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5.4 years ago
CY
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750
Gene expression is a dynamic process. RNA-Seq expression may vary at different time point. I am curious how large the fluctuation is. Is the RNA-Seq profile at single time point be representative? Is there any study done on that?
You can almost never be sure a single measurement is representative because of all sources of variation such as biological and measurement noises. This is why there are replicates in a study. You should define what a time point is because how precisely/reproducibly you sample from a "time point" can explain some of the variations between measurements at a given time point. For example, if your time point is an interval of several hours (such as a cell cycle phase or a developmental stage) you could get different results based on when in that interval your sample is.
My 'time point' is exactly the time point of sample get extracted. Specifically, I am curious about the degree of fluctuation of RNA-Seq profile of a tumor sample between different time point (say, I extract a piece of sample today and extract another piece tomorrow from the same patient (ignore the heterogeneity between sample)).
Today and tomorrow don't define time points very precisely. I can imagine that today, you take a sample two hours after the patient has taken their medication but tomorrow, you'll take the sample just before. This is also without taking into account the effect that taking the first sample can have on the tumor. Maybe there are standard procedures to control for this kind of things in the clinics but my point is that in general temporal variability hides a lot of other sources of heterogeneity.
My concern is the validity of RNA-Seq profile. However, I guess it is ok since RNA-Seq has been widely accepted.
That is quite impossible to answer because it depends on the system you are analysing and how quickly it evolves. A steady state system will probably not be affected by small differences in time whereas fx a infection will develop very fast. Furthermore it also depends on the technology you use, in single cell RNASeq data we can see gene busting (that many genes are not continuously transcribed but rather have subsequent periods of on/off) whereas these effects are averaged out in bulk data.
Yes. I thought about this for a long time because the validity of entire RNA-Seq profile depends on it. Since RNA-Seq has been widely accepted. I can only imagine that the fluctuation of RNA-Seq profile throught time is not that large.