Video tutorials: gene expression databases

The video below demonstrates the use of NCBI’s Gene Expression Omnibus (GEO) database by

  • Searching for hypoxia studies
  • Examining the contents of a study that examines hypoxia inducible transcription factor binding to genes via sequencing (i.e ChIP-seq)
  • Downloading the data files and viewing the sequencing reads in the Integrative Genome Viewer (IGV)

The video below demonstrates how to download raw sequencing files that are associated with high throughput sequencing studies found in NCBI GEO using Unix command line in the HiPerGator environment.  HiPerGator is UF’s research computing cluster.