---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2010-11-24 04:34:09+00:00
layout: post
slug: phenolchloroform-extractions-and-etoh-precipitations-hapii-and-mspi-digests-from-yesterday
title: Phenol:Chloroform Extractions and EtOH Precipitations - HapII and MspI digests
  from yesterday
categories:
  - 2010
  - Miscellaneous
tags:
  - Crassostrea gigas
  - DNA Quantification
  - EtOH precipitation
  - gill
  - gonad
  - HpaII
  - MspI
  - NanoDrop1000
  - Pacific oyster
  - phenol-chloroform cleanup
---

Restriction digests from yesterday were mixed with equal volume (50uL) of phenol:chloroform:IAA (25:24:1) and centrifuged 16,000g for 5mins @ 4C. Aqueous phase was transferred to a clean tube and an equal volume (50uL) of chloroform was added. Samples were mixed and centrifuged 16,000g for 5mins @ 4C. Aqueous phase was transferred to clean tubes and EtOH precipitated, [according to protocol](/protocols#Protocols-Nucleic%20Acid%20Precipitation-Ethanol%20Precipitation%20(DNA)). Samples were resuspended in 25uL of H2O and spec'd.

Samples are labeled as Parent (P), #, tissue, enzyme (MspI = M, HpaII = H, Undigested = U)

Results:

[Here is a link to a spreadsheet with ODs](https://spreadsheets.google.com/ccc?key=0AmS_90rPaQMzdDdkakJ4ekRrOEg0am9KSmItVUJ6T3c&hl=en&authkey=CLWS5LAB). Average recovery was ~734ng, which is only a 36% recovery (started with 2000ng). Will need to discuss with Mac and Steven to see if it's worth continuing with these sample through a second round of digests/phenol:chloroform extraction/EtOH precipitation, as I don't know what quantity of DNA is required/desired for the subsequent methylation specific PCR (MSP), OR if I should/need to perform a repeat of these 1st-round digestions in order to end up with sufficient DNA for MSP.

![](https://eagle.fish.washington.edu/Arabidopsis/20101123%20DNA.JPG)
