Does anyone know of a way to search for integrated GFP strains? - I want to use them as a genetic marker, not particular about the cells, so the wormbase expression pattern search function doesn’t help. Also the Markers section of wormbase appears to be limited to SNPs and phenotypic markers. Is there a site or document that has a good list of GFPs representing each of the six chromosomes? Thanks!
CB5584,ChromII
There is a Worm Breeder’s piece listing a set in this issue (page 20; article-specific Worm Breeder’s links don’t embed well).
I’ve also listed below some integrated transgenes available from the CGC, which I found by looking through our lab’s strain collection and checking whether the CGC had the transgene. Obviously, this is not remotely comprehensive, it’s just what we happen to have locally, in a database I can search more readily than I can the CGC’s. I haven’t seen most of these transgenes, certainly not recently, and I make no guarantees about their suitability for your purposes.
LGI
ayIs4
mIs13
ccIs9753
jsIs1
ruIs34
arIs37
kyis39
kyis39
zdIs5
ynIs45
LGII
otIs39
juIs76
inIs179
otIs77
syIs54
LGIII
juIs73
ruIs32
zhIs4
eIs34
syIs80
ynIs57
ynIs37
LGIV
kyis5
syIs49
jcIs1
edIs6
xrIs87
arIs51
LGV
mIs10
jsIs37
ruIs33
akIs3
cuIs1
qIs56
kyis235
oyIs14
bcIs39
otIs3
zuIs178
It is possible to use the wormbase AQL search to retrieve transgenes by chromosomal location:
e.g. this query searches for transgenes integrated on X.
select l, map from l in class Transgene,
map in l->Map where map = “X”
If you want balancer chromosomes, I believe that the knockout consortium have GFP marked insertions/translocations for some of the chromosomes see:
http://www.zoology.ubc.ca/~alorch/research1_strains.htm
also see Mark Edgeley’s chapter on wormbook.
Freddie
Do you know of lines carrying other fluorescent markers different from GFP?
Couldn’t find them in WormBase.
Thank you
ST53 Chr III another simple marker for crossing
I put a list of transgenes, for which (at least some) mapping data are available on WormBase Wiki:
http://www.wormbase.org/wiki/index.php/Mapped_Transgenes
Hope this will help a bit.
Igor,
I have tried to generate a list like yours but didn’t get the search criteria correct. I would like to export this data to Excel so I can sort by chromosome and search. I am unable to get the data from the html table in the wiki into Excel.
Could you please let me know either the search criteria you used so that I can do the search and export it myself or how to extract the data from the html table?
Thanks!
I used a relatively involved Perl script to generate the table. I don’t think it’s easy to do with one of the query tools in WormBase. So for now I just added a link to an Excel file containing the data - it’s at the top of the page.
Hope this will do, but let me know if you have further question.
Igor.
I would really appreciate if any of you help me with the molecular information about transgene qIs51 used in nT1 translocation marker (IV:V)? Integrated Pharynx GFP used as balanced in Chromosome IV and the data is not there in wormbase.
Thanks,
The best description I know of for qIs51 is in Cui, Kim, and Han (2006), although I’m not sure why it’s in that paper. That paper cites Belfiore et al (2002) for qIs51, and I’ve also seen Siegfried, Kidd, Chesney, and Kimble (2004) cited for qIs51, but unless I’m missing something neither of the two references from the Kimble lab actually seems to describe the transgene in detail.
The description from Cui, Kim, and Han is:
qIs51 is a genomic insertion containing three markers: myo-2::GFP expressed in the pharynx throughout development, pes-10::GFP expressed in the embryo, and F22B7.9::GFP expressed in the intestine