From listmaster animalgenome.org Wed Jan 15 13:41:26 2020
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From: =?iso-8859-1?Q?Tomas_Klingstr=F6m?= <tomas.klingstromslu.se>
Subject: Re: DNA extraction from cattle hair for WGS
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To: Members of AnGenMap <angenmapanimalgenome.org>
Date: Wed, 15 Jan 2020 13:41:26 -0600
Hello Laura
We've been doing some work on the general characteristics of DNA
fragmentation and for degradation after DNA extraction the three simple
things to test is to add a chelating agent, use EDTA + ethanol (never only
EDTA) and check the pH of the storage buffer (even if the last seems
unlikely given the time frame).
We are revising the structure of the paper but the full preprint may be of
help when checking what may be going wrong in your stabilisation of the
sample: https://www.biorxiv.org/...0.1101/254276v3.full
If you have a copy of the protocol you are using or a link to the kit
instructions you are following it would be very appreciated as I am curious
about the issue.
Best regards
-----------------------------------
Tomas Klingstrm, PhD
Coordinator of Gigacow
Sveriges lantbruksuniversitet
Swedish University of Agricultural Sciences
SLU Department of Animal Breeding and Genetics.
Mobile: +46 73-720 31 54
tomas.klingstromslu.se, http://www.slu.se
________________________________________
.From: Elizabeth Ross <e.rossuq.edu.au>
.Sent: 15 January 2020 19:34
.To: Members of AnGenMap <angenmapanimalgenome.org>
.Subject: Re: DNA extraction from cattle hair for WGS
Hi Laura, we have never noticed a problem with degredation. I know VicDPI
were using it for long term dna storage and it is sold as "archive
quality". We do get shorter DNA from hair than semen but there doesn't
appear to be any further shearing once the DNA is extracted.
For long read sequencing we have added a few tweaks to the protocol. If you
are doing ont or pacbio we are happy to share info on that, just let me
know and I can email it though when I am back in Aus (currently at PAG).
Cheers.
On Jan 16, 2020 3:30 AM, Laura Iacolina <lauraiacolinagmail.com> wrote:
Liz, is it stable? We sometimes have problem with Qiagen kits (never tried
the Gentra though) and sources as hair and bone. Results are ok, but we
need to perform the analysis within a short time 7-10 days otherwise it
degrades and is no longer suitable.
Thanks,
Laura
--
PhD Laura Iacolina
Mammalian Biology subject editor
https://www.researchgate.net/.../Laura_Iacolina/info
https://lauraiacolina.wordpress.com/
Il giorno mer 15 gen 2020 alle ore 18:16 Elizabeth Ross ha scritto:
We use Gentra Puregene Tissue Kit from qiagen on tail hair and use the DNA
for nanopore sequencing. It gives great purity and excellent length if you
are gentle with it.
Cheers
Liz
On Jan 16, 2020 1:32 AM, Rick Tearle wrote:
Does anyone have a good method for extracting DNA from cattle hair? We need
it for whole genome sequencing so has to be high MW. Methods that work for
genotyping do not appear to work for WGS,
Dr Rick Tearle Senior Bioinformatician Davies Research Centre University of
Adelaide Roseworthy Campus rick.tearleadelaide.edu.au +61 432 07 58 07
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