---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2015-02-09 22:36:05+00:00
layout: post
slug: library-prep-quantification-of-c-gigas-larvae-oa-1000ppm-library
title: Library Prep - Quantification of C.gigas larvae OA 1000ppm library
categories:
  - 2015
  - Crassostrea gigas larvae OA (2011) bisulfite sequencing
tags:
  - BS-seq
  - Crassostrea gigas
  - DNA Quantification
  - FLx800 plate reader
  - larvae
  - library prep
  - OA
  - ocean acidification
  - Pacific oyster
  - Quant-iT DNA BR Kit
---

The completed BS Illumina [library made on Friday](https://robertslab.github.io/sams-notebook/posts/2015/2015-02-06-bisulfite-ngs-library-prep-bisulfite-conversion-illumina-library-construction-of-c-gigas-larvae-dna/) (1000ppm) was quantified via fluorescence using the Quant-iT DNA BR Kit (Life Technologies/Invitrogen).  Also quantified [Jake's libraries](https://heareresearch.blogspot.com/2015/02/2-6-2015-library-creation-for-bs-samples/). Used 1μL of  each sample and the standards.  All standards were run in duplicate.  Due to limited sample, the libraries were only processed singularly, without replication.  Fluorescence was measured on a FLx800 plate reader (BioTek), using the Gen5 (BioTek) software for all calculations.

Results:

[20150209_CgigasOA_BSlibrraryQuants_OluridaLibraryQuants](https://docs.google.com/spreadsheets/d/1HhnEA6Wwj3Kci-Lsh0wE2OTCxEc56KCVC3PF8bHzvJM/edit?usp=sharing)

The good news is that the standard curve looked fine, with an R²=0.998.

The bad news is that there's no detectable DNA in the sample, [just like last time](https://robertslab.github.io/sams-notebook/posts/2015/2015-01-28-bisuflite-ngs-library-prep-c-gigas-larvae-oa-bisulfite-library-quantification/).

Possibly something is totally shot with this sample?  Will quantify [the sheared DNA](https://robertslab.github.io/sams-notebook/posts/2015/2015-01-09-dna-isolation-c-gigas-larvae-from-2011-noaa-oa-experiment/) and decide what to do.

I quantified the sheared DNA and there's nothing there! Where did it go? I just don't get it. It was sheared, speed-vac'd and resuspended.  All the DNA should still be in the tubes...
