Table 1 Library building techniques and mapping statistics across mouse faecal small RNA sequencing studies
From: An optimised faecal microRNA sequencing pipeline reveals fibrosis in Trichuris muris infection
Sample information | Liu et al. (n = 15) | Tomkovich et al. (n = 21) | He et al. (n = 11) | Layton et al. (current n = 31) |
|---|---|---|---|---|
Faecal storage prior to extraction | Snap frozen | Snap frozen | N.S. | 4 °C in RNAlater immediate extraction |
Extraction kit and RNA enrichment | MirVana total RNA | MirVana small RNA | MirVana total RNA | MirVana total RNA |
Library kit | Nextflex | NEBnext | NEBnext | NEBnext |
Sequencing machine | NextSeq | MiSeq | HiSeq | HiSeq |
Raw reads (range) | 33,775,633 (20,170,514–55,664,440) | 794,663 (354,995–1,595,598) | 21,620,070 (19,922,251–23,545,474) | 26,246,329 (13,603,079–39,286,425) |
Reads passing QC & filtering | 25.14% (8,530,128) | 29.24% (233,169) | 41.54% (8,910,852) | 38.8% (10,267,557) |
tRNA reads after filtering | 0.21% (17,868) | 1.23% (3,156) | 0.62% (55,163) | 0.27% (27,905) |
rRNA reads after filtering and tRNA removal | 8.4% (729,226) | 57.95% (132,593) | 18.91% (1,775,245) | 24.56% (2,581,720) |
Reads mapping to mouse genome after filtering, tRNA and rRNA removal | 16.75% (1,310,227) | 45.11% (41431) | 21.17% (1,367,993) | 25.48% (1,922,223) |
Raw miRNA reads as % of total reads passing QC | 0.19% | 0.62% | 0.40% | 0.46% |
Raw miRNA reads (range) | 16,562 (1444–51,429) | 1,351 (174–4113) | 30,262 (16,812–47,642) | 43,989 (10,172–122,794) |
Normalised miRNA reads (range) | 10,735 (9434–14,099) | 878 (699–1083) | 28,522 (21,285–37,969) | 35,225 (28,948–42,443) |
miRNA species detected at >10 raw counts in 5 samples | 83 | 25 | 121 | 120 |
