---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2015-01-09 22:40:24+00:00
layout: post
slug: dna-isolation-c-gigas-larvae-from-2011-noaa-oa-experiment
title: DNA Isolation - C.gigas larvae from 2011 NOAA OA Experiment
categories:
  - 2015
  - Crassostrea gigas larvae OA (2011) bisulfite sequencing
tags:
  - Crassostrea gigas
  - DNA Isolation
  - DNA Quantification
  - DNA Shearing
  - larvae
  - OA
  - ocean acidification
---

DNA was isolated from the following samples:
<table width="263" style="height: 244px;" >
<tbody >
<tr >

<td style="text-align: center;" >SAMPLE ID
</td>

<td style="text-align: center;" >DATE
</td>

<td style="text-align: center;" >TREATMENT (ppm)
</td>

<td style="text-align: center;" ># LARVAE
</td>
</tr>
<tr >

<td style="text-align: center;" >6B5
</td>

<td style="text-align: center;" >20110513
</td>

<td style="text-align: center;" >400
</td>

<td style="text-align: center;" >5,000
</td>
</tr>
<tr >

<td style="text-align: center;" >1B2
</td>

<td style="text-align: center;" >20110513
</td>

<td style="text-align: center;" >1000
</td>

<td style="text-align: center;" >5,000
</td>
</tr>
<tr >

<td style="text-align: center;" >6B2
</td>

<td style="text-align: center;" >20110513
</td>

<td style="text-align: center;" >400
</td>

<td style="text-align: center;" >10,000
</td>
</tr>
<tr >

<td style="text-align: center;" >1B1
</td>

<td style="text-align: center;" >20110513
</td>

<td style="text-align: center;" >1000
</td>

<td style="text-align: center;" >10,000
</td>
</tr>
<tr >

<td style="text-align: center;" >1B1
</td>

<td style="text-align: center;" >20110519
</td>

<td style="text-align: center;" >1000
</td>

<td style="text-align: center;" >NA
</td>
</tr>
<tr >

<td style="text-align: center;" >1B2
</td>

<td style="text-align: center;" >20110519
</td>

<td style="text-align: center;" >1000
</td>

<td style="text-align: center;" >NA
</td>
</tr>
<tr >

<td style="text-align: center;" >6B2
</td>

<td style="text-align: center;" >20110519
</td>

<td style="text-align: center;" >400
</td>

<td style="text-align: center;" >NA
</td>
</tr>
<tr >

<td style="text-align: center;" >6B1
</td>

<td style="text-align: center;" >20110519
</td>

<td style="text-align: center;" >400
</td>

<td style="text-align: center;" >NA
</td>
</tr>
</tbody>
</table>


Some tubes contained a high quantity of algae, based on quantity of material in tube and overall green color.

Samples 1B1 & 1B2 from 20110519 have excessive quantities of algae.

Samples 6B1 & 6B1 from 20110519 have a fair amount of algae.

See pic:



[caption id="" align="alignnone" width="676"]![](https://eagle.fish.washington.edu/Arabidopsis/20150109%20-%20Gigas_Larvae_OA_tubes.JPG) Sample tubes after brief spin, prior to DNA isolation.[/caption]

Prior to isolation, samples were briefly spun (12,000g, 15s @ RT). Supernatants were discarded.






## DNA Isolation


DNA was isolated using the DNeasy Blood & Tissue Kit (Qiagen).

Samples were resuspended in 180uL of Buffer AL and 20uL of Proteinase K. Samples were mixed by vortexing and incubated @ 56C O/N.

The manufacturer's protocol (_Purification of Total DNA from Animal Tissues (Spin-Column Protocol)_) was followed.

Due to low quantities of starting tissue, samples were eluted with 200μL of Buffer EB to maximize DNA recovery.




## DNA Quantification


Samples were prepared for quantification via fluorescence using the Quant-iT DNA BR Kit (Life Technologies/Invitrogen). The manufacturer's protocol was altered to use 5μL of sample and 5μL of standards (instead of 10μL) in each well. All samples/standards were run in duplicate and read on a FLx800 plate reader (BioTek).

Mean fluorescence of the standards were plotted with a best-fit line. The resulting equation from the best-fit line was used to determine sample concentrations from their mean fluorescence.




#### Results:


![](https://eagle.fish.washington.edu/Arabidopsis/20150109%20-%20CgigasOAquantsEquation.jpg)

Calcs and resulting quantities are here:

[https://docs.google.com/spreadsheets/d/1e7EF05akWeBtO7Xz0UWXhIzRlkVU5HA_rjCE3c4SPEw/edit?usp=sharing](https://docs.google.com/spreadsheets/d/1e7EF05akWeBtO7Xz0UWXhIzRlkVU5HA_rjCE3c4SPEw/edit?usp=sharing)

``



All samples have yields great enough to proceed with shearing and bisulfite conversion.

Samples 1B1 and 1B2 from 20110519 have extremely large yields.  This is not surprising, considering the amount of algae present in the source tubes.  Will process only 500ng from each sample.






## DNA Shearing


Adjusted volume of all samples to 190μL using Buffer EB (Qiagen) in 1.5mL snap-cap tubes.

Samples were sonicated/sheared in the Bioruptor (Diagenode) with the following cycling protocol:

25 cycles of:

30s on

30s off

Cycling params were adjusted from [the last time I performed this](https://genefish.wikispaces.com/Sam%27s+Working+Notebook+August+-+December+2014#sjw20141126), since I felt the final sheared size was a bit on the small size.

After shearing, samples were stored @ 4C until I could SpeedVac them to reduce their volumes, as the bisulfite treatment step requires volumes < 24uL.



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