Contents

Sources for biological data

GEO (Gene Expression Omnibus)

  • GEO lets you construct a very specific query for microarray data, with inclusion and exclusion criteria.

  • Link to a tutorial.

TCGA (The Cancer Genome Atlas)

  • TCGA has lots of publicly available RNA-seq.

  • Some of this requires access, but most is publicly available.

  • You can build a query and specify open access only.

  • Example query for open access, colon cancer RNA-seq data:

       files.access in ["open"] and files.cases.primary_site in ["colon"] and files.data_category in ["transcriptome profiling"] and files.data_type in ["Gene Expression Quantification"] and files.experimental_strategy in ["RNA-Seq"]