Table 1.
Number of Reads for Each Sample that Match rRNA or Either One of the Two Organisms’ Genomes
| Sample | Raw Reads | rRNA (Mtb + Mouse) | Mouse | M. tuberculosis | |||
|---|---|---|---|---|---|---|---|
| rRNA | % of Raw Reads | Aligned to GRcm38 – Rel. 94 | % of Raw Reads | Aligned to Erdman GCA000668235.1 | % of Raw Reads | ||
| AM 1 ∼25,000 infected cells | 131.5 M | 19.5 M | 14.8% | 96.2 M | 73% | 1.2 M | 0.9% |
| AM 2 ∼18,000 infected cells | 176.5 M | 41.1 M | 23.3% | 96.6 M | 55% | 1.3 M | 0.75% |
| AM 3 ∼12,000 infected cells | 309.8 M | 107.7 M | 34.8% | 51.4 M | 17% | 0.95 M | 0.3% |
| IM 1 ∼25,000 infected cells | 140.6 M | 15.3 M | 10.9% | 72 M | 51% | 1.2 M | 0.85% |
| IM 2 ∼40,000 infected cells | 47.5 M | 6.6 M | 13.9% | 33.2 M | 70% | 0.9 M | 1.9% |
| IM 3 ∼35,000 infected cells | 83.7 M | 12.2 M | 14.6% | 54.3 M | 65% | 1 M | 1.2% |
| Mtb broth 1 | 12.1 M | 1.8 M | 14.7% | – | – | 10 M | 83% |
| Mtb broth 2 | 13.7 M | 1.4 M | 10.4% | – | – | 12 M | 87.5% |
| Mtb broth3 | 15.1 M | 0.8 M | 5.4% | – | – | 12.4 M | 82% |
| Mtb – BMDM 1 | 32.6 M | 0.08 M | 0.25% | – | – | 28.5 M | 87% |
| Mtb – BMDM 2 | 35 M | 0.11 M | 0.31% | – | – | 31.6 M | 90% |
| Mtb – BMDM 3 | 25.5 M | 0.11 M | 0.47% | – | – | 23.6 M | 93% |
For the in vivo samples, the number of sorted cells is reported in the “Sample” column. As a result of the difference in the number of infected cells between AMs and IMs at 14 days post-infection, a lower bacterial RNA enrichment and higher sequencing depth were preferred in some AM samples to compensate for the reduced RNA yield.