---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2010-09-10 03:59:22+00:00
layout: post
slug: qpcr-hard-clam-primers-on-cdna-from-yesterday
title: qPCR - Hard Clam Primers on cDNA from yesterday
categories:
  - 2010
  - Miscellaneous
tags:
  - BigDef
  - C1qTNG
  - CA
  - CFX96
  - CytP450-like
  - ferritnin
  - graphs
  - GST
  - Hard clam
  - HemoDef
  - HSP 70
  - Immomix
  - lysozyme
  - MA
  - MAX
  - Mercenaria mercenaria
  - Mercenaria_Rel
  - metallothionein
  - Mm_TRAF6
  - NADHIV
  - qPCR
  - RACK1
  - SenescentProt
  - STI
  - SYTO 13
  - TfAP1
  - TLR
---

Performed qPCR on Friedman Lab machine targeting immune-related genes in hard clam. [Rough plate layout/master mix calcs are here](https://eagle.fish.washington.edu/Arabidopsis/Notebook%20Workup%20Files/20100709-01.jpg). [qPCR report from Friedman Lab machine is here](http://eagle.fish.washington.edu/Arabidopsis/Notebook%20Workup%20Files/20100909-01%20qPCR%20Report.pdf) (PDF) and shows cycling params, plate layout and Cts.

Results:

[CFX96 Data file is here](https://purplepelican.fish.washington.edu/~srlab/qpcr/Sam/CFX96/Sam_2010-09-09%2009-22-55_CC009827.pcrd).

The following primer sets failed to produce an amplicon:

Mm_TRAF6

Mercenaria_Rel

TLR

STI

CytP450-like

Raw fluorescence data was extracted (No baseline subtraction) and processed with PCR Miner. [Data workup/analysis is here](https://spreadsheets.google.com/ccc?key=toOwWKJGN1aUHuSTaHbiEnQ&authkey=COnVirEI&hl=en#gid=1). Here is a graph of those primer sets producing an amplicon. All were normalized to actin, which exhibited the smallest amount of deviation across all three samples of the normalizing/housekeeping genes analyzed.

![](https://eagle.fish.washington.edu/Arabidopsis/Notebook%20Workup%20Files/20100909%20qPCR%20graphs.jpg)



# 



As a preliminary run with these genes, there are a number of promising candidates that could yield some interesting data regarding the physiological response of hard clam to exposure to QPX.
