---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2015-11-20 04:47:07+00:00
layout: post
slug: dna-sonication-oly-gdna-for-mbd
title: DNA Sonication - Oly gDNA for MBD
categories:
  - 2015
  - MBD Enrichment for Sequencing at ZymoResearch
tags:
  - bioanalyzer
  - Bioruptor 300
  - electropherogram
  - hc1_2B
  - hc1_4B
  - hc2_15B
  - hc2_17
  - hc3_1
  - hc3_10
  - hc3_11
  - hc3_5
  - hc3_7
  - hc3_9
  - Hood Canal
  - olympia oyster
  - Ostrea lurida
  - Oyster Bay
  - sonication
  - ss2_14B
  - ss2_18B
  - ss2_9B
  - ss3_14B
  - ss3_15B
  - ss3_16B
  - ss3_20
  - ss3_3B
  - ss3_4B
  - ss5_18
---

In preparation for MBD enrichment, fragmented Olympia oyster gDNA with a target size of ~350bp.

Genomic DNA samples were isolated and provided to us by Katherine Silliman at UIC. Selected samples will compare Hood Canal (HC) and Oyster Bay (SS, South Sound) populations.

Used the Seeb Lab's Bioruptor 300 (Diagenode) sonicator.

![](https://eagle.fish.washington.edu/Arabidopsis/20151119_bioruptor_settings.JPG)(http://eagle.fish.washington.edu/Arabidopsis/20151119_bioruptor_settings.JPG)

After sonication, samples were run on a the Seeb Lab's 2100 Bioanalyzer (Agilent) on DNA 12000 chips.

Results:

HOOD CANAL SAMPLES

![](https://eagle.fish.washington.edu/Arabidopsis/Bioanalyzer%20Data/20151119_bioanalyzer_oly_hood_canal_all_electropherograms.jpg)(http://eagle.fish.washington.edu/Arabidopsis/Bioanalyzer%20Data/20151119_bioanalyzer_oly_hood_canal_all_electropherograms.jpg)



OYSTER BAY SAMPLES

![](https://eagle.fish.washington.edu/Arabidopsis/Bioanalyzer%20Data/20151119_bioanalyzer_oly_oyster_bay_all_electropherograms.jpg)(http://eagle.fish.washington.edu/Arabidopsis/Bioanalyzer%20Data/20151119_bioanalyzer_oly_oyster_bay_all_electropherograms.jpg)

More detailed analysis (including average fragment size for each samples) will be coming soon...