View source for RT-PCR primer design for ChIP

# Locate the potential gene regions you believe your protein is bound to (for ChIP-seq peaks refer to [[Locating ChIP-seq peaks from ENCODE]]. Make sure this the genetic sequence is species appropriate.  If not, you can use the BLAT option from the UCSC website [https://genome.ucsc.edu/index.html] and choose the desired species from the drop-down menu. 
# The genetic region entered for primer search should be around 400 bp.
# Go to NCBI primer design [http://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi?ORGANISM=9606&INPUT_SEQUENCE=NM_001618.3]
# Enter your sequence in the first box.
# PCR product size should be set to 70-150bp.
# Make sure to select the proper species in the “organism” section.
# Click ‘Get Primers’.
# Choose a primer pair that is towards the middle region, if available.
# Like always you should print off this page and keep it in your records, indicating the primer pair you ordered, the NM# (if one is associated) and the sequences and locations of the forward and reverse primers. Remember to record these primers in the primer database as well.
# Order primers from IDT [https://www.idtdna.com/site]. It is important to indicate on the primer database and in the name on the label that these are ChIP primers so as not to be confused with normal qPCR primers.

[[ Category: Immunoprecipitation‏‎ ]]
[[ Category: Transcription ]]
[[ Category: PCR ]]