---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2018-10-18 21:03:55+00:00
layout: post
slug: qpcrs-ronits-c-gigas-ploidydessicationheat-stress-cdna-15-dilution
title: qPCRs - Ronit's C.gigas ploidy/dessication/heat stress cDNA (1:5 dilution)
categories:
  - 2018
  - Miscellaneous
tags:
  - cfx connect
  - Cg_18s_F
  - Cg_18s_R
  - Cg_DNMT1_F
  - Cg_DNMT1_R
  - Cg_hsc70_F
  - Cg_hsc70_R2
  - Cg_Hsp90_F
  - Cg_Hsp90_R
  - Cg_Prx6_F
  - Cg_Prx6_R
  - Crassostrea gigas
  - dessication
  - EF1_qPCR_3'
  - EF1_qPCR_5'
  - heat shock
  - Pacific oyster
  - ploidy
  - qPCR
  - 'SR ID: 1381'
  - 'SR ID: 1382'
  - 'SR ID: 1396'
  - 'SR ID: 1408'
  - 'SR ID: 1409'
  - 'SR ID: 1416'
  - 'SR ID: 1510'
  - 'SR ID: 1511'
  - 'SR ID: 1532'
  - 'SR ID: 1533'
  - 'SR ID: 308'
  - 'SR ID: 309'
  - SsoFast EvaGreen Supermix
---

IMPORTANT: The cDNA used for the qPCRs described below was a 1:5 dilution of [Ronit's cDNA made 20181017](https://robertslab.github.io/sams-notebook/posts/2018/2018-10-17-reverse-transcription-ronits-c-gigas-dnased-ctenidia-rna/) with the following [primers](https://docs.google.com/spreadsheets/d/14m2kkFhxcoKWWIGoAD_7VOVsAg9wilME2UcSLqfnqLI/edit?usp=sharing&authkey=CP736rQK)! Diluted cDNA was stored in his -20<sup>o</sup>C box with his original cDNA.

The following primers were used:

18s





  * Cg_18s_F (SR ID: 1408)



  * Cg_18s_R (SR ID: 1409)






EF1 (elongation factor 1)





  * EF1_qPCR_5′ (SR ID: 309)



  * EF1_qPCR_3′ (SR ID: 308)






HSC70 (heat shock cognate 70)





  * Cg_hsc70_F (SR ID: 1396)



  * Cg_hsc70_R2 (SR ID: 1416)






HSP90 (heat shock protein 90)





  * Cg_Hsp90_F (SR ID: 1532)



  * Cg_Hsp90_R (SR ID: 1533)






DNMT1 (DNA methyltransferase 1)





  * Cg_DNMT1_F (SR ID: 1511)



  * Cg_DNMT1_R (SR ID: 1510)






Prx6 (peroxiredoxin 6)





  * Cg_Prx6_F (SR ID: 1381)



  * Cg_Prx6_R (SR ID: 1382)






Samples were run on Roberts Lab CFX Connect (BioRad). All samples were run in duplicate. See qPCR Report (Results section) for plate layout, cycling params, etc.

qPCR master mix calcs (Google Sheet):





  * [20181018_qPCR_Cgigas_ploidy_cDNA](https://docs.google.com/spreadsheets/d/1B6_yzSxigiw1Ra_sflRSxHJRtecaQvXo-_gDVp_TUyM/edit?usp=sharing)





* * *





# RESULTS



No analysis here. Will analyze data and post in different notebook entry. This entry just contains the qPCR setup, resulting data, and a glimpse of how each primer performed.

Nothing is broken down based on sample ploidy or experimental conditions.



###### 18s



qPCR Report (PDF):





  * [sam_2018-10-18 2011-28-40_BR006896_18s.pdf](https://owl.fish.washington.edu/Athaliana/qPCR_data/qPCR_reports/sam_2018-10-18%2011-28-40_BR006896_18s.pdf)



qPCR File (PCRD):



  * [sam_2018-10-18 2011-28-40_BR006896_18s.pcrd](https://owl.fish.washington.edu/scaphapoda/qPCR_data/cfx_connect_data/sam_2018-10-18%2011-28-40_BR006896_18s.pcrd)



qPCR Data (CSV):



  * [sam_2018-10-18_11-28-40_BR006896_-__Quantification_Cq_Results_18s.csv](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2018-10-18_11-28-40_BR006896_-__Quantification_Cq_Results_18s.csv)





###### Amplication Plots



![](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2018-10-18%2011-28-40_amp_plots_18s.png)



###### Melt Curves



![](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2018-10-18%2011-28-40_melt_plots_18s.png)



* * *





###### DNMT1



qPCR Report (PDF):





  * [sam_2018-10-18 2010-03-33_BR006896_DNMT1.pdf](https://owl.fish.washington.edu/Athaliana/qPCR_data/qPCR_reports/sam_2018-10-18%2010-03-33_BR006896_DNMT1.pdf)



qPCR File (PCRD):



  * [sam_2018-10-18 2010-03-33_BR006896_DNMT1.pcrd](https://owl.fish.washington.edu/scaphapoda/qPCR_data/cfx_connect_data/sam_2018-10-18%2010-03-33_BR006896_DNMT1.pcrd)



qPCR Data (CSV):



