Introducing Single Cell Genomics, this course covers several aspects of single cell workflows, from experimental design to laboratory hands-on, including cell sorting and processing for production of quality samples for sequencing, generation of sequencing data.
We will provide an overview of tools and metrics for assessing the data quality, focussing on typical data QC reports.
Laboratory practical sessions will involve cell sorting using FACS (AriaFusion), including considerations for different cell types, preparation of samples for Smart-seq2 library construction, QC and sample pooling.
We will also include an overview of the differences in sample preparation for sequencing on the 10X instrument, including loading of samples. Delegates will have the opportunity to review sequencing reports and discuss to determine data quality, understand the workflow for library and pre-processing QC, produce matrices, and how to identify any filtering required with subsequent demultiplexing.
All theory lectures and hands-on sessions will include best practices and tips as learned first-hand by EI's own faculty.
The course will consist of a mixture of conceptual lectures, methodological lectures, hands-on sessions in the laboratory, with walk-throughs of initial quality control, as well as ample time for group discussions.
What will I learn?
- Cell sorting, including an introduction to different platforms at EI
- How to generate cDNA for RNASeq using the Smart-seq2 workflow
- Library construction using Nextera XT protocol
- Quality control at cDNA and library stages with exemplars of good and bad libraries
- 10X genomics chip loading demonstration
- Understand how to assess data quality and troubleshoot problematic samples
- Understand basic QC assessment at different stages of data production
- Introductory overview of data management and downstream use of scRNAseq data
Course Prerequisites
Delegates are expected to be confident and competent in Good Laboratory Practice and with standard laboratory equipment, for example familiarity with best practice for pipetting.
If you have certificates for competency training, please email these to training@earlham.ac.uk or we ask that your line manager emails us with a description of techniques/equipment that you are familiar with.
A basic understanding of NGS including indexes and pooling would be beneficial. For those with minimal laboratory experience, we will ask you to complete a short laboratory induction. For more information on requirements, please email training@earlham.ac.uk.
Who is this event for?
Those in the process of writing grant applications, or those in experimental planning stages of a project involving single-cell genomics, who want to gain wet lab experience in single-cell techniques.
Early career researchers (PhD and early career postdocs), research assistants, technicians and group leaders are all welcome.
