Course outside EMBL-EBI
EMBL-EBI Workshop in Stanford University: Transcriptomics data and resources
This is a one-day workshop to provide an overview of data management and ontology principles in addition to hands-on experience with functional genomics resources at the EBI which cover data submission, archive and visualisation. These resources are: Annotare, ArrayExpress and the transcriptomics knowledgebases Expression Atlases (bulk and single-cell).
- ArrayExpress: public database for functional genomics
- Expression Atlas: Gene expression across species and biological conditions
Who is this course for?
This workshop is aimed at wet-lab scientists and bioinformaticians. Participants should have degree-level understanding of molecular biology/genetics and be proficient at using web browsers.
What will I learn?
Learning outcomes
After this course participants should be able to:
- Summarize good data management concepts and incorporate them into their research practice
- Explain and use data submission process at the EBI with the web tool Annotare
- Investigate datasets in ArrayExpress relevant to users’ research
- Access and download the raw data and accompanying metadata
- Interpret the results of data visualisation in Expression Atlas and its counterpart Single Cell Expression Atlas to draw conclusions about available data as well as downloading the results of the data analysis
- Define different methods for producing single cell data and the considerations underlying these decisions
Trainers
Nancy George
EMBL-EBI, UK
Programme
Day 1 – Tuesday 21st January 2020
09:30-09:45
Welcome and Introduction to EMBL-EBI resources and tools
Nancy George
09:45-10:45
Data quality: standards and ontologies
Nancy George
10:45-11:00
Break
11:00-12:00
Discover and submit functional genomics data with Annotare and ArrayExpress
Nancy George
12:00-13:00
Lunch
13:00-14:00
Discover and submit functional genomics data with Annotare and ArrayExpress: Advanced search and practical session
Nancy George
14:00-15:00
Explore gene expression data with Expression Atlas
Nancy George
15:00-15:30
Break
15:30-16:30
Explore gene expression data with Expression Atlas: Practical session
Nancy George
16:30-17:15
Single Cell Expression Atlas: a new tool for single cell transcriptomics
Nancy George
17:15-17:30
RNA-seqer: Programmatic access to data
Nancy George
17:30-17:45
Wrap-up and feedback
Nancy George
17:45
End of workshop
Registration is being administered by Michael Newman. If you have questions about registration, please contact Michael for further information.
EMBL-EBI, UK
Programme
Day 1 – Tuesday 21st January 2020 |
||
---|---|---|
09:30-09:45 | Welcome and Introduction to EMBL-EBI resources and tools | Nancy George |
09:45-10:45 | Data quality: standards and ontologies | Nancy George |
10:45-11:00 | Break | |
11:00-12:00 | Discover and submit functional genomics data with Annotare and ArrayExpress | Nancy George |
12:00-13:00 | Lunch | |
13:00-14:00 | Discover and submit functional genomics data with Annotare and ArrayExpress: Advanced search and practical session | Nancy George |
14:00-15:00 | Explore gene expression data with Expression Atlas | Nancy George |
15:00-15:30 | Break | |
15:30-16:30 | Explore gene expression data with Expression Atlas: Practical session | Nancy George |
16:30-17:15 | Single Cell Expression Atlas: a new tool for single cell transcriptomics | Nancy George |
17:15-17:30 | RNA-seqer: Programmatic access to data | Nancy George |
17:30-17:45 | Wrap-up and feedback | Nancy George |
17:45 | End of workshop |
Registration is being administered by Michael Newman. If you have questions about registration, please contact Michael for further information.