Files in this Data Supplement:

• Supplementary Figure 1 (PDF, 68KB) - Individual genotyping of CD1 -/- mice The figure shows the genotype of 9 CD1-/- mice with representative EAE development used in the experiments. Each individual’s genotype is represented in one column and the three most right columns show the wild type reference allele sizes. The figure demonstrates that the 10N CD1-/- founder mice harbor fragments from three different ancestors, namely ES-129, BALB/c and B6. In case an allele could be positively identified the strain name has been indicated, while the allele size is shown if a marker is not informative between two strains. The fcgr1 SNP has been identified by Pyrosequencing, the SNP leads to a C/G polymorphism. All mice have a clearly identifiable linked minimal fragment (dark gray) from the ES 129-D3 cell line and flanking regions that are also likely to be ES-129 (light gray). Following the genotypes telomeric, BALB/c alleles can be detected in some of the mice, indicating genetic heterogeneity among the 10N CD1-/- founder mice. Surprisingly, the marker D3Mit 216, which clearly types for a homozygous 129-D3 allele size for most of the mice, has been placed at 126 Mb on the physical map, respectively 58,8 cM. This position seems highly unlikely and the marker is probably closely linked to the CD1-/- fragment. The physical map is based on the Celera mouse genome database; the cM positions are retrieved from the MGI mouse list. Failed genotypings are indicated as (-).
• Supplementary Figure 2 (PDF, 56KB) - Individual scores of the screened mice As three of the mice are sacrificed at day 17 individual scores are only shown until this time point, a significant difference between the CD1-/- and the CD1+/+ mice are already established at day 11. The homogeneity of the results show that the significant difference in EAE score between CD1-/- and CD1+/+ mice is due to the CD1-/- region and that the BALB/c contaminations telomeric of this region, including the eae3, have no strong effect in this model.
• Supplementary Figure 3 (PDF, 73KB) - Genotype screening on other chromosomes The CD1-/- mice have been screened for contamination on different chromosomes focusing on positions where QTLs in different EAE models have been described. No ES-129 or BALB/c alleles could be detected indicating the backcross success to B6 despite the genetic heterogeneity on chromosome 3.