Get Standardized protein concentration (ug/mL) protein_test<-read.csv(file="/Users/oliviacattau/Documents/data/BSA_Nov22_mantle+gill.csv") A<-protein_test$Absorbance...570..1.0s...A. protein<-(A*2500)-1700 #from GLM standard equation protein_test<-cbind(protein_test, protein) protein_test<-protein_test[protein_test$protein >= 0,] M1= subset(protein_test, protein_test$label=='M_1') M2= subset(protein_test, protein_test$label=='M_2') G1= subset(protein_test, protein_test$label=='G_1') G2= subset(protein_test, protein_test$label=='G_2') M_1<-mean(M1$protein) M_2<-mean(M2$protein) G_1<-mean(G1$protein) G_2<-mean(G2$protein) protein_list<-c(M_1, M_2, G_1, G_2) tissue_label<-c("mantle_1", "mantle_2", "gill_1", "gill_2") protein_content<-as.table(cbind(tissue_label, protein_list)) print(protein_content) CS activity (nmol/min/uL) CS_Nov22<-read.csv(file="/Users/oliviacattau/Documents/data/CS_Nov22.csv") CS_Nov22<-CS_Nov22[!(CS_Nov22$Well=="B06" | CS_Nov22$Well=="B03"),] A<-CS_Nov22$Absorbance...405..0.1s...A. blank=subset(CS_Nov22, CS_Nov22$label==0) zero<-mean(blank$A) new_A<-A-0.0664 #subtract blank well CS_Nov22<-cbind(CS_Nov22, new_A) M1= subset(CS_Nov22, CS_Nov22$label=='m1') M2= subset(CS_Nov22, CS_Nov22$label=='m2') G1= subset(CS_Nov22, CS_Nov22$label=='g1') G2= subset(CS_Nov22, CS_Nov22$label=='g2') CS_tissue<-rbind(M1, M2, G1, G2) #plot data library(ggplot2) GSH<-ggplot(data=CS_tissue)+geom_point(aes(x=as.factor(Time), y=new_A, color=label))+theme_bw() GSH time_0<-subset(CS_tissue,CS_tissue$Repeat==1) time_30<-subset(CS_tissue, CS_tissue$Repeat==30) time_0$delta<-time_30$new_A-time_0$new_A #delta OD to get GSH standard_CS<-read.csv(file="/Users/oliviacattau/Documents/data/standard_curve_small.csv") cs_model<-lm(standard_CS$New_A~(standard_CS$GSH.well)) summary(cs_model) cs_equation<-paste("y=",coef(cs_model)[[1]], "+", coef(cs_model)[[2]], "*x") cs_equation time_0$nmol<-0.0753742256190483 + 0.0465124174107143*delta #equation from GSH standard curve standard_cs_plot<-ggplot(data=standard_CS,(aes(x=New_A, y=GSH.well)))+geom_point()+geom_smooth(method="lm", se=FALSE, formula = y ~x)+xlab("OD")+ylab("GSH")+theme_bw()+stat_regline_equation(label.x=1, label.y=8) standard_cs_plot #get CS activity B<-21*delta-0.73 V<-50 #uL D<-1 time<-27 #min SampleCSactivity<-B/(time*V)*D time_0$CSactivity<-SampleCSactivity #(nmol/min/uL) |tissue_label| OD (delta A)| GSH nmol| CSactivity (nmol/min/uL)| protein (ug/mL)| protein (ug/uL)| relative CS activity (nmol/min/ug)| |—|—|—|—|—|—|—| |mantle_1| 0.116| 1.706|...
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BSA check
bovine serum albumin (BSA) test
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Lab work Mondays
Check to see if BioRad bovine serum albumin (BSA) Protocol works with oyster tissue
link to BSA protocol
if it does, use the results from the assay run to calculate total protein concentration per sample (ug/mL)
I am going to want to use various dillutions of the samples so I can get the protein concentration in the linear range (<2000 ug/mL)
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Goals for November
experimental work
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Functional Annotation of P. Generosa transcriptome
Inspect P. generosa genome for candidate genes. First step is to extract output data from kallisto:
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