RIKEN Center for Life Science Technologies


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Labs & Technologies

Genomics Miniaturization Technology Unit

Population transcriptomics

Unit Leader
Charles Plessy  Ph.D.

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


>>> Lab Site

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.

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).

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

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