---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2010-03-10 18:58:20+00:00
layout: post
slug: pcr-test-lexies-mercenaria-18s-contamination-issue
title: PCR - Test Lexie's Mercenaria 18s contamination issue
categories:
  - 2010
  - Miscellaneous
tags:
  - 18s
  - Apex Red Master Mix
  - cDNA
  - gel
  - Hard clam
  - Mercenaria mercenaria
  - PCR
  - troubleshooting
---

Lexie's PCR with this primer set and a pool of Mercenria cDNA has yielded contamination in all of her waters. Performed two sets of PCR: one with her existing primer working stocks and the other with a fresh aliquot of primer working stocks. Used my own reagents/water. [PCR set up and cycling params are here](https://eagle.fish.washington.edu/Arabidopsis/Notebook%20Workup%20Files/20100310-01.jpg). PCR ran O/N.

Results:

![](https://eagle.fish.washington.edu/Arabidopsis/20100311.jpg)

Lane 1 - 100bp ladder

Lane 2 - H2O (Lexie's primer stocks)

Lane 3 - H2O (Lexie's primer stocks)

Lane 4 - cDNA (Lexie's primer stocks)

Lane 5 - H2O (fresh primer stocks)

Lane 6 - H2O (fresh primer stocks)

Lane 7 - cDNA (fresh primer stocks)

All water samples look clean and there's a nice bright band in the cDNA samples. Lexie's contamination issue is probably a technique issue and not one of reagent contamination.