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Figure S1. Individual genes and functional gene categories with significant changes in expression between BALB/c and C57BL/6 strains. A. Two-dimensional scatter plot depicting the microarray-based comparison of genes expressed by 4 C57BL/6 mice versus 4 BALB/c mice on FD. Averaged expression of genes is represented by dots. The binary logarithm of normalized data was plotted. Genes on the identity line (diagonal) denote no changes in expression. The cutoffs for 2-fold increases and decreases are indicated by the two parallel lines above and below the diagonal, respectively. Genes with a fold change greater than 2 or smaller than 0.5 fall outside these boundaries. B. Categories of genes that are differentially expressed between BALB/c and C57BL/6 strains. The 12 IPA-sorted categories with highest p-values are shown. This analysis is based on the candidate gene list in Table S6. Values after the bars indicate the number of genes in each category. C. Total RNA was isolated from duodenum and used to amplify the Pla2g2a cDNA from BALB/c and C57BL/6 mice, as indicated in Materials and Methods, followed by BamH1 digestion. Digestion of the BALB/c 98 bp product generates fragments of 74 and 24 bp. The 24 bp band is seen after overexposure (data not shown). In C57BL/6, the 99 bp amplicon (distinct size from BALB/c due to mutation, a single-base pair insertion) is left uncut because the BamH1 site is abolished by the insertion. D. Genomic DNA diagnostic test for the frameshift mutation in Pla2g2a exon 3, for BALB/c or C57BL/6 mice. C and B6 stand for BALB/c and C57BL/6, respectively. Amplicons from Pla2g2a exon 3 and flanking intronic sequences were amplified from mouse intestinal genomic DNA, as described in Materials and Methods, and digested with BamH1. BALB/c mice generated PCR products that are digested by BamHI into fragments of 270 and 122 bp. BALB/c and C57BL/6 strains showed indistinguishable PCR products before digestion by BamHI, for all amplified cDNAs (98 and 99 bp, respectively; data not shown) and genomic DNAs (392 and 393 bp, respectively).

Table S1. Primers for genotyping the Mom1 locus in Pla2g2a.

Table S2. Primer pairs for qRT-PCR for the 13 genes in Table 1 and the internal control, Gapdh.

Table S3. Oligonucleotide primers for verification of potential Ppara exon skipping b).

Table S4. Pyrosequencing primers.

Table S5. Oligonucleotidesa) in the EpiTYPER analysis.

Table S6. List of 164 differentially expressed genes, resulting from the microarray-based comparison of Mthfr+/- C57BL/6 mice and Mthfr+/- BALB/c mice.

Table S7. Genes activated by PPARA and involved in fatty acid ß-oxidation a) that showed significantly (p < 0.05) higher expression b) in BALB/c compared to C57BL/6.

Table S8. Genes involved in oxidative stress response that showed significantly (p < 0.05) higher Expression in BALB/c compared to C57BL/6, as expected a,b) from higher PPARA activation.

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