光遗传学：光遗传学项目的分析脚本

% Here, I want to compare two optogenetics datasets with or without % illumination with the blue light. % What I ultimately want to have is Figure 4, Garcia 2013 analysis for % these optogenetic Bcd constructs driving the hbP2P.V1-MS2-lacZ % expression. %% Load the datasets (using LoadMS2sets) NoBlueData = LoadDataSets('noBlue') BlueData = LoadDataSets('Blue') %% Plot the accumulated mRNA over AP, in nc13 and nc 14. % I will use the IntegratemRNA.m to calculate the accumulated mRNA [TotalProd_NoBlue,TotalProdError_NoBlue,TotalProdN_NoBlue,... MeanTotalProd_NoBlue,SDTotalProd_NoBlue,SETotalProd_NoBlue] = IntegratemRNA([NoBlueData.Particles],1,1); [TotalProd_Blue,TotalProdError_Blue,TotalProdN_Blue,... MeanTotalProd_Blue,SDTotalProd_Blue,SETotalProd_Blue] = IntegratemRNA([BlueData.Particles],1,1); %% Plot to compare different quantities % 1) Total mRNA per nucleus at nc 13 figure(1) hold on errorbar(0:0.025:1, nanmean(TotalProd_NoBlue(1:3,:,13),1),nanmean(TotalProdError_NoBlue(1:3,:,13),1),'r')%,TotalProdError_NoBlue(1,:,13)./sqrt(TotalProdN_NoBlue(1,:,13)),'r') errorbar(0:0.025:1, nanmean(TotalProd_Blue(1:3,:,13),1),nanmean(TotalProdError_Blue(1:3,:,13),1),'b')%,TotalProdError_Blue(1,:,13)./sqrt(TotalProdN_Blue(1,:,13)),'b') hold off xlabel('AP bin') ylabel('Integrated mRNA (AU)') title('Integrated mRNA over AP @ nc 13') %legend('Control','Export') % plot settings, like a title, x,y labels, etc. % 2) Total mRNA per nucleus at nc 14 figure(2) hold on errorbar(0:0.025:1, nanmean(TotalProd_NoBlue(1:3,:,14),1),nanmean(TotalProdError_NoBlue(1:3,:,14),1),'r')%,TotalProdError_NoBlue(1,:,14)./sqrt(TotalProdN_NoBlue(1,:,14)),'r') errorbar(0:0.025:1, nanmean(TotalProd_Blue(1:3,:,14),1),nanmean(TotalProdError_Blue(1:3,:,14),1),'b')%,TotalProdError_Blue(1,:,14)./sqrt(TotalProdN_Blue(1,:,14)),'b') hold off xlabel('AP bin') ylabel('Integrated mRNA (AU)') title('Integrated mRNA over AP @ nc 14') legend('Control','Export') % 3) %% Plot single embryos figure(1) hold on %errorbar(0:0.025:1, nanmean(TotalProd_NoBlue(1:3,:,13),1),nanmean(TotalProdError_NoBlue(1:3,:,13),1),'r')%,TotalProdError_NoBlue(1,:,13)./sqrt(TotalProdN_NoBlue(1,:,13)),'r') errorbar(0:0.025:1, TotalProd_NoBlue(1,:,13),TotalProdError_NoBlue(1,:,13),'r')%,TotalProdError_NoBlue(1,:,13)./sqrt(TotalProdN_NoBlue(1,:,13)),'r') errorbar(0:0.025:1, TotalProd_NoBlue(2,:,13),TotalProdError_NoBlue(2,:,13),'r') errorbar(0:0.025:1, TotalProd_NoBlue(3,:,13),TotalProdError_NoBlue(3,:,13),'r') %errorbar(0:0.025:1, nanmean(TotalProd_Blue(1:3,:,13),1),nanmean(TotalProdError_Blue(1:3,:,13),1),'b')%,TotalProdError_Blue(1,:,13)./sqrt(TotalProdN_Blue(1,:,13)),'b') errorbar(0:0.025:1, TotalProd_Blue(1,:,13),TotalProdError_Blue(1,:,13),'b')%,TotalProdError_NoBlue(1,:,13)./sqrt(TotalProdN_NoBlue(1,:,13)),'r') errorbar(0:0.025:1, TotalProd_Blue(2,:,13),TotalProdError_Blue(2,:,13),'b') errorbar(0:0.025:1, TotalProd_Blue(3,:,13),TotalProdError_Blue(3,:,13),'b') xlabel('AP