TROPLIST: Troplist summary 2: Xeno Affy data ortholog conversions, combininginsulators and SceI transgenesis, Trop Gal lines

[Kristen Kroll]

Troplisters:
Here is a 2nd summary with some other replies to the previous thread.  On
the topic of converting large sets of affymetrix laevis array hits to their
corresponding orthologs, Paul Mead's bioinformatics folks have generated a
converter to do this that people may find useful--hopefully can link this
weblink to the Xenbase genomics page for others to easily find.  As an
alternative, Itai Yanai developed some perl scripts to pull the orthologs
for all existing Xenopus laevis unigenes into one spreadsheet.  This
spreadsheet provided an "instant fix" for many of my  prior ortholog
annotation woes, so if other people need this, now or in the future, drop me
an email. The conversion is still imperfect in that it relied on mapping
laevis to trop ensemble listings and many of the trop genes are not yet
annotated to orthologs. Still, that said, both approaches helped us to get
the job done.

> The address to get Paul's converter is:
> http://www.hartwellcenter.org/hcnetdat/webFront/searchFrogOrtholog.php
> 
> 
Matt Guille also had a few comments about the new stock center--sounds like
the website will be up soon.

Itai's ortholog conversion:

> Dear Kris,
> 
> I'm glad this approach seems to be working. It's easy to run so feel free
to> send sets anytime. I ran the third set (attached) but couldn't run the
> second because I don't have the Affy probe to unigene mappings handy. If
you> send the unigenes for these I can easily run those too. Also I'm
attaching> the orthologs for all of the unigenes for your records (attached,
probably> the most useful file of all ;)
> 
> It's not too hard to learn how to get data from Ensmart and then push it
> through my perl scripts. I'm happy to show you how so feel free to call
> (617-320-0360) and I can walk you through the steps and also send along my
> perl scripts. That said don't hesitate to also just send more sets.
> 
> About a web accessible converter: I don't really know how to do that. I'm
> sure it's not that hard but since I have no experience with I'd rather
hold> off on that for now.
> 
> About the mappings from laevis to tropicalis: I checked a couple unigenes
> (Xl.11203 and Xl.12606) by hand and confirmed that they really cannot be
> matched to any ensemble tropicalis gene which most probably reflects the
> problems with current the tropicalis annotation (those genes have to be
> there right?)
> 
> Cheers,
> Itai

-----Original Message-----
From: Kristen Kroll [mailto:kkroll@wustl.edu]
Sent: Friday, November 09, 2007 8:06 PM
To: Itai Yanai
Subject: Re: TROPLIST: Xeno Affy data ortholog conversions,combining
insulators and SceI transgenesis, Trop Gal lines

Dear Itai,
You are right; using your ortholog conversion table that contains info for
all laevis unigenes, I could easily pull up the data for any array dataset
we have. Wonderful!

For this, I can just use the excel numerical/lookup functions, which is
easy, whereas for me writing a script to pull it from the web databases or
batch blast would not be...

Don't worry about a web converter; if Paul spruces his up that will be
useful to link to Xenbase; your all-ortholog conversion table may also, for
others using the arrays in the short term and running into this issue.

Many thanks again and have a great weekend--Cheers,
Kris

Hi Kris,
I'm glad this helped! Have a great weekend too.
Cheers,
Itai
Kris,
> Hi Kris,
> 
> As you may remember we've now got the European stock centre up and
> running here and one of the experiments we're actually in the middle
of> is testing the CTCF insulators in Sce1 transgenics -  I shall be
going to> nurture the embryos from yesterday as soon as I press send. In
terms of > trops, I don't think we have the driver line you're looking for
yet> people are just starting to send us lines but if you're really
desperate> to try some proven egg layers our embryo quality is excellent in
house> and we could arrange to ship some -  won't be the cheapest exercise
> though due to crossing the pond.
> 
> best wishes,
> 
> Matt
>  
> 
> Dr Matt Guille

>>> Kristen Kroll <kkroll@wustl.edu> 11/11/07 2:29 PM >>>
Hi Matt,
Thanks for the info-- Have to say, I hadn't considered the possibility
Of getting frogs from the UK, just because I have organized shipping trops
And laevis within the US a couple of times but never overseas so I'm not
Sure what must be done logistically or how well this works. Have you folks
shipped some animals to the US?

It would certainly be very useful to know which stocks you carry.
Perhaps Xenbase could add a link to your site/stock list under the "obtain
frogs" page. I didn't spot the website in a look through your or the U.
Portsmouth web pages or via google, but maybe I'm just missing it. I think
on the proven egg layers, I may just be patient for the moment, it is hit-
or-missbut not always miss and we need to get a population bred in house
anyway.

Good luck on the insulator expts-- should be useful for many of us to
Know whether it is worth it to add those to our plasmids for generating
transgenics. 

Best wishes,
Kris
 
Hi Kris,

We've shipped frogs from the US but not to - however I'm sure the same
firm would do it. The centre's website will be up and running in the
next few weeks - its the last thing for us to get into place and the
link from Xenbase will be there too. I'll let you know how the
insulators work. If you're in Europe in the near future and want to
visit please drop me a line - it would be great to see you.

all the best,

Matt 
 

Dr Matt Guille
Head of School
School of Biological Sciences
King Henry Building
University of Portsmouth
Portsmouth 
PO1 2DT

Tel: (44) 2392 842491
Fax: (44) 2392 842053

Husbandry advice fm Mustafa Khokha-

Sorry for the late reply.  One other thing I might suggest in
addition to the comments by lyle - you might try priming the frogs first.
We often give 10 u  hCG to females 24-72
hours prior to when we want to ovulate.  Sometimes they lay a few
eggs with this priming dose but we boost them anyway.  There was a time
"back in the day" when we  did this routinely.
However, we found that as we started ovulating regularly (like
monthly to every other month), they remained "primed" and a priming dose
could lead to them laying  all of their eggs.  But this
might be after 4-6 regular ovulations.

However, if these are new frogs or you are not using them on a
regular clock then I would encourage you to prime them.  It does take some
pre-planning.  If you   then find that the ladies start laying all their
eggs with a priming dose, then   stop, but my guess is at that point, eggs
will be raining down on you...

Regarding the reptomin Lyle, when did they change the formulation?
Have you seen any problems since?  In some sense, it might make sense just
to vary the   diet - sometimesnasco, sometimes reptamin.  Have you tried the
HBH tad+froglet   bites?  our froglets seem
to love it but too small for adults...

thanks for the digest.  very useful to see the responses.
M 

 

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