Fan Gao, Ph.D., The Picower Institute for Learning and Memory at MIT
Fan is a staff bioinformatician with PILM. Before moving to MIT, Fan was working as a research associate at University of Southern California, with a joint appointment at Zilkha Neurogenetic Institute and Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research.
This workshop is suitable for postdocs and graduate students who would like to learn the basics of regular RNA-Seq library preparation and [...]
This workshop is suitable for postdocs and graduate students who would like to learn the basics of regular RNA-Seq library preparation and RNA-Seq data analysis. Prior knowledge of RNA is needed to participate in this workshop. The workshop will consist of a short lecture followed by demonstrations.
RNA-Seq library preparation
RNA-Seq is the latest next-generation sequencing method that quantitatively profiles the whole transcriptome. Compared to microarray approach, RNA-Seq offers broader dynamic range, increased specificity and sensitivity, and unbiased detection of novel splicing and gene fusion events. In this workshop, we will briefly review the bench protocol (Illumina TruSeq total RNA prep kit and BIOO mRNA prep kit) for sequencing library preparation.
RNA-Seq data analysis
In the workshop, we will start with the raw FASTQ format files obtained from Illumina sequencers, and go through data QC, read mapping, gene (transcript, exon) quantification, normalization, gene differential expression analysis and data visualization with Picower bioinformatics server. We will use recently published RNA-Seq data of excitatory neurons and PV neurons for the demo.
Please note that the workshop will last for 1 hour, and all the participants are REQUIRED to bring their own MAC computers for hands-on practice.
Philip L. De Jager is the Steven R. and Kathleen P. Haley Distinguished Chair for the Neurosciences at the Brigham & Women’s Hospital and is an associate professor of neurology at Harvard Medical School. He is the director for basic and translational research at the Institute for the Neurosciences at the Brigham & Women’s Hospital and is an associate member of the Broad Institute of Harvard University and the Massachusetts Institute of Technology. He continues to practice clinical neurology, seeing patients within the Partners Multiple Sclerosis Center that is affiliated with the Brigham & Women’s Hospital and Massachusetts General Hospital in Boston. In 2008, Philip received the prestigious Harry Weaver Neuroscience Scholar Award from the National Multiple Sclerosis Society. His work focuses on understanding the genomic, epigenomic, and neuroimmunologic architecture of neurodegenerative diseases such as multiple sclerosis, Alzheimer’s disease, and age-related cognitive decline.
Philip received his BS (summa cum laude) in molecular biophysics & biochemistry and French literature from Yale University. He received his PhD in neurogenetics from The Rockefeller University and his MD from Cornell University Medical College. He also completed an MMSc program in clinical investigation at Harvard Medical School and the Massachusetts Institute of Technology. In addition, he completed subspecialty training in neuroimmunology at the Brigham and Women’s Hospital and in human genetics at the Broad Institute.