24-26 April 2018

San Francisco, USA

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Workshop A
April 24, 2018

09.00am - 12.00pm
Exploring Single-Cell Transcriptomes Using Bioinformatics Solutions from QIAGEN
Workshop Leader: Jean-Noel Billaud, Senior Principal Scientist, QIAGEN Workshop Leader: Nirav M. Amin, Bioinformatics Scientist, QIAGEN

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:

  • Run single-cell RNA-sequencing pipelines within OmicSoft Array Studio to analyze and visualize gene expression differences in different cell types, or within a unique cell type.
  • Analyze disease versus normal gene expression signatures in IPA to pinpoint significant genes, in this case associated with Beta cells in T1D.
  • Identify significant differentially-expressed isoforms and their association with disease.
  • Generate hypotheses about novel regulatory networks that suggest drivers of the expression changes observed in the disease state in single cells.
  • Gain additional insights about single cell biology by readily comparing this T1D dataset in IPA to thousands of additional public datasets which have been curated and processed in OmicSoft.

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.

Workshop B
April 24, 2018

13.00pm - 16.00pm
RNA-Seq data in the UCSC Genome Browser – New Display Modes
Workshop Leader: Robert Kuhn, Associate Director, Genome Browser UCSC

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:

  • Learn some useful navigation features of the Genome Browser, including exon-only display
  • Upload RNA-seq data to the UCSC Genome Browser and visualize in the context of UCSC-resident data such as GTEx
  • Configure data tracks from multiple sources for co-visualization
  • Display sum and difference datasets by subtracting controls from experimental in real time on-screen

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