Institute Genomic Analysis Laboratory
For the supplementary Table S10, the name of the table is "Table S10:
Arabidopsis transcripts only observed upon exosome depletion". So does
these data mean that comparing to previous tiling array results (as "Arabidopsis Tiling Array Transcriptome" shown on
http://signal.salk.edu/cgi-bin/atta), the listed sequences are not expressed before
but now expressed upon exosome depletion? or they are only not expressed so much previously?
In the case of this analysis, many of these transcripts were not
detected (determined to be not expressed) in our previous tiling array
experiments, but also some of these regions did show very low levels
of expression that go up in a statistically significant amount upon
exosome depletion. Additionally, these regions were determined to be
intergenic based on the TAIR annotation of "genes".
Is it the reason which makes many short sequences in the table
the second one "10309174-10309180"? If so, then after combining
sequences with the initial expressed segments, they will be much
These up-regulated regions are short in nature due to the extremely
stringent criteria that we used for our analysis (which can be found
in the supplemental material that accompanies our manuscript).
However, for designation of a locus. all regions falling in the same
interegenic space were combined as a single locus, which is why ~1000
regions correspond to far less exosome-specific loci.
3. Q: You gave out an example sequence in Figure 6G, could we have
the its base components or its coordinates on the genome?
The genomic coordinates for the example used in Figure 6G are
chr2:13509319-13513609, which corresponds to an ~4300 bp sense/anti-
sense transcript pair. If you go to http://signal.salk.edu/cgi-bin/exosome
and type in these coordinates you will see that there are large
transcription units emanating from both strands.