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Using the in-Silico PCR (isPCR) tool in the UCSC Genome Browser

Difficulty level
Beginner
Duration
8:01
Topic

This tutorial describes the isPCR tool and demonstrates how to use it for predicting the size and location of PCR products and visualizing the genomic location on the genome. The tool operates on DNA templates for all organisms and DNA or RNA on human and mouse. It also demonstrates how to use the Browser to obtain DNA sequences from the genome.

Topics covered in this lesson
  • Set the Genome Browser to hg19 defaults
  • Navigate to a gene (CYP2D6) to obtain DNA for primers
  • Get DNA with exons annotated
  • Obtain primers for PCR from exons
  • Use primers to predict amplicon size from genome assembly
  • Observe amplified DNA in Genome Browser
  • Use primers to predict amplicon size from RNA template
  • Observe RNA results in Genome Browser