Figure 3. Genetic variation occurs in the Cxcr4 locus in B6.SJL-CD45.1 compared to B6.CD45.2 mice.

(A-F) CD4⁺ or (A, B) CD8⁺ T cells were isolated from B6-CD45.2, B6.SJL-CD45.1, or SJL mice from Jax and polarized in Th1 conditions. (A) Western analysis monitoring Cxcr4 protein expression, with STAT4 shown as a control. (B) Flow cytometry analyzing Cxcr4 cell surface expression. (C) qRT-PCR analyses with primer sets monitoring different regions of the Cxcr4 transcript. Data were processed as in Fig. 2D, and p-values were calculated with an unpaired Student’s t test (*** ≤ 0.001 and ** ≤ 0.01). (D) Primer sequence locations (color arrows) used in (C) and Sanger sequencing for a partial Cxcr4 transcript. (E) Graphs of normalized counts for RNA-seq datasets from B6-CD45.2 (dark blue), B6.SJL-CD45.1 (light blue) and SJL (orange) mice processed with default (solid bars) or stringent (hatched bars) parameters. DESeq2 performs a Benjamini-Hochberg test to calculate adjusted p-values (*** ≤ 0.001 and ** ≤ 0.01). (F) IGV browser display of RNA-seq alignment files from default parameters with nucleotide changes from the mm10 genome shown by color lines (red (T), blue (C), green (A), orange (G)). (A-F) Data are compiled from, or representative of, at least (D) 2, (A, E, F) 3, (C) 4, or (B) 6 independent biological replicates. See also Fig. S2.