Table 5. Targeted RNA-seq of Peromyscus leucopus with and without Borrelia hermsii infection.
Table 5—source data 1. Targeted RNA-seq of blood with normalization by Ptprc of P. leucopus with and without infection by Borrelia hermsii.
elife-90135-table5-data1.xlsx (14.1KB, xlsx)
| Variable | Uninfected (n=3) mean (95% CI)* | Infected (n=4) mean (95% CI)* | Fold change | FDR p value |
|---|---|---|---|---|
| B. hermsii qPCR of spleen | . | 13615 (1882–98,476) | . | . |
| B. hermsii reads blood† | . | 3487 (743–16,362) | . | . |
| % spleen/body mass | 0.15 (0.12–0.19) | 0.36 (0.26–0.51) | 2.4 | 1E-02 |
| Targeted RNA-seq | ||||
| Akt1 | 184 (135–253) | 347 (191–630) | 1.88 | 3E-01 |
| Akt2 | 92.9 (72.4–119) | 141 (89.4–222) | 1.52 | 3E-01 |
| Arg1 | 247 (96.9–630) | 1375 (848–2230) | 5.57 | 4E-02 |
| Cd14 | 308 (119–799) | 598 (357–1002) | 1.94 | 3E-01 |
| Cd177 | 2.11 (0.71–6.27) | 35.9 (11.9–108) | 17.0 | 4E-02 |
| Cd69 | 133 (114–155) | 65 (33.6–128) | 0.49 | 2E-02 |
| Cxcl10 | 0.33 (0.14–0.76) | 4.85 (2.74–8.59) | 14.7 | 2E-02 |
| ERV env | 26.8 (22.4–32.1) | 29.2 (14.8–57.8) | 1.09 | 9E-01 |
| ERV gag-pol | 1853 (1351–2542) | 1578 (820–3037) | 0.85 | 8E-01 |
| Fcgr2a | 44.8 (24.0–83.6) | 715 (303–1689) | 16.0 | 2E-02 |
| Fcgr2b | 47.3 (30.2–74.3) | 578 (167–2000) | 12.2 | 5E-02 |
| Fcgr3 | 30.6 (18.6–50.4) | 392 (171–897) | 12.8 | 2E-02 |
| Gapdh | 1985 (1142–3447) | 5366 (2383–12,081) | 2.70 | 2E-01 |
| Gbp4 | 126 (82.3–193) | 289 (130–644) | 2.30 | 3E-01 |
| Ifit1 | 223 (107–465) | 604 (303–1203) | 2.71 | 2E-01 |
| Ifng | 0.58 (0.09–3.92) | 2.28 (0.86–6.06) | 3.94 | 3E-01 |
| Il10 | 0.25 (0.07–0.87) | 1.49 (0.31–7.28) | 5.94 | 3E-01 |
| Il12 | 0.43 (0.23–0.81) | 1.13 (0.45–2.88) | 2.63 | 3E-01 |
| Il1b | 477 (174–1308) | 2828 (1325–6034) | 5.93 | 7E-02 |
| Irf7 | 93.3 (13.4–65) | 626 (196–1998) | 6.71 | 2E-01 |
| Isg15 | 302 (30.1–3030) | 1922 (623–5934) | 6.36 | 3E-01 |
| Itgam | 72.2 (44.5–117) | 322 (211–492) | 4.45 | 2E-02 |
| Mmp8 | 7.1 (2.74–18.6) | 537 (148–1952) | 75.2 | 2E-02 |
| Mx2 | 152 (48.6–476) | 167 (48.0–582) | 1.10 | 9E-01 |
| Nos2 | 0.16 (0.08–0.30) | 0.32 (0.13–0.80) | 2.01 | 4E-01 |
| Oas1 | 51.3 (6.75–390) | 159 (39.2–643) | 3.10 | 5E-01 |
| Rigi (Ddx58) | 38.7 (18.9–79.2) | 55.7 (33.9–91.5) | 1.44 | 5E-01 |
| S100a9 | 1739 (657–4596) | 18430 (6546–51,883) | 10.6 | 5E-02 |
| Saa3 | 0.49 (0.13–1.87) | 212 (25.9–1733) | 431 | 2E-02 |
| Slpi | 0.41 (0.18–0.95) | 166 (49.0–566) | 401 | 1E-02 |
| Sod2 | 104 (51.4–211) | 2011 (804–5028) | 19.3 | 2E-02 |
| Tlr2 | 83.2 (59.7–116) | 371 (234–587) | 4.46 | 2E-02 |
| Tlr4 | 44.8 (26.1–77.0) | 256 (138–474) | 5.71 | 3E-02 |
| Ratios | ||||
| Akt1/Akt2 | 2.0 (1.7–2.3) | 2.5 (2.1–2.9) | 1.25 | 1E-01 |
| Cd14/Fcgr3 | 11.3 (4.8–17.9) | 1.7 (0.72–2.8) | 0.15 | 2E-02 |
| IL12/IL10 | 2.3 (0.00–5.0) | 2.8 (0.0–7.6) | 1.21 | 9E-01 |
| Nos2/Arg1 | 0.001 (0.0–0.002) | 0.0001 (0.0–0.0004) | 0.28 | 2E-01 |
*
For targeted RNA-seq it is mean unique reads for given gene normalized for reads for Ptprc (Cd45) gene for a sample. The 95% confidence intervals (CI) are asymmetric. Actual [gene]/Ptprc ratios are x 10–3.
†
† Normalized PE150 reads mapping to cp6.5 plasmid of B. hermsii.