Guest post by Anastassia Voronova
Sequencing platforms and techniques are undergoing a revolutionary and transformational progress. As a stem cell researcher, I value the opportunity for continued professional education to maintain a grip on the latest technologies. In late February, I had such an opportunity, and participated in the Stem Cell Network’s first -OMICS Workshop focused on “acquiring, analyzing and interpreting next generation sequencing data”. The workshop was held over three days at the Institute of Biomaterials and Biomedical Engineering in downtown Toronto.
For those not familiar with OMICS, it is a term used to describe the technologies used to study the many roles and actions of molecules present within cells, such as genomics (the study of genes), proteomics (study of proteins) and transcriptomics (study of mRNA) using high-throughput methods like microarray and sequencing. This course offered a unique and highly in-demand basic training for stem cell researchers and trainees interested in harnessing the power of OMICS data in their own research.
In the stem cell field, the ability to analyze different cell populations, especially if they are rare or difficult to obtain, is an ever-growing need. The emergence of better cell isolation techniques and deeper sequencing technologies enables researchers to ask questions about stem cell biology and human development in a global and systemic way. For this reason, the workshop was designed to provide stem cell researchers not only with the type of questions to ask, but also the answers through an introduction to the robustness of OMICS experiments.
The theoretical part on day one of the workshop consisted of lectures by several wet and dry lab researchers Drs. Bill Stanford, Richard Wintle, Julie Brind’Amour, Theodore Perkins and Messrs. Gareth Palidwor and Matt Tanner from Ontario and British Columbia. The focus was multi-disciplinary in nature, ranging from experimental design for genomic DNA, RNA or ChIP-seq, history and power of genome sequencing, to tips on microarray, RNA- and ChIP-seq data analysis. The “hands on” part of the workshop on days two and three, was led by Dr. Daniele Merico, who gave trainees an opportunity to manipulate large datasets to identify gene ontology and pathway enrichment maps, perform statistical analysis and gain practical meaning from the results. This was cemented through the visualization of definitive networks with software such as Cytoscape.
The workshop was an excellent introduction for anyone with little or limited experience in OMICS research. For me, the workshop helped to expand the scope and breadth of genomic sequencing experiments and microarray data analysis. I now have a comprehensive overview of next generation sequencing experimental design, in particular, the importance of biological replicates, depth of analysis, and library normalization.
For the data analysis, the focus was on testing different algorithms to obtain rigorous conclusions. The ability to experiment with different gene set enrichment models provided a more robust perspective on the power of statistical analysis and data interpretation and was complemented by an in-depth discussion on multiple test correlation strategies and their applications. Finally, networks and interaction data analysis offered an understanding of different types of networks, interactions and databases one can work with to get more meaningful visual interpretations of OMICS data.
By the end of this workshop, I (and I am sure all of my colleagues at the workshop) learned several tools and tricks not previously in my repertoire and which I will incorporate into my own data analysis and representation. In my own research, I study the environmental and epigenetic regulation of stem cells in developing brain. With the skills I gained, I can now plan to use RNA-seq and ChIP-seq to start elucidating the roles of autism spectrum disorder associated genes in different progenitor populations of the developing brain cortex. Moreover, I can revisit microarray datasets I already have to reanalyze them using statistical analyses and gene-set enrichment strategies introduced at the workshop, as well as employ different visualization tools for my future manuscripts.
Perhaps the strongest message that I will take away with me is that a wealth of next generation sequencing data already exists in public repositories such as GEO, and that stem cell researchers may be able to develop more focused hypotheses by tapping into this rich resource. Personally, I will make sure to browse through the available experiments before picking up a pipette – even if they are done in different conditions or cell lines, they can inform my future hypotheses and experimental approaches.
Anastassia Voronova obtained her Ph.D. degree from University of Ottawa under the tutelage of Dr. Ilona Skerjanc, where she studied the transcriptional regulation of stem cell differentiation programs by Hedgehog signalling. Anastassia has since then transferred her expertise to the laboratory of Dr. Freda Miller at the Hospital for Sick Children, where her research focuses on environmental and epigenetic regulation of brain stem cells, more specifically in the developing cortex. Anastassia is a recipient of CIHR, Multiple Sclerosis Society of Canada and Hospital for Sick Children Research Training Centre postdoctoral fellowships. Aside from lab work, Anastassia is also involved in promoting a better life for Canadian graduate students and postdoctoral fellowships through her involvement at the Canadian Society for Molecular Biosciences, where she is a Board Director.