---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2009-09-02 04:59:58+00:00
layout: post
slug: qpcr-hrm-lake-trout-snp-primer-test
title: qPCR - HRM Lake Trout SNP primer test
categories:
  - 2009
  - Miscellaneous
tags:
  - lake trout
  - LTP01
  - qPCR
  - SNPs
---

Tested out the plate of Lake Trout primers (LTP01 - forward and reverse combined) for SNP detection. qPCR was performed using Roche 2x HRM M.M. [qPCR set up is here](https://eagle.fish.washington.edu/Arabidopsis/Notebook%20Workup%20Files/20090901-01.jpg). Cycling params are as follows:

95C - 10mins

40 cycles of:

95C - 10s

60C - 15s

72C - 25s

Plate layout matches the [primer plate layout](https://spreadsheets.google.com/ccc?key=tg7mtIbECmdwRrBdQr3lOnA).

Results: The following wells have signals and good, clean melting curves: A1, C1, H1, B2, A3, D2, G3, A4, E4, B5, A7, D7, H7, B8, C8, F10, G10, C11, H11, A12, E12. These are potential candidates for SNP analysis. Will test HRM analysis using these primers, each on a subset of Lake Trout DNA samples to see whether or not they'll be truly useful for analyzing the full plate of DNA.