---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2015-09-02 01:43:05+00:00
layout: post
slug: agarose-gel-geoduck-olympia-oyster-gdna-integrity-check
title: Agarose Gel - Geoduck & Olympia Oyster gDNA Integrity Check
categories:
  - 2015
  - Geoduck Genome Sequencing
  - Olympia Oyster Genome Sequencing
tags:
  - gDNA
  - gel
  - geoduck
  - O'geneRuler DNA Ladder Mix
  - olympia oyster
  - Ostrea lurida
  - Panopea generosa
---

Ran 0.8% agarose 1x modified TAE gel stained with EtBr to assess the integrity of [geoduck gDNA (from 20150828)(2015/08/28/genomic-dna-isolation-geoduck-adductor-muscle-foot.html) and [Olympia oyster gDNA (from 20150901)](https://robertslab.github.io/sams-notebook/posts/2015/2015-09-02-genomic-dna-isolation-olympia-oyster-adductor-musle-mantle/).

Ran 500ng of each sample:

Geoduck adductor muscle: 4.87μL

Geoduck foot: 4.50μL

Oly adductor muscle: 4.22μL

Oly mantle: 2.51μL

Results:

![](https://raw.githubusercontent.com/sr320/LabDocs/master/protocols/Commercial_Protocols/ThermoFisher_OgeneRuler_DNA_Ladder_Mix_F100439.jpg)(https://raw.githubusercontent.com/sr320/LabDocs/master/protocols/Commercial_Protocols/ThermoFisher_OgeneRuler_DNA_Ladder_Mix_F100439.jpg)[![](http://eagle.fish.washington.edu/Arabidopsis/20150901_gDNA_geoduck_oly.jpg)](http://eagle.fish.washington.edu/Arabidopsis/20150901_gDNA_geoduck_oly.jpg)





The gel was loaded in the same order as the sample volumes listed above.

The gel is a bit disappointing.



#### Geoduck adductor



High molecular weight band present, but extremely faint. Not too much smearing, but accumulation of low molecular weight smudge suggests residual RNA. This is despite the fact that the kit used for isolation (E.Z.N.A. Mollusc DNA Kit) has a RNase treatment. This residual RNA could explain why the amount loaded on the gel appears to be so little compared to other samples (the RNA is contributing to the absorbance at 260nm, thus inflating the calculated concentration of gDNA).



#### Geoduck foot



High molecular weight band present and bright. Some smearing (i.e. degradation) present, along with degarded DNA visible at ~500bp. This sample may require a Bioanalyzer run to accurately quantify the high molecular weight DNA, as the lower molecular weight DNA (i.e. degarded DNA) is "artificially" inflating the concentration of the DNA in the sample.



#### Oly adductor



High molecular weight band present and bright. Some smearing (i.e. degradation) present, along with degarded DNA visible at ~500bp. This sample may require a Bioanalyzer run to accurately quantify the high molecular weight DNA, as the lower molecular weight DNA (i.e. degarded DNA) is "artificially" inflating the concentration of the DNA in the sample.



#### Oly mantle



High molecular weight band present, but extremely faint. Some smearing and a smudge around 500bp, indicating degraded DNA. The low visibility of this sample on the gel suggests that the concentration determined by the NanoDrop1000 is inaccurate. However, unlike the geoduck adductor sample, it doesn't appear that RNA carryover is responsible, as there is no noticeable low molecular weight (~100bp) smudge.



Overall, the geoduck foot and the Oly adductor samples are likely usable. Currently awaiting clarification from BGI for DNA quantity requirements for the genome sequencing of these two species.
