Talk:SHAPE

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SHAPE entry

Hi Nando

(not sure if this is where this talk should go in wiki)

For your new SHAPE entry, I like the information so far. Perhaps we should note that SHAPE is one of several chemical methods used for RNA probing; as I believe DMS and perhaps others shows up in the data (RMDB, etc.). 

 


 

Typically, discussions about a page should go in its dedicated discussion page, in this case Talk:SHAPE.

Agreed. There are still a few articles missing on the topic of secondary structure determination...

And I was also thinking that the EteRNA-centric side of the topic should be mentioned somewhere, like how lab results are presented in the interface (shades of blue and yellow) and their relation to design scores.

-- ElNando888 (talk) 05:14, 11 July 2013 (UTC)

Added reference to SHAPE in Lab. not much but a sort of stub

 

Scope

I'm a little unsure whether we should put all the informations we have about the Cloud Lab inside this SHAPE article. I actually love this overview you wrote down, Omei, it's better presented than I could have ever done. But while the content is undoubtedly valuable, I'm not sure if we should be putting all of this here. Personally, I'd rather stay on-topic and limit this content to 

  • its nature (chemical structure of the probe itself)
  • details about the chemical reaction
  • the consequence of bulky adducts (block the RT, results in "truncated" cDNA)
  • the measurement method(s)

 

Thoughts?

-- ElNando888 (talk) 08:43, 3 September 2013 (UTC)


Good question; I certainly don't have any definitive answer.

I have only a murky notion of "What are the most important things an EteRNA player needs to understand if they are going to move beyound the notion that the SHAPE data is a direct measurement of the extent to which a base is either paired or not paired?".  Given that I tend to approach program design (as opposed to program implementation) top-down, that's generally how I write as well.

As for specifics, I had been thinking that since the actual measurement (i.e. counting) is made on DNA, not RNA, someone had to at least know what reverse transcription was if they were were going to understand the measurement process at all.  On the other hand, DNA amplification (PCR) and forwardl transcription are important parts of the experimental process, but perhaps are not so necessary in terms of understanding the results.

It may well be that the article I've been envisioning shouldn't be the main "SHAPE" entry in the wiki, but rather have a title like "The EteRNA Player's Guide to Understanding Lab SHAPE Data".  On the other hand, if we break it out now, we'll lose some of the synergy that comes form working on something together.  I propose we continue to treat it as one page for now, each adding, editing and reorganizing according to what we think is important.  If and when it becomes apparent two document -- speaking to different audiences -- is better, we can split it.

Omei (talk) 22:26, 3 September 2013 (UTC)


Agreed. And I really like the way you go about this :)

At 2am, I tend to not be at my best though, so I will refrain from touching anything until tomorrow ;)

-- ElNando888 (talk) 00:10, 4 September 2013 (UTC)


 

RMDB

It seems, the database lists annotations about the experimental conditions. For instance, on http://rmdb.stanford.edu/repository/detail/ETERNA_R76_0000 I can find:

annotation name value
chemical  MgCl2:10mM
chemical  HEPES:50mM(pH8.0)
MAPseq  tag:RTB001
modifier  1M7
temperature  24C
processing  overmodificationCorrectionExact
processing  ligationBiasCorrection:0.174
processing  backgroundSubtraction
processing  normalization:GAGUA

 

Among the questions I'd like to ask to the labcoats:

  • details about the "processing" entries, which are obviously related to the numerical data processing (in which order, details of algorithms)
    Edit: I just discovered that https://sites.google.com/site/rmdbwiki/hitrace paragraph 10 gives a little information about background subtraction and overmodification correction. 
  • how does 10mM MgCl2 compare with 1M NaCl (which is the assumption of the Turner parameters if I recall correctly)
    Edit: some in-depth information here: http://vfold.missouri.edu/paps/es.06BJ.pdf

 

-- ElNando888 (talk) 15:31, 4 September 2013 (UTC)


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