Table 1. Classification of unique small RNA reads.
| Classification | Total | HB | AB | HA | AA | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Number of unique reads | Percentage (%) | Total sequences | Percentage (%) | Number of unique reads | Percentage (%) | Total sequences | Percentage (%) | Number of unique reads | Percentage (%) | Total sequences | Percentage (%) | Number of unique reads | Percentage (%) | Total sequences | Percentage (%) | Number of unique reads | Percentage (%) | