---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2012-01-13 02:01:40+00:00
layout: post
slug: rna-isolation-c-gigas-larvae-from-20110412-20110705
title: RNA Isolation - C.gigas Larvae from 20110412 & 20110705
categories:
  - 2012
  - Miscellaneous
tags:
  - Crassostrea gigas
  - larvae
  - NanoDrop1000
  - Pacific oyster
  - RNA
  - RNA isolation
  - RNA quantification
  - TriReagent
  - troubleshooting
---

RNA was isolated from C.gigas larvae collected from Taylor Shellfish hatchery on the dates noted above. Samples were in RNA Later. RNA Later was removed. Attempted homogenization with a pestle proved futile, as a significant quantity of larvae were sticking to the pestle and were nearly impossible to wash off using TriReagent as a rinsing agent. Due to this, all samples were vortexed for 1min in 1mL of TriReagent. It should be noted that the TriReagent took on a cloudy appearance and even showed some separation into two layers upon letting the samples sit. This was not normal and I was immediately concerned about the high salt content from residual RNA Later. Samples were treated normally with the following changes:





  * Aqueous phase after chloroform treatment was clear, but grey in color. This is not necessarily unusual.



  * Addition of isopropanol triggered immediate precipitation of a dark grey material.



  * "Pelleting" of the RNA after the isopropanol precipitation resulted in a gooey grey material that did NOT pellet, and a clear supernatant. The grey goo was transferred to a clean tube. An additional 500uL of isopropanol was added to the clear supernatant of two samples (#140 & #142), as well as to the grey goo. The addition of isopropanol to the clear supe resulted in an immediate precipitation of white salt-like material. The isopropanol appeared to have no effect on the grey goo. All samples were stored @-20C in their existing conditions until 20120116.



  * Since the two samples that were treated with an additional 500uL of isopropanol produced an excess of salt precipitation, I instead added 1mL of 70% EtOH to all the remaining samples; both the clear supernatants and the grey goo. The idea being that the higher water content in the 70% EtOH would help to keep the salts in solution, while precipitating the RNA. Samples were pelleted. All of the grey goo samples produced a white pellet. The grey goo seemed unchanged. Supernatants (including grey goos) were discarded and the resulting pellets from all samples were washed in this fashion were washed three more times.



  * Pellets were resuspended in 25uL of 0.1% DEPC-H2O and stored @ -80C until 20120123.



  * Samples were spec'd on the Roberts' Lab NanoDrop 1000.






Results:

[Spreadsheet of OD readings is here](https://docs.google.com/spreadsheet/ccc?key=0AmS_90rPaQMzdEt1XzlQc1AtdThjVktNSEVxck12cmc&hl=en_US#gid=0).

Since samples were split into two (clear supernatant and grey goo), they were kept separate through the remainder of the process. Sample names are appended with "-1" or "-2". "-1" samples are grey goo samples and the "-2" samples are the clear supernatant samples.

Overall, most of the grey goo samples appear to have produced the highest yields and highest quality of RNA, although this is not true for all of the samples.
