CCMI - Workshop

UC San Diego – 2020 Transcriptomics Data and Resources at EMBL-EBI

Hosted by Dr. Nancy George, Gene Expression team at EMBL-EBI

This one-day workshop will 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, archival and visualisation. The workshop is primarily targeted at wet-lab researchers.

The content of the workshop will include the following:

  • 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
  • (If time permits) RNA-seqer API: programmatic access to publicly available processed RNA-seq data from ENA

A typical one-day workshop will consist of all the above modules with the last module depending on timing.

By the end of the course participants should be able to:

  • understand good data management concepts and incorporate them into their research practice
  • understanding data submission process at the EBI with the web tool Annotare
  • investigate datasets in ArrayExpress to investigate 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
  • be aware of different methods for producing single cell data and the considerations underlying these decisions

The only prerequisites for this workshop are a general knowledge of molecular biology and genomics and a laptop with a web browser, preferably Chrome or FireFox.


  • 9:00 am - Welcome and introduction to EMBL-EBI resources and tools
  • 9:15 am - Data quality: standards and ontologies
  • 10:15 am - Coffee break
  • 10:30 am  - Discover and submit functional genomics data with Annotare and ArrayExpress
  • 12:00 pm - Lunch break (box lunches provided)
  • 1:00 pm - Explore gene expression data with Expression Atlas
  • 2:00 pm - Explore gene expression data with Expression Atlas: Practical session
  • 3:00 pm - Coffee break
  • 3:30 pm - Single Cell Expression Atlas: a new tool for single cell transcriptomics
  • 4:15 pm - Programmatic access to data


Parking at UC San Diego requires a valid permit. Hourly rates are posted at pay stations; credit cards are accepted. A map of the MET Building and nearby parking lots can be viewed here. The nearest parking lots are the Osler Parking Structure, the Gilman Parking Structure, and lots P602 and P603. If using the UC San Diego Shuttle, exit at Gilman Dr and Meyers Ln, then walk south towards School of Medicine.

No Show Policy

If you are unable to attend for any reason, please cancel your registration at least two business days prior to the event. Your cooperation ensures our programs can be made available to interested attendees and remain fiscally sustainable. A no-show may limit your ability to book our events in the future. Thank you for your understanding. 

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