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ISMB/ECCB
ISMB/ECCB Stockholm 2009: ISMB/ECCB
HL58: Caroline Friedel - A new method for high-resolution gene expression analysis
July 1, 2009 - Comment - Share
Metabolic tagging of newly transcribed RNA - Diego M. Riaño-Pachón
Able to measure decay and de novo synthesis - Diego M. Riaño-Pachón
this methods tries to solve a long standing problem in transcriptomics, ] - Diego M. Riaño-Pachón
i.e., bias for differential expression of short-lived RNAs - Diego M. Riaño-Pachón
and thus in subsequent analysis - Diego M. Riaño-Pachón
solution is to perform gene expression analysis of newly transcribed RNA - Diego M. Riaño-Pachón
using 4-thiouridine - Diego M. Riaño-Pachón
after tagging,normal analysis techniques for microarray or RNA-seq can be sused - Diego M. Riaño-Pachón
bur of course new methods could exploit features specific for the tagging of newly transcribed RNA - Diego M. Riaño-Pachón
directly observe changes in de novo transscription - Diego M. Riaño-Pachón
observe changes relative to basal transcription - Diego M. Riaño-Pachón
no bias for short-lived trnascripts - Diego M. Riaño-Pachón
It can offer evidence of the stability of RNA (decay) - Diego M. Riaño-Pachón
(room pretty full) - Diego M. Riaño-Pachón
New methods for normalization are necessary when comparing total RNA to newly transcribed RNA - Diego M. Riaño-Pachón
after normalization the RNA half-life can be calculated using and exponential decay model - Diego M. Riaño-Pachón
the exp. technique with the new normalization increases the precision on the estimation of RNA half-life - Diego M. Riaño-Pachón
Q: is 4-thiouridine toxic to the cell? A: No, at least in the time points looked at. - Diego M. Riaño-Pachón
Q: is there a bias towards transcript length? A: They did not see any significant correlation - Diego M. Riaño-Pachón
(only to get the blog on top of the ISCB portal site; the figures messed up our layout) - Reinhard Schneider