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Single-Cell Transcriptomic Analysis Plateform by DROP-SEQ

Goal

The goal of scGenAP is to generate and share genomic data obtained by sequencing the transcriptome of single-cells isolated from retinal tissue. This approach known as single-cell RNA sequencing (scRNAseq) has been optimised in our laboratory in collaboration with Dr Andelfinger at the Sainte-Justine Research Center.

Description

The scRNAseq technology allows investigating the transcriptome (polyA mRNA) in live cells at the single cell resolution, from retina (or any other organs of interest) at different developmental stages or conditions (physiological or pathological), and in any species with an annotated genome available (in order to align sequencing data).

Currently, data are available for the analysis of mouse retina from postnatal day 5 to 17, in normal or retinopathic condition (OIR). Two different genetic background are available (C57 and S129). Additional analyses are on their way, using other time points or cell sorting approaches to enrich for specific cell type. Human fetal retina analysis is also considered.

Impact

Compared to classical RNAseq (“Bulk” RNAseq), the scRNAseq technology allow to investigate tissue heterogeneity in term of transcriptomic profile between cell types, which is inherent to any multicellular organisms. This disruptive technology in the field of transcriptomic analysis, both at the technical and theoretical level, allows a much greater interpretability of the cellular variability and is becoming the predominant approach to analysis tissue gene expression.

Accessibility

The scGenAP is available to any member of the RRSV. It is important to use the data in a collaborative way in order to take advantage from the large amount of information offered by the scRNAseq technology. Such competitive advantage allows researchers to test their hypothesis using an in silico approach to strengthen their grant proposal or manuscripts. RRSV members can either take advantage of the pre-existing datasets or create new datasets for scRNAseq analysis if they are to engage into long term research project.

We have established an online portal so that members can access data in either a public or private way. Each PI would have the choice to give access to their own dataset based on collaborative agreement. We believe that sharing data will increase networking opportunities and ultimately strengthen the RRSV leadership in vision research.

Infrastructure administrator

Jean-Sébastien Joyal, MD, FRCPC, PhD, Assistant Professor, Department of Pediatrics, Accredited Professor, Department of Pharmacology, Université de Montréal; Adjunct Professor, Department of Pharmacology and Therapeutics, McGill University; Pediatric intensive care physician, CHU-Sainte Justine

Contact information

Gael Cagnone – singlecellacademy@gmail.com

Funding

Vision Health Research Network