View source for Primer Design for qPCR

==Finding Known Primer Sets==
* Check papers, especially supplementary tables
* Check PrimerBank http://pga.mgh.harvard.edu/primerbank/index.html

==Making Your Own Primers From Entrez==
# Find your RNA sequence on entrez by starting with the gene at http://www.ncbi.nlm.nih.gov/gene (make sure its the correct species).  Then pick the mRNA you want to probe, based on the isoform structure on that page.  Click on that nucleotide
# Under analyse this sequence click '''Pick Primers'''
# Under PCR Product Size pick 70-150 as the range
# Under Exon/intron selection -> Intron Inclusion check the box by '''Primer pair must be separated by at least one intron on the corresponding genomic DNA'''
# If you want to look at a specific region of the mRNA and an appropriate primer pair in that region is not selected, change the range under PCR template on the top
# Click '''Get Primers''' on the bottom and wait for results
# Print this out, for future reference and when you order primers name them as follows species-Gene-direction-seq.start-seq.end, for example '''mm-SREBF1-FWD-127-254'''.
# Enter both primers in ExperimentDB

[[ Category: qPCR ]]
[[ Category: mRNA ]]
[[ Category: Transcription ]]
[[ Category: Molecular Biology ]]