Single-cell RNA sequencing has emerged as an important technology with which to examine gene expression that distinguishes different cell types. This workshop will provide in-depth coverage of
bioinformatics solutions from QIAGEN that are used to analyze and interpret whole transcriptome datasets from single-cell sequencing experiments. Using a public dataset (pancreatic cells from T1D patients), we will demonstrate best practices on (i) how to import and process raw FASTQ expression data using OmicSoft Array Studio software, and (ii) how to interpret and explore the underlying biology using Ingenuity Pathway Analysis (IPA).
You will learn how OmicSoft Array Studio can be leveraged by biologists and bioinformaticians alike to integrate datasets from different platforms. We will also demonstrate how to optimize the transcriptome data, and how using IPA you can gain insights into biological signatures—to identify the transcriptional drivers, the affected pathways, biological processes, and more—by comparing T1D Beta cells versus normal pancreatic Beta cells as a test case.
In this workshop you will learn how to:
Jean-Noel Billaud, Senior Principal Scientist, QIAGEN
Before joining QIAGEN Bioinformatics, Dr. Billaud joined Ingenuity Systems 2008 as staff scientist for in silico research programs in oncology and infectious diseases. Jean-Noël Billaud holds a Ph.D. in Blood Cell Biology from Paris VII, and has done his post-doctoral work at the Scripps Research Institute (San Diego, CA) studying the impact of Feline Immunodeficiency Virus and Borna Disease Virus on brain cells. He pursued his career at the Vaccine Research Institute of San Diego where he co-developed a universal vaccine platform using the core antigen of Hepatitis B Virus in order to target infectious (viral and parasitic) diseases as well as metabolic diseases and cancer.
Nirav M. Amin, Bioinformatics Scientist, QIAGEN
Nirav is a Bioinformatics Scientist at QIAGEN. He obtained his PhD in Genetics and Development from Cornell University (Ithaca, NY), and conducted post-doctoral work in cardiac development at the University of North Carolina at Chapel Hill (Chapel Hill, NC). Nirav joined OmicSoft (now a QIAGEN company) in 2017, specializing in customer support and development.
The workshop will be a hands-on demonstration of the UCSC Genome Browser, a widely used visualization tool that offers myriad resident datasets to aid in the interpretation of your own uploaded data. Exon-only display mode allows narrowing the view to show only the relevant parts of the genome.
A preview of a soon-to-be released feature that allow users to group datasets into composite tracks that can be configured together, subtracted or added to each other, and displayed as “transparent overlay” — together on the same axes. Data can be combined across multiple data sources, from user-uploaded private data, track data hubs all over the internet and from UCSC.
In this workshop you will learn:
Robert Kuhn, Associate Director, Genome Browser UCSC
Robert Kuhn received his PhD at the University of California, Santa Barbara in Biochemistry and Molecular Biology, where he studied the centromeres of yeast. Following a postdoctoral at UC Berkeley/USDA Plant Gene Expression Center, he taught biochemistry, molecular biology and genetics at UC Santa Cruz. He joined the UCSC Genome Browser project in 2003, where he is now Associate Director, helping bring the fruits of the Human
(and other) Genome Project(s) to scientists worldwide