---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2015-12-10 23:26:21+00:00
layout: post
slug: sample-submission-2brad-libraries-for-genewiz
title: Sample Submission - 2bRAD Libraries for Genewiz
categories:
  - 2015
  - 2bRAD Library Tests for Sequencing at Genewiz
  - Olympia oyster reciprocal transplant
  - Samples Submitted
tags:
  - 2bRAD
  - olympia oyster
  - Ostrea lurida
  - RAD
  - RAD-seq
---

Pooled the libraries into a single sample for sequencing on Illumina HiSeq2500 by Genewiz.

Here's the list of samples that were pooled:

<table cellpadding="0" cellspacing="0" border="0" dir="ltr" > 
<tbody >
<tr >

<td data-sheets-value="[null,2,"SJW_Oly_2bRAD"]" >SAMPLE NAME
</td>

<td data-sheets-value="[null,2,"Oly RAD 02"]" >LIBRARY NAMES
</td>

<td data-sheets-value="[null,2,"CGTGAT"]" >INDEX 1 (i7)
</td>

<td data-sheets-value="[null,3,null,6]" data-sheets-formula="=LEN(R[0]C[-1])" >LENGTH (bp)
</td>

<td data-sheets-value="[null,2,"ATGCAT"]" >INDEX 2 (i5)
</td>

<td data-sheets-value="[null,3,null,6]" data-sheets-formula="=LEN(R[0]C[-1])" >LENGTH
</td>
</tr>
<tr >

<td data-sheets-value="[null,2,"SJW_Oly_2bRAD"]" >SJW_Oly_2bRAD
</td>

<td data-sheets-value="[null,2,"Oly RAD 02"]" >Oly RAD 02
</td>

<td data-sheets-value="[null,2,"CGTGAT"]" >CGTGAT
</td>

<td data-sheets-value="[null,3,null,6]" data-sheets-formula="=LEN(R[0]C[-1])" >6
</td>

<td data-sheets-value="[null,2,"ATGCAT"]" >ATGCAT
</td>

<td data-sheets-value="[null,3,null,6]" data-sheets-formula="=LEN(R[0]C[-1])" >6
</td>
</tr>
<tr >

<td data-sheets-value="[null,2,"SJW_Oly_2bRAD"]" >SJW_Oly_2bRAD
</td>

<td data-sheets-value="[null,2,"Oly RAD 03"]" >Oly RAD 03
</td>

<td data-sheets-value="[null,2,"ACATCG"]" >ACATCG
</td>

<td data-sheets-value="[null,3,null,6]" data-sheets-formula="=LEN(R[0]C[-1])" >6
</td>

<td data-sheets-value="[null,2,"ATGCAT"]" >ATGCAT
</td>

<td data-sheets-value="[null,3,null,6]" data-sheets-formula="=LEN(R[0]C[-1])" >6
</td>
</tr>
<tr >

<td data-sheets-value="[null,2,"SJW_Oly_2bRAD"]" >SJW_Oly_2bRAD
</td>

<td data-sheets-value="[null,2,"Oly RAD 04"]" >Oly RAD 04
</td>

<td data-sheets-value="[null,2,"GCCTAA"]" >GCCTAA
</td>

<td data-sheets-value="[null,3,null,6]" data-sheets-formula="=LEN(R[0]C[-1])" >6
</td>

<td data-sheets-value="[null,2,"ATGCAT"]" >ATGCAT
</td>

<td data-sheets-value="[null,3,null,6]" data-sheets-formula="=LEN(R[0]C[-1])" >6
</td>
</tr>
<tr >

<td data-sheets-value="[null,2,"SJW_Oly_2bRAD"]" >SJW_Oly_2bRAD
</td>

<td data-sheets-value="[null,2,"Oly RAD 06"]" >Oly RAD 06
</td>

<td data-sheets-value="[null,2,"TGGTCA"]" >TGGTCA
</td>

<td data-sheets-value="[null,3,null,6]" data-sheets-formula="=LEN(R[0]C[-1])" >6
</td>

<td data-sheets-value="[null,2,"ATGCAT"]" >ATGCAT
</td>

<td data-sheets-value="[null,3,null,6]" data-sheets-formula="=LEN(R[0]C[-1])" >6
</td>
</tr>
<tr >

<td data-sheets-value="[null,2,"SJW_Oly_2bRAD"]" >SJW_Oly_2bRAD
</td>

<td data-sheets-value="[null,2,"Oly RAD 07"]" >Oly RAD 07
</td>

<td data-sheets-value="[null,2,"CACTGT"]" >CACTGT
</td>

<td data-sheets-value="[null,3,null,6]" data-sheets-formula="=LEN(R[0]C[-1])" >6
</td>

