--- 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 -20oC 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)