Data Repositories

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The Rockefeller University

Bioinformatics Resource Centre

Getting hold of HTS data

• From public repositories
• From collaborators
• By sequencing some of your own material!

Public Repositories

• Several public sources of HTS data exist.
• First concentrating on those acting as repositories.
  • GEO (Gene Expression Omnibus)
  • ENA (European Nucleotide Database)
  • SRA (Short Read Archive)

GEO (https://www.ncbi.nlm.nih.gov/geo/)

• GEO holds different types of biological datasets.
• Very popular for submission of data accompanying publication.
• Captures metadata,  processed files and raw data.
• GEO was not built for HTS data 

GEO - Quick Tour

SRA (www.ncbi.nlm.nih.gov/sra)

• NCBI's HTS specific repository.
• Sequencing specific metadata.
• Stores Raw data (in SRA format)
• SRA format - requires SRA Toolkit
• Lost then regained funding?

SRA - Quick Tour

ENA (https://www.ebi.ac.uk/ena)

• ENA acts as a european HTS repository.
• Mirrors much of SRA.
• Stores Raw data
• No SRA formats - fastq by default.

ENA - Quick Tour

Other Repositories

• Many repositories contain processed or unprocessed data.
• These typically are the result or a consortium's data release policies.
• Good example is Encode site. (https://www.encodeproject.org/)
• UCSC has many useful links to genomics data in various formats. (http://hgdownload.soe.ucsc.edu/downloads.html)

Other Repositories

• Other specialist repositories exist.
• ReCount database provides standardised counts for user analysis.
• Other databases like Immgen/Bodymap provide RNAseq for specific cells/tissues.

Reference data

• Reference Genome available from many locations.
• Different assemblies
  • Major Revisisons - Change locations
  • Minor Revisions - Update annotation
• Genome sequence stored as FASTA.
• Gene build as GFF3 or GTF.
• IGenomes contains full annotation files for many genomes.