I do not have delta delta Ct values because I have only untreated samples (the aim is to assess the abundance of a gene in a range of cell lines). I'm sure I can present deltaCt values in a table and explain that higher values mean lower abundance. But is there any good way to plot them, like in a bar chart? I thought about plotting 2^-deltaCt values but I haven't seen this in publications so I’m not sure if it is a good idea. I’ll appreciate any help.
Plotting as relative quantities should be fine (this is effectively what 2^dCt is), and this is used very frequently in the literature because it's far more immediately understandable (nobody likes doing log2 calculations in their heads just to understand a figure).
Alternatively, you could plot as absolute transcript numbers if you wish: just create a standard curve from a serial dilution of plasmid or PCR product of your template and read off your sample Cts from that (remember to double your final value to account for cDNA being single stranded).
Thank you John Hildyard. I always see researchers plotting 2^-deltadeltaCt but when I know they do not have treated x untreated samples, I see that they plot "relative expression" but I was not sure if it represented 2^-deltaCt. That makes things easier, plus the bars look good as well! Thanks.
Dear Caroline
if you just take one of your untreated samples and assign the expression in that sample as '1' then you can plot other cell lines relative to this one sample. Plot as a bar chart with error bars representing +/- 1 x SD; This tends to be the standard convention
I have has situations where my 'calibrator' = sample where you assign the expression as '1' and then plot relative expression of other samples has been one type of cell line or alternatively my untreated control. It doesn't really matter as long as the comparison makes sense in the context of your gene and cell line
See attached where I have compared the expression of a particular gene in 1 cell line - assigned as '1' with another cell line
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