Ruler array paper edits:
1.) We detected a total of 114 additional indels between the genomes beyond the 106 selected for
conformation based on the _nal _1278b assembly (see supplemental material). (This portion is much
more clearly written now) One suggestion is explicitly state the size of the 114 additional indels that were
found. Reading this it sounds as if they might be over 100 base pairs but I cannot be certain.
2.) Two ruler array replicates identified roughly 75% of the PCR confirmed changes (28 and 25 of 36)
and many (28 and 20 out of 114) of the set of 100bp changes. Why do we only find 20-15% of the
changes in the set of 114? Is this because we believe that many of these changes are in fact not real and
thus the ruler array is not calling them correctly or are we just not finding them? If so this should be stated
and potentially tested if we never ran those PCRs. If we are just not finding them that is weird because I
would predict that we should find an equal percentage of the 36 and the 114 if an equal percentage of the
differences are in fact real and the size of the difference is roughly the same. Either way this statement
needs a small amount of clarification.
3.) These repeats may also cause reduced signal in downstream sequence. This statement could be
eliminated. I think that it is obvious that if the polymerase falls off more readily at those repeats then it will
cause decreased signal downstream, and I don’t know if it really says anything about the ruler arrays
utility. If you think that it needs to be stated then I have no problem leaving it, just an opinion. I have
more comments on this later on in the figures section.
4.) Second, an insertion may carry a restriction site that counters an expected intensity drop. I am not
crazy about the word counters here. I think something more along the lines of “complicates the analysis
of an expected intensity drop”. Counters seems to imply something more specific where as a we want to
convey that if a restriction site is introduced that we do not know about it can complicate the analysis.
5.) I think that mentioning the high false positive rate at the end here may be enough explanation. If we
are not trying to sell this as technology that is going to come in and blow up the existing paradigm but
instead complement a robust infrastructure that is already in place I think that the false positive rate can
be left as something to be worked out in the next generation of the technology.
6.) Adapter Design paragraph has some weird spacing issues. This may have just come through in my
copy, just make it looks like you want it to on your end.
7.) 65 C needs the little circle thing (don’t know what it is called)
8.) DAB is funded by A.L.S. grant PF-09-072-01-MBC Should be ACS
9.) At the end of the citations there is a big title Figure Legends, it does not seem to be attached to the
figures and if it is meant as a title for the figure and legends we should probably put Figures and Legends
or Figures and Figure Legends. If the Journal wants it designated as Figure Legend than obviously
leave.
10.) Figure 1 came through weird on my computer, many of the words look jagged. Not sure why, just
make sure they look clean on the copy you send out. Also the extension product lines are all different
thicknesses and the letter e is much smaller than a, b, c, and d not sure how that happened might be
something weird in the translation to my computer.
11.) Figure 2, doesn’t matter to me but the journal will probably make you label all three EcoR1 sites or
label a single EcoRI site.
12.) Figure 3, label site might want to be changed to restriction site, we don’t people to think that the we
are only labeling at the beginning of the transcript but instead throughout.
13.) Figure 4, chromosome IV is labeled two different ways 4 and IIII both of which seem weird. I
personally would go with IV since in figure 2 we start with Roman Numerals and this is carried through in
other figures.
14.) Figure 5, I don’t know if two examples are necessary. If so they should be labeled a and b. Also
where the AT repeats are in the trace should be highlighted so that very obvious where to look to find
these changes. The bottom panel gene names are very small as well. In addition the upper panel is a bit
odd because the intensity ratio jumps but then settles back down towards a ratio of 1. This suggests that
the polymerase that stays on is more processive, which is probably true or that polymerase is reengaging
unlikely but difficult to rule out. Either way it is a bag of worms we don’t need to get into thus in my
opinion we should just clean up the font in the bottom panel an only show that one. These are just
opinions and you have other ideas about better ways to address this I would like to hear them. This
comment goes along with what I had said in comment 3.
Let me know if you have any questions or if you would like to discuss any of these comments.