Table 1.
Seven genes significantly changed in E8.5 Slc7a5‐null embryos
| Gene_ID | Gene | logFC | P‐value | FDR | Description |
|---|---|---|---|---|---|
| ENSMUSG00000110631 | Gm42047 | −11.1 | 0 | 0 | lincRNA |
| ENSMUSG00000040010 | Slc7a5 | −4.95 | <10−16 | <10−16 | Solute carrier family 7 (cationic amino acid transporter, y+ system), member 5 |
| ENSMUSG00000074052 | BC048644 | −4.35 | 4.6 × 10−12 | 4.0 × 10−8 | cDNA sequence BC048644 |
| ENSMUSG00000112478 | AC153370.2 | −3.59 | <10−16 | 2.8 × 10−14 | lincRNA |
| ENSMUSG00000040263 | Klhdc4 | −1.14 | <10−16 | <10−16 | Kelch domain containing 4 |
| ENSMUSG00000010154 | Spire2 | −0.948 | 3.1 × 10−11 | 2.4 × 10−7 | Spire homolog 2 (Drosophila) |
| ENSMUSG00000032815 | Fanca | −0.387 | 7.2 × 10−6 | 0.038 | Fanconi anaemia, complementation group A |
| ENSMUSG00000040618 | Pck2 | 0.594 | 7.3 × 10−10 | 4.8 × 10−6 | Phosphoenolpyruvate carboxykinase 2 (mitochondrial) |
| ENSMUSG00000032715 | Trib3 | 1.851 | 6.9 × 10−8 | 0.00040 | Tribbles pseudokinase 3 |
| ENSMUSG00000027313 | Chac1 | 3.431 | 1.2 × 10−13 | 1.2 × 10−9 | ChaC, cation transport regulator 1 |
RNA‐seq data based on 5 wild‐type littermates and 5 Slc7a5‐null E8.5 embryos identified 7 genes showing significant change in expression (and see Appendix Table S1). Slc7a5 was downregulated with a log2 fold change of 4.948 (equivalent to > 99.9% reduction in mRNA expression (Fig 4H)). Klhdc4 (Kelch domain containing 4) and Spire2 (spire‐type actin nucleation factor 2) genes were both downregulated to a much lesser extent with log2 fold changes of ~ 1, confirmed by reductions in mRNA expression to ~ 50% of wild‐type level. Klhdc4 is a highly abundant transcript, and Spire2 is functionally redundant with Spire1 (Pfender et al, 2011; Fig 4H), so the observed changes in their expression levels seem unlikely to be functionally significant (and may be associated with their close proximity to the Slc7a5 locus on chromosome 8). Upregulated genes, Chac1, Trib3 and Pck2, are all metabolic stress‐related genes (see text). Correlation between samples was high (r > 0.98), and additional analysis without one WT outlier had a small effect on the significant gene list, adding several further genes associated with metabolic stress (Appendix Table S2).