Washington University School of Medicine SNP Research Facility
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RFLP assays (snip-SNPs) - Genetic Mapping Resource for C. briggsae

We have developed restriction fragment length polymorphism (RFLP) assays to facilitate inexpensive genetic mapping in C. briggsae.

Identification of snip-SNPs

We screened the latest build of HK104 SNPs for substitutions that altered the recognition sequence of restriction enzymes. To make this a practical resource, we limited the analysis to 30 restriction enzymes from REBASE that are known to be reliable and inexpensive. In the end, 25 of these had at least one RFLP assay per chromosome (see table below).

Primer Design and Assay Development

PCR assays were designed to our standard protocols: amplicon sizes of 500 to 1000 bp, primer TM's of 54-56. In silico fragment analysis of the PCR products was performed to predict band sizes for AF16 and HK104; assays with more than 4 bands in either strain were removed. Some 3,723 snip-SNPs passed PCR primer design. These spanned 137 cb25 ultra-contigs, 84 of which were in the current genetic map. Our final set contained 1,987 RFLP assays, now positioned on the "cb3" sequence assembly, that can be used for genetic mapping in C. briggsae.

RFLP Assay Sets By Enzyme
EnzymeChromosome (Map v3.3)Total
IIIIIIIVVX
AluI191613332231134
ApaI12161314
BclI137781238
BglII53657430
BstUI9109178962
ClaI432611834
Csp6I41720182834121
DpnII132425292935155
DraI282821432648194
EcoRI116522142078
EcoRV56516121054
HaeIII6129292827111
HindIII78613101559
HpaII98716141872
MspI98716141872
NcoI42422115
PstI14321415
PvuII43284425
RsaI41720182834121
SacI267210734
Sau3AI132425292935155
SspI101215243136128
TaqI102021263548160
XbaI47121171556
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