---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
layout: post
title: qPCR - C.gigas PolyIC Diploid MgCl2
date: '2023-08-17 06:38'
tags: 
  - qPCR
  - CFX Connect
  - Crassostrea gigas
  - Pacific oyster
  - polyIC
categories: 
  - 2023
  - Miscellaneous
---
Using [diploid MgCl<sub>2</sub> control cDNA from 20230816](https://robertslab.github.io/sams-notebook/posts/2023/2023-08-16-Reverse-Transcription---C.gigas-PolyIC-Diploid-MgCl2/), performed qPCR on the following [primer sets selected by Steven](https://github.com/RobertsLab/resources/issues/1686) (GitHub Issue), along with `Cg_Actin` as a potential normalizing gene:

| SRID   | Primer              |
|--------|---------------------|
| 1170/1 | Cg_Actin            |
| 1830/1 | Cg_DICER            |
| 1172/3 | Cg_GAPDH            |
| 1832/3 | Cg_IRF2             |
| 1834/5 | Cg_SACSIN           |
| 1828/9 | Cg_VIPERIN          |
| 1826/7 | Cg_cGAS             |
| 1383/4 | Cg_citrate_synthase |

qPCR calcs:

- [20230817 - qPCR Calcs polyIC gigas cDNA](https://docs.google.com/spreadsheets/d/1z5UOomTMgyO6ZKArKC1tP6kAum7OXgc2JT2YwXZF56M/edit?usp=sharing) (Google Sheet)


Reactions were run on white, low-profile, 96-well qPCR plates (USA Scientific). A total of two plates were run. One was run on a CFC Connect (BioRad) and the other on a CFX96 (BioRad). See the qPCR Report in the [RESULTS](#results) section below for cycling params, plate layouts, etc.

Due to time and sample constraints, samples were just run in _singular_. No template controls were run in duplicate.


---

# RESULTS

Brief note(s) on results:

- Sample D14 comes up later than the other three samples in all of the primer sets.

- Have not compared to [the diploid poly:IC-inject qPCRs results](https://robertslab.github.io/sams-notebook/posts/2023/2023-07-26-qPCR---C.gigas-polyIC/) (Notebook) yet.


qPCR Results file (CSV)

- [sam_2023-07-26_13-06-28_Connect-Quantification%20-Cq-Results.csv](sam_2023-08-17_11-58-46_Connect-Quantification-Cq-Results.csv)

qPCR Data file (QPCRD - CFX Maestro required)

- [sam_2023-07-26_13-06-28_Connect.pcrd](https://owl.fish.washington.edu/scaphapoda/qPCR_data/cfx_connect_data/sam_2023-08-17_11-58-46_Connect.pcrd)

qPCR Report (PDF)

- [sam_2023-07-26_13-06-28_Connect.pdf](https://owl.fish.washington.edu/Athaliana/qPCR_data/qPCR_reports/sam_2023-08-17_11-58-46_Connect.pdf)


---

#### PLOTS






| SR ID  | Primer              | Amplification Plot                                                                                                                                               | Melt Curve                                                                                                                                                        |
|--------|---------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 1830/1 | Cg_DICER            | ![Cg_DICER amplification plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-08-17_11-58-46_Connect-Cg_DICER-amp-plots.png)                       | ![Cg_DICER melt plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-08-17_11-58-46_Connect-Cg_DICER-melt-plots.png)                       |
| 1172/3 | Cg_GAPDH            | ![Cg_GAPDH amplification plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-08-17_11-58-46_Connect-Cg_GAPDH-amp-plots.png)                       | ![Cg_GAPDH melt plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-08-17_11-58-46_Connect-Cg_GAPDH-melt-plots.png)                       |
| 1832/3 | Cg_IRF2             | ![Cg_IRF2 amplification plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-08-17_11-58-46_Connect-Cg_IRF2-amp-plots.png)                         | ![Cg_IRF2 melt plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-08-17_11-58-46_Connect-Cg_IRF2-melt-plots.png)                         |
| 1834/5 | Cg_SACSIN           | ![Cg_SACSIN amplification plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-08-17_11-58-46_Connect-Cg_SACSIN-amp-plots.png)                     | ![Cg_SACSIN melt plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-08-17_11-58-46_Connect-Cg_SACSIN-melt-plots.png)                     |
| 1828/9 | Cg_VIPERIN          | ![Cg_VIPERIN amplification plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-08-17_11-58-46_Connect-Cg_VIPERIN-amp-plots.png)                   | ![Cg_VIPERIN melt plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-08-17_11-58-46_Connect-Cg_VIPERIN-melt-plots.png)                   |
| 1170/1 | Cg_actin            | ![Cg_actin amplification plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-08-17_11-58-46_Connect-Cg_actin-amp-plots.png)                       | ![Cg_actin amplification plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-08-17_11-58-46_Connect-Cg_actin-melt-plots.png)                       |
| 1826/7 | Cg_cGAS             | ![Cg_cGAS amplification plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-08-17_11-58-46_Connect-Cg_cGAS-amp-plots.png)                         | ![Cg_cGAS amplification plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-08-17_11-58-46_Connect-Cg_cGAS-melt-plots.png)                         |
| 1383/4 | Cg_citrate_synthase | ![Cg_citrate_synthase amplification plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-08-17_11-58-46_Connect-Cg_citrate_synthase-amp-plots.png) | ![Cg_citrate_synthase amplification plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-08-17_11-58-46_Connect-Cg_citrate_synthase-melt-plots.png) |