Table 2.
Summary of SMRF-seq data comparing footprinted sites with or without RNase H pretreatment. The total number of independent reads and R-loop footprints (peaks) are shown broken down by strand for each locus. The overall percentages of R-loop footprints with and without RNase H pretreatment are shown below.
| Gene | Strand | No RNase H |
RNase H-treated |
||||||
|---|---|---|---|---|---|---|---|---|---|
| Total (+) strand reads |
(+) strand peaks |
Total (−) strand reads |
(−) strand peaks |
Total (+) strand reads |
(+) strand peaks |
Total (−) strand reads |
(−) strand peaks |
||
| CALM3 | + | 1598 | 199 | 355 | 6 | 1685 | 36 | 173 | 0 |
| FUS | + | 2037 | 1084 | 2488 | 0 | 1052 | 0 | 2500 | 5 |
| SNRPN70 | + | 1450 | 767 | 2060 | 5 | 1092 | 0 | 1778 | 0 |
| MRFAP1L1 | − | 1833 | 0 | 762 | 491 | 1249 | 0 | 1018 | 0 |
| Total stranded peaks | 2541 | Total stranded peaks | 36 | ||||||
| Total stranded reads | 5847 | Total stranded reads | 4847 | ||||||
| % peaks | 43.46% | % peaks | 0.74% | ||||||
SMRF-seq, single-molecule R-loop footprinting coupled with PacBio sequencing; RNase, ribonuclease H.