Table 1. Systematic and iterative integration of experimentally derived components for meta-structure elucidation.
| Integration | High-throughput data | Iteration | |||
|---|---|---|---|---|---|
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|
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| Round1 | Round2 | Round3 | Round4 | ||
| Step 1 | Probe expressed | 103,518 | 108,288 | 114,738 | 118,767 |
| RTS1 | 2,357 | 2,524 | 2,650 | 2,685 | |
| RTS coverage (bp)2 | 3,150,825 | 3,397,450 | 3,685,476 | 3,758,989 | |
| RTS density3 | 84% | 82% | 82% | 83% | |
| RTS mean size (bp) | 1,336 | 1,346 | 1,390 | 1,400 | |
|
| |||||
| Step 2 | Solexa reads | 3,824,517 | 4,118,539 | 4,445,749 | ND |
| Known TSS4 | 1,047 (84%) | 1,069 (85%) | 1,089 (87%) | ND | |
| TSS5 | 3,969 | 4,062 | 4,133 | (4,133) | |
| TSS-associated RTS | 2,200 (93%) | 2,360 (94%) | 2,490 (94%) | 2,525 (94%) | |
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| Step 3 | Peptide detected | 22,856 | 38,968 | 54,549 | ND |
| pORF | 2,015 | 2,391 | 2,542 | (2,542) | |
| Protein-coding RTS6 | 1,657 | 1,702 | 1,733 | (1,742) | |
| ORF assigned | 2,002 | 2,376 | 2,525 | ND | |
RNAP-binding regions to determine RNAP-guided transcript segments (RTS) was 2,955.
RTS genomic coverage (bp) was determined as the ratio between total base pair of RTS and E. coli genome (4,639,668 bp).
RTS density (average, %) was defined as the ratio of the number of the probes expressed against the total number of probes in the RTS.
The known TSS (1,252 in total) was compared with the high-throughput TSS data within 10-bp window region.
TSS was determined within 200-bp window size and 60% cut-off followed by manual curation (see Online Method).
Protein-coding RTS indicates RTS having peptide fragments. Each round indicates the integration of results obtained from experimental conditions (1, log phase; 2, log phase + heat-shocked condition; 3, log phase + heat-shocked condition + stationary growth phase; 4, log phase + heat-shocked condition + stationary growth phase + glutamine growth condition). ND, not determined.