---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2011-04-06 21:40:54+00:00
layout: post
slug: 53-race-pcrs-cox2-sequence-on-5-3-race-libraries-from-20080619
title: 5'/3' RACE PCRs - COX2 Sequence on 5' & 3' RACE Libraries (from 20080619)
categories:
  - 2011
  - Miscellaneous
tags:
  - COX
  - COX2
  - Crassostrea gigas
  - cyclooxygenase
  - Pacific oyster
  - PCR
  - PGS
  - PGS2
  - prostaglandin synthase
  - RACE
---

Ran PCRs on both the 5' & 3' RACE libraries created 20080619 with a new COX2 gene-specifc (GSP) primer designed by Steven (CgPGSRACEsrGSP1; SR ID: 1208). Although this primer was designed to obtain additional 5' sequence, it was used with both 5' and 3' libraries as a precaution in case it accidentally designed on the wrong strand. PCR rxn was set up according to the Clontech SMARTer RACE cDNA Amplification Kit. [Master mix calcs are here](https://eagle.fish.washington.edu/Arabidopsis/Notebook%20Workup%20Files/20110406-01.jpg). PCR cycling followed "Program 1" from the Clontech manual for 25 cycles.

After PCR completion, 5uL were transferred to a clean tube and saved, in case this PCR didn't work and a nested PCR would need to be performed. This is according to the Clontech protocol. Samples were run on a 1.2% agarose gel, as instructed in the Clontech manual.

Results:

No bands of any kind in any sample, including the negative controls (gel not shown). Will perform nested PCR on both libraries in hopes of getting bands.