bin') ylabel('Integrated mRNA (AU)') title('Integrated mRNA over AP @ nc 14') figure(2) hold on %errorbar(0:0.025:1, nanmean(TotalProd_NoBlue(1:3,:,13),1),nanmean(TotalProdError_NoBlue(1:3,:,13),1),'r')%,TotalProdError_NoBlue(1,:,13)./sqrt(TotalProdN_NoBlue(1,:,13)),'r') errorbar(0:0.025:1, TotalProd_NoBlue(1,:,14),TotalProdError_NoBlue(1,:,14),'r')%,TotalProdError_NoBlue(1,:,13)./sqrt(TotalProdN_NoBlue(1,:,13)),'r') errorbar(0:0.025:1, TotalProd_NoBlue(2,:,14),TotalProdError_NoBlue(2,:,14),'r') errorbar(0:0.025:1, TotalProd_NoBlue(3,:,14),TotalProdError_NoBlue(3,:,14),'r') %errorbar(0:0.025:1, nanmean(TotalProd_Blue(1:3,:,13),1),nanmean(TotalProdError_Blue(1:3,:,13),1),'b')%,TotalProdError_Blue(1,:,13)./sqrt(TotalProdN_Blue(1,:,13)),'b') errorbar(0:0.025:1, TotalProd_Blue(1,:,14),TotalProdError_Blue(1,:,14),'b')%,TotalProdError_NoBlue(1,:,13)./sqrt(TotalProdN_NoBlue(1,:,13)),'r') errorbar(0:0.025:1, TotalProd_Blue(2,:,14),TotalProdError_Blue(2,:,14),'b') errorbar(0:0.025:1, TotalProd_Blue(3,:,14),TotalProdError_Blue(3,:,14),'b') xlabel('AP bin') ylabel('Integrated mRNA (AU)') title('Integrated mRNA over AP @ nc 14') %% RNAP II Loading rate (by FitMeanAPSymmetric) % Also average this rate, and calculate the total SD for all embryos. noBlueFit = load('D:\Data\YangJoon\LivemRNA\Data\DynamicsResults\2018-02-05-P2PV1-MCP-mCherry-LEXY-mCi-Bcd_noBlue\MeanFits.mat') BlueFit = load('D:\Data\YangJoon\LivemRNA\Data\DynamicsResults\2018-02-05-P2PV1-MCP-mCherry-LEXY-mCi-Bcd_Blue2\MeanFits.mat') noBlueFit_nc13 = nan(1,41); noBlueFit_nc14 = nan(1,41); BlueFit_nc13 = nan(1,41); BlueFit_nc14 = nan(1,41); noBlueFit_nc13_SD = nan(1,41); noBlueFit_nc14_SD = nan(1,41); BlueFit_nc13_SD = nan(1,41); BlueFit_nc14_SD = nan(1,41); for i=8:22 noBlueFit_nc13(i) = noBlueFit.FitResults(i,2).RateFit; noBlueFit_nc13_SD(i)=noBlueFit.FitResults(i,2).SDRateFit; noBlueFit_nc14(i) = noBlueFit.FitResults(i,3).RateFit; noBlueFit_nc14_SD(i) = noBlueFit.FitResults(i,3).SDRateFit; BlueFit_nc13(i) = BlueFit.FitResults(i,2).RateFit; BlueFit_nc13_SD(i) = BlueFit.FitResults(i,2).SDRateFit; BlueFit_nc14(i) = BlueFit.FitResults(i,3).RateFit; BlueFit_nc14_SD(i) = BlueFit.FitResults(i,3).SDRateFit; end %% Plot RNAP II loading rate hold on