SSLP Codes

An explanation of codes used in Roopenian SSLP tables

Allele codes (listed by strain name - 129, BALB, PWD, etc.)

In our gel-based genotyping assays, we have no need to determine exact product sizes in base pairs (bp).  Location of the amplified product in the mouse genome and C57BL/6J (B6) product size are determined by testing the primers with Ensembl BLAST or USCS In-Silico PCR.

For Roopenian markers:

  • S = product is smaller than B6
  • L = product larger than B6
  • Y = product different from B6 (either larger or smaller)
  • N = product not appreciably different from B6 (as measured by our assay)
  • Z = unknown (for comparing two other strains, not including B6)

0 = product same size as B6, 1 = slightly different, 2 = larger difference, 3 = larger still,  4 = larger still.  Usually size differences of 1 are not enough to distinguish for genotyping purposes.

So if, for example, 129 is S1 and BALB is S2, then 129 and BALB both give smaller products than B6, with BALB being the smaller of the two (more different compared to B6).  The example marker should be usable for genotyping B6 compared to BALB, but probably not for B6 compared to 129.

Band Strength codes

  • 0 = amplification failed, no visible product
  • 1 = faint band, probably not usable for genotyping
  • 2 = sufficient band strength for genotyping purposes
  • 3 or 4 = robust product, very good band strength