Analysis of single cell RNASeq data from 10x Genomics, Leuven
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methods are required and some of the underlying assumptions for the methods developed for bulk RNASeq experiments are no longer valid.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.
Trainers
Janick Mathys
Janick tries to help VIB scientists analyze their data by offering bioinformatics training and support. Next to organizing trainings, creating e-learning courses and teaching statistics, R, Python, Linux, HPC, bulk and single cell RNA-Seq analysis, she consults scientists and develops pipelines for omics analyses. Before joining VIB, she worked as a post-doc at KULeuven, doing research on transcriptomics and transcription regulation. She coordinated the Master of Bioinformatics program of KULeuven and taught the course on Biological Databases.
Niels Vandamme
Niels Vandamme heads the VIB Single Cell Core to cover complete experimental and computational workflows for single cell multi-omics. During his PhD, he studied heterogeneity and population dynamics in neural crest biology and cancer cell plasticity, using in vitro systems and genetically engineered mouse models at a single cell resolution. During his postdoctoral training, he gained expertise in computational models to analyze high-throughput single-cell data.
Program
Practical info
20 April 2023 - 27 April 2023
Leuven - Campus Gasthuisberg
Herestraat 49
3000 Leuven
Belgium
20 April 2023 - 27 April 2023
Leuven - Campus Gasthuisberg
Leuven train station is approximately 4 km from the campus Gasthuisberg. Buses depart very regularly to the Gasthuisberg Campus from Leuven train station.
For tickets and up to date schedules visit website De Lijn or use the De Lijn App.
Exit at the very last bus stop ‘Gasthuisberg Campus) make sure not to exit at ‘Gasthuisberg Kliniek =
hospital)
Once you get off the bus, go to your right and go up the street until you see stairs to your left. Climb the stairs all the way up between two buildings. Look for the signs containing blue circles and white numbers and follow them all the way from 2 up to number 12. You will cross several buildings and the walk will take max. 10 minutes. When you reach number 12, you have reached O&N 5, where you can find the reception.
20 April 2023 - 27 April 2023
Leuven - Campus Gasthuisberg
The Gasthuisberg campus is west of the Leuven ring. Our buildings are situated behind the hospital (see black arrow near ‘RING NOORD’ on the map). If you come from the city center, you will arrive on campus from the east side (taking Mgr. Van Waeyenberglaan and roundabout Het Teken). If you come from Heverlee or Campus Arenberg, you will arrive from the west side (taking the Celestijnenlaan and Taborweg). When you arrive uphill at the intersection with the Rega Institute and the Red Cross building, you need to take the road down to the bicycle parking at Rega Institute (see map) where you can park. Next, follow the ‘Onderwijs & Navorsing blue route’ description below (start point is #9).
20 April 2023 - 27 April 2023
Leuven - Campus Gasthuisberg
You arrive via the E314 highway – EXIT 16
After 200 m, keep left to drive underneath the roundabout and into the tunnel.
Keep left and follow the arrows to Parking West.
You arrive via the Leuven ring road
At the roundabout, take the exit towards ‘Spoed / Ziekenhuis’.
Follow the ring around Campus Gasthuisberg and pass the entrance of SPOED.
Continue right until you arrive at a second roundabout.
Follow the directions for E314.
Near the Fire Brigade Station, make a U-turn and follow the directions for ‘Ziekenhuis’.
Keep left and drive downhill, underneath the roundabout and into the tunnel.
Keep left and follow the arrows to Parking West.
Next, leave the parking at level +1 using the big stairs near the vending machines.
Follow the red carpet and arrows to 'Onco Dagcentrum' to get to the O&N buildings. Take the stairs on your left after exiting Parking West. You are now in front of the O&N4 building; on the left you will find O&N5.