errorbar(0:0.025:1,noBlueFit_nc13,noBlueFit_nc13_SD,'r') errorbar(0:0.025:1,BlueFit_nc13,BlueFit_nc13_SD,'b') hold off xlabel('AP bin') ylabel('RNAP Loading Rate (AU)') title('RNAP Loading Rate @ nc 13') legend('Control','Export') figure(2) hold on errorbar(0:0.025:1,noBlueFit_nc14,noBlueFit_nc14_SD,'r') errorbar(0:0.025:1,BlueFit_nc14,BlueFit_nc14_SD,'b') xlabel('AP bin') ylabel('RNAP Loading Rate (AU)') title('RNAP Loading Rate @ nc 14') legend('Control','Export') %% Things to check % 1) offset of MCP-mCherry % noBlue = load('D:\Data\YangJoon\LivemRNA\Data\DynamicsResults\2018-01-11-P2PV1-MCP-mCherry-LEXY-mCi-Bcd_noBlue\CompiledParticles.mat') % Blue = load('D:\Data\YangJoon\LivemRNA\Data\DynamicsResults\2018-01-15-P2PV1-MCP-mCherry-LEXY-mCi-Bcd_Blue\CompiledParticles.mat') % % hold on % plot(noBlue.ElapsedTime(noBlue.nc13:noBlue.nc14),noBlue.MeanOffsetVector(noBlue.nc13:noBlue.nc14)) % plot(Blue.ElapsedTime(Blue.nc13-21:Blue.nc14-21),Blue.MeanOffsetVector(Blue.nc13:Blue.nc14)) % 2) Bicoid concentration % 3) Averaging the Rate fit for multiple embryos with proper error bar % 4) Find the AP bins where the Bicoid concentration profile is similar % (for Blue and no Blue), then see how the output looks like. %% Nuclear fluorescence % This also needs averaging over multiple embryos. % Bcd concentration (to check whether it was homozygous) % noBlueNuc = load('D:\Data\YangJoon\LivemRNA\Data\DynamicsResults\2018-02-05-P2PV1-MCP-mCherry-LEXY-mCi-Bcd_noBlue\CompiledNuclei.mat') % BlueNuc = load('D:\Data\YangJoon\LivemRNA\Data\DynamicsResults\2018-02-05-P2PV1-MCP-mCherry-LEXY-mCi-Bcd_Blue2\CompiledNuclei.mat') % Define the time points (for synchronization) for i=1:length(NoBlueData) noBlue_nc13(i) = NoBlueData(i).Particles.nc13; noBlue_nc14(i) = NoBlueData(i).Particles.nc14; NucFluo_noBlue{i} = NoBlueData(i).Nuclei.MeanVectorAP(noBlue_nc13(i):end,:); NucFluo_STD_noBlue{i} = NoBlueData(i).Nuclei.SDVectorAP(noBlue_nc13(i):end,:); NucFluo_N_noBlue{i} = NoBlueData(i).Nuclei.NParticlesAP(noBlue_nc13(i):end,:); end for i=1:length(BlueData) Blue_nc13(i) = BlueData(i).Particles.nc13; Blue_nc14(i) = BlueData(i).Particles.nc14; NucFluo_Blue{i} = BlueData(i).Nuclei.MeanVectorAP(Blue_nc13(i):end,:); NucFluo_STD_Blue{i} = BlueData(i).Nuclei.SDVectorAP(Blue_nc13(i):end,:); NucFluo_N_Blue{i} = BlueData(i).Nuclei.NParticlesAP(Blue_nc13(i):end,:); end % Averaging the Nuc fluo over multiple embryos % For all timepoints, for all embryos % No Blue NucFluo_NoBlueTotal=zeros(71,41); NucFluo_Var_NoBlue=zeros(71,41); for i=1:length(NoBlueData) NucFluo_NoBlueTotal = NucFluo_NoBlueTotal + NucFluo_noBlue{i}(1:71,:); NucFluo_Var_NoBlue = NucFluo_Var_NoBlue + NucFluo_STD