Analysis of single cell RNASeq data
2/04/2024
9/04/2024
General context
Today it is possible to obtain genome-wide transcriptome data from single cells using high-throughput sequencing (scRNASeq). The main advantage of scRNASeq is that the cellular resolution and the genome wide scope makes it possible to address issues that are intractable using other methods, e.g. bulk RNASeq or single-cell RT-qPCR. These scRNASeq datasets can be used to unravel heterogenous cell populations, for the discovery of new cell types and states, the reconstruction of developmental trajectories and fate decisions, all previously masked in bulk transcriptome analyses. However, to analyze scRNASeq data, novel methods are required and some of the underlying assumptions for the methods developed for bulk RNASeq experiments are no longer valid.
In this course we will discuss some of the advantages and pitfalls of scRNASeq and go through the whole scRNASeq analysis pipeline. We will teach you how to do proper quality control and filtering on gene level and cell level, how to do create tSNE plots, how to get potential markers for a subset of cells ...
Participants should have some experience with R. You can attend the Basic statistics in R training to get sufficient R background. Contact janick.mathys@vib.be if you want to follow the R introduction training.
Trainers
Janick Mathys
Program
9h30-12h00 Analysis via R of publicly available data: scater pipeline
12h00-13h00 Lunch
13h00-17h00 Analysis via R of publicly available data: Seurat pipeline
9h30-12h00 Follow up to Seurat pipeline: topics depend on needs of participants
12h00-13h00 Lunch
13h00-17h00 Analysis of own data under guidance of experts from Single Cell Core
Practical info
02 April 2024 - 09 April 2024
Antwerp - Campus Drie Eiken UAntwerpen
Universiteitsplein 1
2610 Antwerpen
Belgium
02 April 2024 - 09 April 2024
Antwerp - Campus Drie Eiken UAntwerpen
02 April 2024 - 09 April 2024
Antwerp - Campus Drie Eiken UAntwerpen
02 April 2024 - 09 April 2024
Antwerp - Campus Drie Eiken UAntwerpen
Neuron Room, Building V of the University of Antwerp (UA), Parking 4, Universiteitsplein 1, 2610 Antwerpen.
Via public transport: from Antwerp Central Station take bus 17 to UZA and get out at the last stop. Walk around the hospital building via the right side and pass building T (see map in the link below).
By car: see map