Table 1.
APOBEC1/APOBEC3A/APOBEC3B expression in small and large intestines across bulk and single-cell RNA-seq datasets
| Dataset | Data type | Gene | Small intestine | Large intestine | Small intestine/large intestine | Adj P value |
|---|---|---|---|---|---|---|
| The HPA38 project | Bulk RNA-seq (nTPM) | APOBEC1 | 26 | 1.1 | 23.6 | – |
| APOBEC3A | 0.8 | 1.5 | 0.53 | – | ||
| APOBEC3B | 4.3 | 12.1 | 0.36 | – | ||
| The GTEx project | Bulk RNA-seq (nTPM) | APOBEC1 | 11.9 | 1.1 | 10.8 | – |
| APOBEC3A | 0.8 | 1.4 | 0.57 | – | ||
| APOBEC3B | 2.1 | 6 | 0.35 | – | ||
| Gut Cell Survey39–41 epithelial | scRNA-seq (relative read count) | APOBEC1 | 0.27 | 0.028 | 9.72*** | 0 |
| APOBEC3A | 0.016 | 0.082 | 0.20*** | 5.0 × 10−91 | ||
| APOBEC3B | 0.016 | 0.053 | 0.31*** | 9.25 × 10−205 | ||
| Gut Cell Survey39–41 stem cells | scRNA-seq (relative read count) | APOBEC1 | 0.024 | 0.00058 | 41.6*** | 9.0 × 10−4 |
| APOBEC3A | 0.0026 | 0.015 | 0.17 | 1 | ||
| APOBEC3B | 0.022 | 0.036 | 0.62 | 0.73 | ||
| Tabula Sapiens42 epithelial | scRNA-seq (relative read count) | APOBEC1 | 0.12 | 0.012 | 9.29*** | 2.3 × 10−79 |
| APOBEC3A | 0.17 | 0.021 | 8.29*** | 5.3 × 10−55 | ||
| APOBEC3B | 0.030 | 0.0086 | 3.48*** | 2.2 × 10−13 | ||
| Tabula Sapiens42 stem/amplifying cells | scRNA-seq (relative read count) | APOBEC1 | 0.022 | 0 | Infinity | 1 |
| APOBEC3A | 0.080 | 0.025 | 3.16 | 0.38 | ||
| APOBEC3B | 0.056 | 0.038 | 1.50 | 1 | ||
| HPA collection43,44 epithelial | scRNA-seq (relative read count) | APOBEC1 | 0.62 | 0.062 | 10.0*** | 7.3 × 10−246 |
| APOBEC3A | 0.021 | 0.22 | 0.095 | 0.86 | ||
| APOBEC3B | 0.0047 | 0.059 | 0.080*** | 7.0 × 10−9 | ||
| HPA collection43,44 undifferentiated cells | scRNA-seq (relative read count) | APOBEC1 | 0.11 | 0.0047 | 22.3*** | 2.4 × 10−6 |
| APOBEC3A | 0.0059 | 0.053 | 0.11 | 1 | ||
| APOBEC3B | 0.012 | 0.028 | 0.45 | 1 |
Relative read count was calculated under a scale factor of 104 and averaged across all cells. All single-cell data were obtained by 10X Genomics droplet-based sequencing. Gut Cell Survey—73,023/47,020 cells and 6,952/1,065 stem cells from small/large intestine from small/large intestine. Tabula Sapiens—3,112/5,790 cells and 259/318 stem and amplifying cells from small/large intestine. Human Protein Atlas (HPA) collection—6,167/11,167 cells and 1,290/2,104 undifferentiated cells from small/large intestine. P values were calculated from the coefficient two-tailed t-test of negative binomial regression models and were corrected for multiple testing using Benjamini–Hochberg method. Asterisks on the ratio indicate statistical significance. ***: Adjusted P value < 0.001.