From: Charles Plessy Date: Mon, 15 Jun 2020 08:46:03 +0000 (+0900) Subject: More links X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=60c11bab201648a66e92b65ee46c3e53ebe05474;p=source.git More links --- diff --git a/open-source-biologist.mdwn b/open-source-biologist.mdwn index 80ab04d2..e3efec94 100644 --- a/open-source-biologist.mdwn +++ b/open-source-biologist.mdwn @@ -26,32 +26,35 @@ artefacts and unwanted sequences generated by ribosomal RNAs using low-complexity “pseudo-random” reverse-transcription primers ([Arnaud and coll., 2016](https://pubmed.gov/27071605)). -On April 2013, I started a new development cycle as the leader of the -Genomics Miniaturization Technology Unit at RIKEN Center for Life -Sciences, Division of Genomics Technology, to expand this work on -single cells following a **population transcriptomics** approach (Plessy -et al., 2013) focused on sampling the largest possible number of -cells. In our ongoing developments, we have reached **single-cell and +On April 2013, I started a new development cycle as the leader of the Genomics +Miniaturization Technology Unit at RIKEN Center for Life Sciences, Division of +Genomics Technology, to expand this work on single cells following a +**population transcriptomics** approach ([Plessy and coll., +2013](https://pubmed.gov/23281054)) focused on sampling the largest possible +number of cells. In our ongoing developments, we have reached **single-cell and single molecule resolution** through the introduction of transposase -fragmentation and unique molecular identifiers (Poulain et al., -2017). The protocol exists in two versions, one for FACS-isolated -cells, and one for the Fluidigm C1 platform (Kouno et al., 2019). +fragmentation and unique molecular identifiers ([Poulain and coll., +2017](https://pubmed.gov/28349422)). The protocol exists in two versions, one +for FACS-isolated cells, and one for the Fluidigm C1 platform ([Kouno and coll., +2019](https://pubmed.gov/30664627)). -I have complemented my work on CAGE with the development of a -gene-centred technique for detecting promoters, termed Deep-RACE -(Olivarius et al., 2009, Plessy et al., 2012), which we used to -validate our discovery of the pervasive expression of retrotransposons -detected by CAGE (Faulkner et al., 2009). To study transcription start -activity at nucleotide resolution in zebrafish transfected with -chimeric transgenes containing a copy of an endogenous promoter, I -combined Deep-RACE, CAGE and paired-end sequencing in a technology -that we called “Single-Locus CAGE” (Haberle et al., 2014). With my -contributions related to CAGE development and analysis, I have been a -**member of the FANTOM consortium** since FANTOM3. +I have complemented my work on CAGE with the development of a gene-centred +technique for detecting promoters, termed Deep-RACE ([Olivarius and coll., +2009](https://pubmed.gov/19317658), [Plessy and coll., +2012](http://dx.doi.org/10.1002/9783527644582.ch4)), which we used to validate +our discovery of the pervasive expression of retrotransposons detected by CAGE +([Faulkner and coll., 2009](https://pubmed.gov/19377475)). To study +transcription start activity at nucleotide resolution in zebrafish transfected +with chimeric transgenes containing a copy of an endogenous promoter, I +combined Deep-RACE, CAGE and paired-end sequencing in a technology that we +called “Single-Locus CAGE” ([Haberle and coll., +2014](https://pubmed.gov/24531765)). With my contributions related to CAGE +development and analysis, I have been a **member of the FANTOM consortium** +since FANTOM3. Together with my colleagues at RIKEN and collaborators in the field of neuroscience, I have applied nanoCAGE to the study of single neuron -cell types, for instance the **olfactory neurons** (Plessy et al., 2012), +cell types, for instance the **olfactory neurons** ([Plessy et al., 2012), or in dopaminergic cells, where we could demonstrate the expression of haemoglobin in the midbrain (Biagioli et al., 2009). We are also exploring the sub-cellular localisation of RNA in **Purkinje neurons**