Single cell transcriptomics – University of Copenhagen

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Single cell transcriptomics

Course Content

  • Single cell transcriptomics using plate-based method, Smart-Seq2, and droplet-based method, 10x Chromium
  • Whole cell and nucleus transcriptomics
  • Processing of single cell data using Seurat and Pagoda (for the data processing part, the participants will be subdivided into unexperienced and experienced users)
  • Participants are expected to present their projects in form of oral presentation

Brief course program
Wet-lab: Tissue processing for single cell or single nucleus analysis
Wet-lab: Smart-seq2 cDNA library preparation with follow-up RNA sequencing
Wet-lab: Single cell analysis by 10x Chromium
Dry lab: Clustering of single cell transcriptomics data by cell type using Seurat and Pagoda
Dry lab: Developmental and maturation trajectories
Dry lab: Grouping of genes into co-expressed modules

Detailed day-to-day program will be available to the participants in advance

Participants
PhD students at any year of their studies, with some experience in molecular biology (molecular cloning, PCR, work with RNA)
There is no prerequisite knowledge of programming or data analysis tools, and both experienced sequencing data analysis users as well as unexperienced ones can attend the course. However, for the data analysis part, the participants will be subdivided into 2 groups and the training will be provided at beginners and advanced levels.

Organizers
Konstantin Khodosevich, Biotech Research and Innovation Center, University of Copenhagen
Tune H Pers, Center for Basic Metabolic Research, University of Copenhagen                  

Teachers
Group leaders:
Konstantin Khodosevich, Biotech Research and Innovation Center, University of Copenhagen
Tune H Pers, Center for Basic Metabolic Research, University of Copenhagen
Peter Kharchenko, Department of Biomedical Informatics, Harvard Medical School

Postdocs and students:
Andrea Asenjo Martinez, Biotech Research and Innovation Center, University of Copenhagen
Dylan Rausch, Center for Basic Metabolic Research, University of Copenhagen
Julie Lee, Center for Basic Metabolic Research, University of Copenhagen
Nikolaos Barkas, Department of Biomedical Informatics, Harvard Medical School
Pascal Timshel, Center for Basic Metabolic Research, University of Copenhagen
Samuel Demharter, Biotech Research and Innovation Center, University of Copenhagen
Ulrich Pfisterer, Biotech Research and Innovation Center, University of Copenhagen

Dates

27.09.18-03.10.18

Course location
Biotech Research and Innovation Center (BRIC), University of Copenhagen
Biocenter building, Ole Maaløes Vej 5, 4th floor

Registration

Apply for the course with the motivation letter and CV to momed@bric.ku.dk before 15.08.18, the decision will be sent to applicants few days after the deadline.

Sign up deadline 1 Aug 2018