Single Cell Computational Analysis Platform
Funded since 2018
Aim
Our infrastructure offers a bioinformatics service that allows researchers to generate, analyze and share genomic data from individual cells following their isolation and sequencing of their transcriptomes. This approach, better known as “Single-cell RNA sequencing” (abbreviated scRNAseq), is useful for evaluating the transcriptome (mRNA polyA) of each living cell previously dissociated from retinas (or other organ of interest), at different stages of development, both in a physiological and pathological context, and regardless of the species whose genome is available (in order to be able to align the sequencing data). With the advent of spatial transcriptomics, we can also support researchers in this field.
Description of services
Our infrastructure is managed in a collaborative mode, involving Dr. Joyal’s laboratory and the student members of the Single-Cell Academy. This service is available to all RRSV member researchers. 4 types of services are offered :
1) We offer a consulting service for the preparation of dissociated individual cell samples from retinas (animal or human) , as well as their sequencing using the sequencing platform supported by Genome Qc at CHU Sainte-Justine. In the last year, we have transitioned from DROP-seq to a cutting-edge technology supported by 10X Genomics that allows the analysis of different “OMICS” modalities such as transcriptomics (scRNAseq) and epigenomics (scATACseq). This transition offers greater flexibility in the minimum number of cells required and the experimental design (“cell hashing”). We also offer new technological innovations such as “spatial transcriptomics” and “Nanopore long-read sequencing”.
2) The infrastructure allows in a second stage, bioinformatics analysis and data interpretation , as well as the complementary integration of public data if available (“single-cell atlas”). This service will also be offered to network members who have obtained sequencing data in another Center, but whose access to the services of a bioinformatician specialized in retinal/vascular biology is limited. The “in house” data currently available come from analyses made on mouse retinas aged 5 to 17 days, in normal conditions or retinopathies (OIR). The mice analyzed come from lines with different genetic origins (C57B6 WT and S129 WT). Other analyses are possible at different ages and origins and according to targeted cell dissociation and enrichment protocols.
3) In a third step, our infrastructure allows researchers to access single-cell data via a web interface (genap.ca). This web interface allows efficient data mining of these common databases, but initially limited to Network members, in order to offer a competitive advantage to members in developing new research questions, fleshing out a manuscript in preparation or a funding application. The integration of single-cell analysis functions in GenAP was launched in 2020 and contains scRNAseq databases. These data, stored on Compute Canada servers, are easily accessible to all Network researchers via login and password.
4) Finally, the platform, via the Single-cell academy, supports the training of the new generation of bioinformaticians interested in the retina thanks to a consortium of experts at the Sainte-Justine research center and its partners. The Single-cell academy also provides an interface with the Quebec bioinformatics community, notably via its contribution to the single-cell online meetings bringing together Montreal researchers interested in single-cell technology every 3 weeks.
Impact
Compared to conventional RNAseq (“bulk” RNAseq), scRNAseq technology allows the assessment of intra-sample transcriptomic variations that are due to the cellular heterogeneity specific to living tissues. This technology is therefore a departure from RNAseq technology both in terms of transcriptomic analysis and the interpretation of cellular variability within a sample, and is rapidly becoming the predominant tool for the study of tissue gene expression.
Accessibility
This infrastructure is available to all RRSV member researchers. Indeed, it is important to promote access to and use of published or soon-to-be published data in order to foster collaborations within the Network and allow several laboratories to benefit from scRNAseq technology. This competitive advantage allows researchers to test their hypotheses in sillico for the submission of funding applications and to expand their manuscripts by using existing bioinformatics data. New models could be analyzed by scRNAseq for longer-term collaborative projects.
We are setting up a website giving privileged access to Network members to our published (public access) or upcoming (private access) scRNAseq data. Each PI will be able to choose to provide access to a database that is in the process of being published in the context of collaboration. We believe that better data sharing could foster closer collaborations within our Network.
Responsible
Jean-Sébastien Joyal , MD , FRCPC , PhD , Assistant Professor, Department of Pediatrics, Accredited Professor, Department of Pharmacology, University of Montreal; Associate Professor, Department of Pharmacology and Therapeutics, McGill University, Pediatric Intensivist, CHU Sainte-Justine
Contact person
Gael Cagnone – gael.cagnone.1@gmail.com
Source of funding
Vision Health Research Network