<td data-sheets-value="[null,2,"ATGCAT"]" >ATGCAT
</td>

<td data-sheets-value="[null,3,null,6]" data-sheets-formula="=LEN(R[0]C[-1])" >6
</td>
</tr>
<tr >

<td data-sheets-value="[null,2,"SJW_Oly_2bRAD"]" >SJW_Oly_2bRAD
</td>

<td data-sheets-value="[null,2,"Oly RAD 08"]" >Oly RAD 08
</td>

<td data-sheets-value="[null,2,"ATTGGC"]" >ATTGGC
</td>

<td data-sheets-value="[null,3,null,6]" data-sheets-formula="=LEN(R[0]C[-1])" >6
</td>

<td data-sheets-value="[null,2,"ATGCAT"]" >ATGCAT
</td>

<td data-sheets-value="[null,3,null,6]" data-sheets-formula="=LEN(R[0]C[-1])" >6
</td>
</tr>
<tr >

<td data-sheets-value="[null,2,"SJW_Oly_2bRAD"]" >SJW_Oly_2bRAD
</td>

<td data-sheets-value="[null,2,"Oly RAD 14"]" >Oly RAD 14
</td>

<td data-sheets-value="[null,2,"GATCTG"]" >GATCTG
</td>

<td data-sheets-value="[null,3,null,6]" data-sheets-formula="=LEN(R[0]C[-1])" >6
</td>

<td data-sheets-value="[null,2,"ATGCAT"]" >ATGCAT
</td>

<td data-sheets-value="[null,3,null,6]" data-sheets-formula="=LEN(R[0]C[-1])" >6
</td>
</tr>
<tr >

<td data-sheets-value="[null,2,"SJW_Oly_2bRAD"]" >SJW_Oly_2bRAD
</td>

<td data-sheets-value="[null,2,"Oly RAD 17"]" >Oly RAD 17
</td>

<td data-sheets-value="[null,2,"TCAAGT"]" >TCAAGT
</td>

<td data-sheets-value="[null,3,null,6]" data-sheets-formula="=LEN(R[0]C[-1])" >6
</td>

<td data-sheets-value="[null,2,"ATGCAT"]" >ATGCAT
</td>

<td data-sheets-value="[null,3,null,6]" data-sheets-formula="=LEN(R[0]C[-1])" >6
</td>
</tr>
<tr >

<td data-sheets-value="[null,2,"SJW_Oly_2bRAD"]" >SJW_Oly_2bRAD
</td>

<td data-sheets-value="[null,2,"Oly RAD 23"]" >Oly RAD 23
</td>

<td data-sheets-value="[null,2,"CTGATC"]" >CTGATC
</td>

<td data-sheets-value="[null,3,null,6]" data-sheets-formula="=LEN(R[0]C[-1])" >6
</td>

<td data-sheets-value="[null,2,"ATGCAT"]" >ATGCAT
</td>

<td data-sheets-value="[null,3,null,6]" data-sheets-formula="=LEN(R[0]C[-1])" >6
</td>
</tr>
<tr >

<td data-sheets-value="[null,2,"SJW_Oly_2bRAD"]" >SJW_Oly_2bRAD
</td>

<td data-sheets-value="[null,2,"Oly RAD 30"]" >Oly RAD 30
</td>

<td data-sheets-value="[null,2,"AAGCTA"]" >AAGCTA
</td>

<td data-sheets-value="[null,3,null,6]" data-sheets-formula="=LEN(R[0]C[-1])" >6
</td>

<td data-sheets-value="[null,2,"ATGCAT"]" >ATGCAT
</td>

<td data-sheets-value="[null,3,null,6]" data-sheets-formula="=LEN(R[0]C[-1])" >6
</td>
</tr>
</tbody>
</table>

Combined 40ng of all samples, except Oly RAD 30. Used only 20ng of Oly RAD 30 because it was the only sample that produced a single peak in qPCR melt curve analysis (i.e. no primer dimer). As such, it's a rough assumption that [the qPCR quantitation](https://robertslab.github.io/sams-notebook/posts/2015/2015-11-17-qpcr-oly-rad-seq-library-quantification/) of all the other samples is twice as high as they should be due to the contribution of primer dimer amplification.

Calculations for pooling can be seen here (Google Sheet): [20151117_RAD_qPCR_data](https://docs.google.com/spreadsheets/d/1z7UAWm56JkQI04LKJ92dsWFhC0IFR-a9065aLP2jmso/edit?usp=sharing)

The full list of samples (and the individual samples/libraries/indexes) submitted to Genewiz for this project by Katherine Silliman & me can be seen here (Google Sheet): [White_BS1511196_R2_barcodes](https://docs.google.com/spreadsheets/d/1DJP4zpF3OcISOAQ-MM8bW85WcJqdB5EvcExs2wGvzcg/edit?usp=sharing)


