---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2017-12-11 23:24:21+00:00
layout: post
slug: dna-sonication-bioanalzyer-c-virginica-gdna-for-medip
title: DNA Sonication & Bioanalzyer - C. virginica gDNA for MeDIP
categories:
  - 2017
  - Miscellaneous
tags:
  - bioanalyzer
  - Crassostrea virginica
  - DNA 12000 assay
  - DNA Shearing
  - Eastern oyster
  - qsonica
  - sonication
---

I transferred 8ug (136uL) of _Crassotrea virginica_ gDNA ([isolated earlier today](https://robertslab.github.io/sams-notebook/posts/2017/2017-12-11-dna-isolation-quantification-crassotrea-virginica-mantle-gdna/)) to two separate 1.7mL snap cap tubes for sonication/shearing.

I performed shearing at the [NOAA Northwest Fisheries Science Center](https://www.nwfsc.noaa.gov/about/facilities/montlake.cfm), using the Qsonica Q800R. Mackenzie Gavery assisted me.

Target fragment size was ~500bp.

Samples were run at the same time with the following settings:





  * 10 minutes


  * 30 seconds on, 30 seconds off


  * 25% power



![Qsonica settings](http://owl.fish.washington.edu/Athaliana/20171211_qsonica_settings.jpg)

After sonication, fragmentation was assessed using the Seeb Lab's Bioanlyzer 2100 (Agilent) and the DNA 12000 Chip Kit (Agilent). NOTE: All of the reagents and the chips were past their expiration dates (most in June 2016).

![Bioanlyzer DNA chip used](http://owl.fish.washington.edu/Athaliana/20171211_bioanalyzer_DNA12000_chip.jpg)

Results:

Agilent 2100 Bioanalyzer Expert file (XAD): [2100 expert_DNA 12000_DE72902486_2017-12-11_13-45-31.xad](https://owl.fish.washington.edu/Athaliana/2100%20expert_DNA%2012000_DE72902486_2017-12-11_13-45-31.xad)

Fragmentation was successful, and pretty consistent.

Both samples appear to have an average fragment size of ~420bp. Will proceed with MeDIP, once reagents are received.

![Sample 1 sheared electropherogram](http://owl.fish.washington.edu/Athaliana/20171211_electropherogram_sheared_virginica_01.jpg)

![Sample 2 sheared electropherogram](http://owl.fish.washington.edu/Athaliana/20171211_electropherogram_sheared_virginica_02.jpg)

Unsheared gDNA:

![Unsheared DNA electropherogram](http://owl.fish.washington.edu/Athaliana/20171211_electropherogram_virginica_gDNA.jpg)