EMBL-EBI Workshop in UC Davis: Transcriptomics data and resources

Date:

  Friday 24 January 2020

Venue: 

University of California, Davis - Shields Library, Davis, , CA,  95616, United States

Application opens: 

Tuesday 03 December 2019

Application deadline: 

Tuesday 03 December 2019

Participation: 

By invitation

Registration fee: 

Please contact Monica Britton for further information.

Registration closed

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Course Overview

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).

 

Resources

During this course you will learn about: 

  • Introduction to data management good practice, FAIR standards and ontologies
  • *Annotare: submitting functional genomics data to the EBI in-line with good data practice
  • ArrayExpress: how to find and reuse functional genomics data
  • Expression Atlas: overview of the standardised analysis pathway. Introduction to experiment types investigated and features available in visualising bulk RNA-seq data
  • Single Cell Expression Atlas: introduction into single-cell sequencing concepts and experiment types followed by overview of the resource and methods of single cell data visualisation
  • *RNA-seqer API: programmatic access to publicly available processed RNA-seq data from ENA

Audience

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.

Modules

  • arrayexpress-public-database-functional-genomics
  • expression-atlas-gene-expression-across-species-and-biological-conditions

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

Programme

Day 1 – Friday 24th 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