Table 4.
Example of DNA and RNA meta-ome sequencing reproducibility, based on Reads per Million (RPM) values from MG-RAST annotation of bacterial housekeeping genes, obtained from soils FH (high pH peat, pH 7.39) and FL (low pH peat, pH 3.65).
| Gene | FH |
FL |
||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| DNA |
RNA |
DNA |
RNA |
|||||||
| D1 | D2 | D3 | R5 | R6 | D4 | D5 | D6 | R11 | R12 | |
| recA | 212.4 | 208.5 | 208.3 | 114.7 | 164.4 | 221.4 | 221.7 | 221.7 | 23.4 | 18.2 |
| gyrB | 383.1 | 392.1 | 385.6 | 209.5 | 277.1 | 374.8 | 385.7 | 383.8 | 40.6 | 35.5 |
| fusA | 788.4 | 800.3 | 794.6 | 434.9 | 594.1 | 764.9 | 782.9 | 774.7 | 201.2 | 183.6 |
| rpoB | 686.0 | 700.5 | 702.3 | 456.7 | 525.3 | 693.3 | 717.9 | 710.7 | 205.6 | 187.2 |
| infB | 356.8 | 359.2 | 359.3 | 229.5 | 298.0 | 345.6 | 376.5 | 368.0 | 63.0 | 50.4 |
| atpD | 297.5 | 296.5 | 298.0 | 222.9 | 263.9 | 340.7 | 347.9 | 339.5 | 57.3 | 48.1 |
Samples were sequenced using Illumnia HiSeq 2500 technology, and all values were normalized for total read counts to Reads per Million (RPM). DNA samples were sequenced in triplicate (D1–D3, and D4–D6), and RNA samples were sequenced in duplicate (R5–R6, and R11–R12). The genes were identified in MG-RAST using the following annotations: recA (RecA protein), gyrB (DNA gyrase subunit B), fusA (Translation elongation factor G), rpoB (DNA-directed RNA polymerase beta subunit), infB (Translation initiation factor 2), and atpD (ATP synthase beta chain).