---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2009-12-08 00:36:47+00:00
layout: post
slug: rna-fragmentation-herring-liver-mrna-for-solid-libraries
title: RNA Fragmentation - Herring Liver mRNA for SOLiD Libraries
categories:
  - 2009
  - Miscellaneous
tags:
  - 2L
  - 3L
  - 4L
  - 6L
  - bioanalyzer
  - gel
  - mRNA
  - mRNA enrichment
  - NanoDrop1000
  - Pacific herring
  - Ribominus Concentration Module Kit
  - RNA fragmentation
  - RNA Pico 6000
  - RNA quantification
  - total RNA
  - Whole Transcriptome Analysis Kit
---

Samples from [20091203](/Sam%27s+Working+Notebook+Nov-Dec+2009#sjw20091203). 0.5uL was removed from each and transferred to separate tubes and diluted to < 5ng/uL for subsequent Bioanalyzer analysis using the Pico chip. Samples were fragmented using RNase III according to the Ambion WTK protocol and then cleaned up/concentrated using the Invitrogen RiboMinus Concentration Module according to the Ambion WTK protocol.

Samples were spec'd prior to running on the Bioanalyzer:

![](https://eagle.fish.washington.edu/Arabidopsis/RNA%20Spec%20Readings/20091207%20mRNA%20fragmented%20SJW.jpg)

Concentrations/absorbance values are not accurate when using the NanaDrop after using the RiboMinus Concentration module, according to the Ambion WTK protocol. However, yields seem pretty good...

Total, mRNA and fragmented mRNA from each of the four samples was run on the Pico chip with the Eukaryote Total RNA Bioanalyzer protocol.

Results:

![](https://eagle.fish.washington.edu/Arabidopsis/Bioanalyzer%20Data/20091207%20bioanalyzer%20gel.jpg)

The 2L tot (total RNA) and 3L tot (total RNA) samples are clearly very good quality. 2L tot does exhibit some very slight degradation, though. 4L tot (total RNA) and 6L tot (total RNA) show a much greater degree of degradation. All mRNA samples show complete removal of any trace, contaminating rRNA. The fragmented samples (the last four samples on the gel image above) all appear to be perfect. The 4L frag sample simply has less RNA loaded and that is why it is not as dark as the other three fragmented samples. Despite the degradation in the 4L tot and 6L tot samples, the fragmentation profile looks good and we will proceed with making the cDNA libraries for those samples.