---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2015-12-19 07:15:06+00:00
layout: post
slug: bioanalyzer-bisulfite-treated-olyc-gigas-dna
title: Bioanalyzer - Bisulfite-treated Oly/C.gigas DNA
categories:
  - 2015
  - BS-seq Libraries for Sequencing at Genewiz
  - Olympia oyster reciprocal transplant
tags:
  - 1NF11
  - 1NF15
  - 1NF16
  - 1NF17
  - 2NF5
  - 2NF6
  - 2NF7
  - 2NF8
  - bioanalyzer
  - Crassostrea gigas
  - electropherogram
  - Katherine Silliman
  - Katie Lotterhos
  - M2
  - M3
  - NF2_18
  - NF2_6
  - olympia oyster
  - Ostrea lurida
  - Pacific oyster
  - RNA Pico 6000
---

Following the guidelines of the [TruSeq DNA Methylation Library Prep Guide (Illumina)(https://github.com/sr320/LabDocs/blob/master/protocols/Commercial_Protocols/Illumina_truseq-dna-methylation-library-prep-guide-15066014-a.pdf), I ran 1μL of each sample on an RNA Pico 6000 chip on the Seeb Lab's Bioanalyzer 2100 (Agilent) to confirm that [bisulfite conversion from earlier today](https://robertslab.github.io/sams-notebook/posts/2015/2015-12-18-bisulfite-treatment-oly-reciprocal-transplant-dna-c-gigas-lotterhos-dna-for-bs-seq/) worked.

Results:

Data File 1(Bioanlyzer 2100): [2100 expert_Eukaryote Total RNA Pico_DE72902486_2015-12-18_21-05-04.xad](https://eagle.fish.washington.edu/Arabidopsis/Bioanalyzer%20Data/2100%20expert_Eukaryote%20Total%20RNA%20Pico_DE72902486_2015-12-18_21-05-04.xad)

Data File 1(Bioanlyzer 2100): [2100 expert_Eukaryote Total RNA Pico_DE72902486_2015-12-18_21-42-55.xad](https://eagle.fish.washington.edu/Arabidopsis/Bioanalyzer%20Data/2100%20expert_Eukaryote%20Total%20RNA%20Pico_DE72902486_2015-12-18_21-42-55.xad)



![](https://eagle.fish.washington.edu/Arabidopsis/20151218_bioanalyzer_RNApico_oly_bisulfite_01.jpg)(http://eagle.fish.washington.edu/Arabidopsis/20151218_bioanalyzer_RNApico_oly_bisulfite_01.jpg)

![](https://eagle.fish.washington.edu/Arabidopsis/20151218_bioanalyzer_RNApico_oly_bisulfite_02.jpg)(http://eagle.fish.washington.edu/Arabidopsis/20151218_bioanalyzer_RNApico_oly_bisulfite_02.jpg)



Firstly, the ladder failed to produce any peaks. Not sure why this happened. Possibly not denatured? Seems unlikely, but next time I run the Pico assay, I'll denature the ladder aliquot I use prior to running.

Overall, the samples look as they should (see image from TruSeq DNA Methylation Kit manual below), albeit some are a bit lumpy.

![](https://eagle.fish.washington.edu/Arabidopsis/20151218_bioanalyzer_illumina_bisulfite.jpg)(http://eagle.fish.washington.edu/Arabidopsis/20151218_bioanalyzer_illumina_bisulfite.jpg)