[mira_talk] Re: Collecting DNA from bacterial cultures, was: suggestion for sequencing companies

  • From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Fri, 13 Apr 2012 09:51:58 +0100

On Thu, Apr 12, 2012 at 9:19 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On Apr 12, 2012, at 22:16 , 000.calabi.yau.000@xxxxxxxxxxxxxx wrote:
>> here is an example:
>> Srivatsan A, Han Y, Peng J, et al. High-precision, whole-genome sequencing of
>> laboratory strains facilitates genetic studies. PLoS genetics. 
>> 2008;4(8):e1000139.
>> Coverages with varying degree of happiness...
>
> Bingo! That's the one I was thinking of. Thanks Markus.
>
> B.

Open access too :)

Srivatsan A, Han Y, Peng J, Tehranchi AK, Gibbs R, et al. (2008) High-Precision,
Whole-Genome Sequencing of Laboratory Strains Facilitates Genetic Studies.
PLoS Genet 4(8): e1000139. doi:10.1371/journal.pgen.1000139

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000139

The "smile effect" is very clear in Figure 1, quote from the caption:

>>> NCIB 3610 and relA-* were grown to mid log phase, while the other
>>> strains were grown to stationary phase. The different shapes of the
>>> coverage maps might be partly due to these differences in growth
>>> phases. doi:10.1371/journal.pgen.1000139.g001

And from the main text:

>>> The shape of the read coverage curve varies depending on the growth
>>> condition, and is almost flat for stationary phase cells (Figure 1A, C, D, 
>>> E),
>>> indicating that these cells have completely replicated DNA, as expected.
>>> Interestingly, the coverage is slightly higher around the replication 
>>> origin,
>>> and is lowest near the replication terminator, likely because a small
>>> sub-population of cells were still replicating DNA. Importantly, in an
>>> actively replicating sample (Figure 1B, F), we found a much higher
>>> read coverage near the origin (at genomic position 0/4.2 Mbp) rather
>>> than the terminus region (at genomic position 2.1 Mbp).

I haven't found the paper Alan Mcnally mentioned though.

Thanks all!

Peter

-- 
You have received this mail because you are subscribed to the mira_talk mailing 
list. For information on how to subscribe or unsubscribe, please visit 
http://www.chevreux.org/mira_mailinglists.html

Other related posts:

  1. Home
  2. mira_talk
  3. Archive
  4. 04-2012