  * [sam_2018-10-18 2010-03-33_BR006896_DNMT1.pcrd](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2018-10-18_10-03-33_BR006896_-__Quantification_Cq_Results_DNMT1.csv)





###### Amplication Plots



![](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2018-10-18%2010-03-33_amp_plots_DNMT1.png)



###### Melt Curves



![](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2018-10-18%2010-03-33_melt_plots_DNMT1.png)



* * *





###### EF1



qPCR Report (PDF):





  * [sam_2018-10-18 2008-20-51_BR006896_EF1.pdf](https://owl.fish.washington.edu/Athaliana/qPCR_data/qPCR_reports/sam_2018-10-18%2008-20-51_BR006896_EF1.pdf)



qPCR File (PCRD):



  * [sam_2018-10-18 2008-20-51_BR006896_EF1.pcrd](https://owl.fish.washington.edu/scaphapoda/qPCR_data/cfx_connect_data/sam_2018-10-18%2008-20-51_BR006896_EF1.pcrd)



qPCR Data (CSV):



  * [sam_2018-10-18_08-20-51_BR006896_-__Quantification_Cq_Results_EF1.csv](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2018-10-18_08-20-51_BR006896_-__Quantification_Cq_Results_EF1.csv)





###### Amplication Plots - Manual Threshold (Linear)



![](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2018-10-18%2008-20-51_EF1_manual_threshold_linear_amp_plots.png)



###### Amplication Plots - Manual Threshold (Log)



![](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2018-10-18%2008-20-51_EF1_manual_threshold_log_amp_plots.png)



###### Amplication Plots - Automatic Threshold (Linear)



![](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2018-10-18%2008-20-51_EF1_og_threshold_linear_amp_plots.png)



###### Amplication Plots - Automatic Threshold (Log)



![](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2018-10-18%2008-20-51_EF1_og_threshold_log_amp_plots.png)



###### Melt Curves



![](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2018-10-18%2008-20-51_melt_plots_EF1.png)



* * *





###### HSC70



qPCR Report (PDF):





  * [sam_2018-10-18 2011-28-40_BR006896_HSC70.pdf](https://owl.fish.washington.edu/Athaliana/qPCR_data/qPCR_reports/sam_2018-10-18%2011-28-40_BR006896_HSC70.pdf)



qPCR File (PCRD):



  * [sam_2018-10-18 2011-28-40_BR006896_HSC70.pcrd](https://owl.fish.washington.edu/scaphapoda/qPCR_data/cfx_connect_data/sam_2018-10-18%2011-28-40_BR006896_HSC70.pcrd)



qPCR Data (CSV):



  * [sam_2018-10-18_11-28-40_BR006896_18s_-__Quantification_Cq_Results_HSC70.csv](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2018-10-18_11-28-40_BR006896_18s_-__Quantification_Cq_Results_HSC70.csv)





###### Amplication Plots



![](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2018-10-18%2011-28-40_amp_plots_HSC70.png)



###### Melt Curves



![](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2018-10-18%2011-28-40_melt_plots_HSC70.png)



* * *





###### HSP90



qPCR Report (PDF):





  * [cfx_connect_data/sam_2018-10-18 2008-20-51_BR006896_HSP90.pdf](https://owl.fish.washington.edu/Athaliana/qPCR_data/qPCR_reports/sam_2018-10-18%2008-20-51_BR006896_HSP90.pdf)



qPCR File (PCRD):



  * [cfx_connect_data/sam_2018-10-18 2008-20-51_BR006896_HSP90.pcrd](https://owl.fish.washington.edu/scaphapoda/qPCR_data/cfx_connect_data/sam_2018-10-18%2008-20-51_BR006896_HSP90.pcrd)



qPCR Data (CSV):



  * [sam_2018-10-18_08-20-51_BR006896_-__Quantification_Cq_Results_HSP90.csv](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2018-10-18_08-20-51_BR006896_-__Quantification_Cq_Results_HSP90.csv)





###### Amplication Plots



![](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2018-10-18%2008-20-51_HSP90_amp_plots.png)



###### Melt Curves



![](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2018-10-18%2008-20-51_HSP90_melt_plots.png)



* * *





###### Prx6



qPCR Report (PDF):





  * [sam_2018-10-18 2010-03-33_BR006896_Prx6.pcrd](https://owl.fish.washington.edu/Athaliana/qPCR_data/qPCR_reports/sam_2018-10-18%2010-03-33_BR006896_Prx6.pdf)



qPCR File (PCRD):



  * [sam_2018-10-18 2010-03-33_BR006896_Prx6.pcrd](https://owl.fish.washington.edu/scaphapoda/qPCR_data/cfx_connect_data/sam_2018-10-18%2010-03-33_BR006896_Prx6.pcrd)



qPCR Data (CSV):



  * [sam_2018-10-18_10-03-33_BR006896_-__Quantification_Cq_Results_Prx6.csv](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2018-10-18_10-03-33_BR006896_-__Quantification_Cq_Results_Prx6.csv)





###### Amplication Plots



![](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2018-10-18%2010-03-33_amp_plots_Prx6.png)



###### Melt Curves



![](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2018-10-18%2010-03-33_melt_plots_Prx6.png)
