Microsatellite (STRP) Resources

CIDR is no longer offering microsatellite whole genome scans. We will continue to provide access to several human and mouse STRP resources.

Human STRP Resources

CIDR is no longer offering human microsatellite (STRP) whole genome scans. This service has been replaced by SNP Linkage Scans and expanded to include Custom SNP Genotyping. We will continue to provide information about the marker set we used in our STRP production lab. CIDR performed 10 cM genome scan analysis on human DNA using automated fluorescent microsatellite analysis. The CIDR marker set was composed primarily of trinucleotide and tetranucleotide repeats. The marker set evolved over the years but was originally based on the Marshfield Genetics version 8 screening set. The final CIDR marker set consisted of approximate 400 primer pairs with average spacing of 9 cM throughout the genome. There were no gaps in the map larger than 18 cM. The average marker heterozygosity was 0.76. Approximately 15% of the marker loci were different between the final CIDR marker set and version 8. All reverse primer sequences were modified from the version 8 sequences in order to reduce '+A' artifacts. The resulting PCR products were sized using a capillary sequencing platform. CIDR multiplexed at both the pre- and post-amplification stages.

The markers were organized into 38 panels (10-fold multiplexing post-amplification). Each primer pair underwent extensive optimization to improve performance and reliability. Marker optimization was accomplished by varying the type of Taq enzyme (we used Taq Gold from Applied Biosystems and Platinum Taq from Invitrogen), the amount of primer, and the thermocycling parameters.

Download the Human STRP Marker Set

Mouse STRP Resources

CIDR is no longer offering mouse microsatellite (STRP) whole genome scans or marker-assisted breeding strategies (speed congenic and consomic studies). This service has been replaced by SNP Linkage Scans and expanded to include Custom SNP Genotyping. We will continue to provide access to our database of STRP genotypes on a set of inbred strains and the software tool for designing STRP mapping panels specific to particular interstrain crosses. Genotyping data for 54 inbred strains and ~300 markers are available.

Marker Set
List of 54 strains genotyped at CIDR
Interactive Queries
- Informative Markers for a Cross
- Panel Generator
- Informative Markers for Multiple Strains
- Informative Markers for Speed Congenics
Complete data files of all allele call data for all markers and strains in different formats
Lab Protocols (including PCR conditions)