Supplementary Figure 1. Lack of autoimmunity in NKT cell deficient B6.NZBc4L

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1 Supplementary Figure. Lack of autoimmunity in NKT cell deficient L mice. A,.CDd-deficient mice lack CDd-independent NKT cells. B, In the absence of NKT cells,.cdd -/- mice fail to generate high titres of IgM or IgG anti-nuclear (chromatin, ssdna, dsdna) antibodies, as determined by ELISA. C, Splenic and peritoneal Ba cell expansion is unaffected by the absence of NKT cells in mice. All mice were aged to months. Each symbol represents an individual mouse. Horizontal lines indicate the median. The p values for significant differences are shown as, p <.5, p <.5, p <.5, and determined using the Mann- Whitney non-parametric test. Supplementary Figure. Genetic map of bicongenic mice. Bicongenic mice were genotyped using polymorphic microsatellite markers (PMMs) or single nucleotide polymorphisms (SNPs) by PCR. Genotypes of PMMs were differentiated by size on an agarose gel while SNPs were assayed using TaqMan SNP genotyping probes as per the manufacturer s instructions (Applied Biosystems; Carlsbad, CA). In addition to the founding breeders of the.nzbcc bicongenic line, at least five mice from each bicongenic cohort (.NZBcc normb and.nzbcc lowb ) were used to confirm this genetic map. Supplementary Figure. Altered frequency of CDd + B cells and activated B cell subsets in bicongenic mice. A, Snap frozen spleens from month old,,.nzbc,.nzbcc normb, and.nzbcc lowb were sectioned (5 µm), fixed in acetone, blocked with normal goat serum and individually stained with FITC-conjugated

2 anti-igm (green; Jackson Immunoresearch), phycoerythrin (PE)-conjugated anti-cdd (red, B clone; BD Biosciences), and allophycocyanin-conjugated anti-cd (purple, LT clone; BD biosciences) and imaged using a Zeiss Axioplan deconvolution microscope with a X objective lens. B, Percentage of recently activated B cells (CD69 + B + ), germinal centre B cells (PNA + CD lo B + ), and plasmablasts (CD8 + CD - B + ) in the spleens of,,.nzbc, and.nzbcc mice. All mice were aged to months. Each symbol represents an individual mouse. Filled circles represent.nzbcc lowb mice and open circles.nzbcc normb mice. Horizontal lines indicate the median. The p values for significant differences are shown as, p <.5, p <.5, p <.5, and were determined using the Mann- Whitney non-parametric test. Symbols for both cohorts of.nzbcc mice are staggered for clarity, but statistical analysis was conducted on all.nzbcc mice. Supplementary Figure. Absolute numbers of various B and NKT cell populations. Absolute number of A, B cell and B, NKT cell subsets in the spleens or peritoneal cavity of,,.nzbc, and.nzbcc mice. All mice were aged to months. Each symbol represents an individual mouse. Filled circles represent.nzbcc lowb mice and open circles.nzbcc normb mice. Horizontal lines indicate the median. The p values for significant differences are shown as, p <.5, p <.5, p <.5, and were determined using the Mann-Whitney non-parametric test. Symbols for both cohorts of.nzbcc mice are staggered for clarity, but statistical analysis was conducted on all.nzbcc mice.

3 A % NKT cells No. of NKT (x 6 cells).cdd-/-.cdd-/-.cdd-/-.cdd-/- B. IgM. IgG anti-chromatin O.D anti-ssdna O.D anti-dsdna O.D C % CD5 + B lo cells 6 Spleen 8 6 Peritoneal Cavity.CDd-/-.CDd-/-.CDd-/-.CDd-/-.CDd-/-.CDd-/-.CDd-/-.CDd-/- Supplementary Figure

4 .NZBcc rs77579 rs7759 rs776 rs776 DMit9 DMit DMit96 DMit7 DMit8 DMit5 DMit9 DMit8 DMit75 rs7798 DMit78 DMit7 DMit DMit7 rs78 rs78 DMit rs589 rs759 rs759 rs7595 rs7599 rs7599 rs75955 rs75966 rs7598 rs76 rs6757 rs766 rs7669 DMit7 rs769 rs76 rs76 DMit rs76 rs768 rs768 DMit DMit5 DMit96 DMit DMit5 DMit6 DMit5 DMit6 DMit9 DMit5 DMit59 rs767 DMit rs769 Mb Chr Mb Chr. Supplementary Figure

5 A.NZBc IgM CD CDd IgM/CDd.NZBcc normb.nzbcc lowb B % Recently activated B cells 6.NZBc.NZBcc % Germinal centre B cells.nzbc.nzbcc % Plasmablasts cells.nzbc.nzbcc Supplementary Figure

6 Spleen Peritoneal Cavity A No. of B cells (x 6 ) No. of Follicular B cells (x 6 ) NZBc.NZBcc No. of CD lo CD - B cells (x 6 ) No. of Marginal zone B cells (x 6 ) 5 5.NZBc.NZBcc No. of Transitional B cells (x 6 ) No. of Ba cells (x 6 ) 5 5.NZBc.NZBcc No. of Ba cells (x 6 ) 8 6.NZBc.NZBcc B No. of Tet + cells (x 6 ) No. of NK. + CD + Tet - cells (x 6 ) No. of NK. + CD + Tet + cells (x 6 ) NZBc.NZBcc No. of CD - CD8 - NK.+ Tet + cells (x 6 ) NZBc.NZBcc Supplementary Figure