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Frequently Asked Questions
 
1. Q: 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?

   A: 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".
 
 
2. Q: Is it the reason which makes many short sequences in the table such as the second one "10309174-10309180"? If so, then after combining these sequences with the initial expressed segments, they will be much longer?

   A: 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?

   A: 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.
 
 

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