06/06

Main Publications List

Targeted reduction of highly abundant transcripts using pseudo-random primers.

Arnaud O, Kato S, Poulain S, Plessy C
Biotechniques, 60(4), 169-174 (2016).

Digital expression profiling of the compartmentalized translatome of Purkinje neurons

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.
Genome Res, 24(8), 1396-1410 (2014).

Multiplicity of 5 ' Cap Structures Present on Short RNAs

Abdelhamid RF, Plessy C, Yamauchi Y, Taoka M, de Hoon M, Gingeras TR, Isobe T, Carninci P.
PLoS One, 9(7), e102895 (2014).

Two independent transcription initiation codes overlap on vertebrate core promoters.

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.
Nature, 507(7492), 381-385 (2014).

Comparison of RNA- or LNA-hybrid oligonucleotides in template-switching reactions for high-speed sequencing library preparation

Harbers M, Kato S, de Hoon M, Hayashizaki Y, Carninci P, Plessy C.
BMC Genomics, 14, 665 (2013).

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, 35(2), 131-140 (2013).

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, 41(3), e44 (2013).

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, 22(3), 486-497 (2012).

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 , 7(7), 528-534 (2010).

Tunable fractionation of nucleic acids

Salimullah M, Kato S, Murata M, Kawazu C, Plessy C, Carninci P.
Biotechniques, 47(6), 1041-1043 (2009).

High-throughput verification of transcriptional starting sites by Deep-RACE.

Olivarius S, Plessy C, Carninci P.
Biotechniques, 46(2), 130-132 (2009).

>>>All Publications

Member *concurrent

Charles Plessy
Unit Leader
Stéphane Poulain
Research Scientist

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