--- 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 MgCl2 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) |