INSPEcT: How to get the RNA dynamics for steady-state with INSPEcT minus
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MK • 0
@user-24137
Last seen 4 days ago
United Kingdom

Hi, a reviewer has asked us to compare some RNA dynamics between samples collected at steady-state. I have previously used INSPEcT+ with matched 4sU samples and now I want to try using INSPEcT- for some samples without matched 4sU samples.

I took a look at the paper Furlan et al., 2020 Genome Res, which states that INSPEcT "can now unveil RNA dynamics from steady-state or time course data, with or without the profiling of nascent RNA." In Table 1 of that paper, it says that INSPEcT- (without labelled RNA) can provided aggregate data for processing and degradation rates. This is what I'm looking to achieve.

I followed the docs to produce an INSPEcT noNascent obect (see code below). I was expecting there to be some output of the k3/k2 values available with this "INSPEcT_steadyNoNascent" object, but it seems like it has no slots for any rates, only 'premature', 'mature', and their associated variances.

Am I correct in understanding that the k3/k2 values (degradation/processing rate) could be derived by premature/mature values (equation shown in Fig. 1B of Furlan et al., 2020)? If so, this is easy enough for me to calculate myself with the 'premature' and 'mature' values stored in the INSPEcT_steadyNoNascent object. Thanks!


matureInspObj<-newINSPEcT(tpts = tpts
                           ,labeling_time = NULL
                           ,nascentExpressions = NULL
                           ,matureExpressions = totExp_plgem)

class(matureInspObj)
# "INSPEcT_steadyNoNascent"

tpts
[1] "0mock"    "60mock"
# tpts is a character vector with the names of the different steady-state conditions corresponding to the columns in the totExp_plgem matrices

# version: INSPEcT_1.26.0
INSPEcT • 20 views
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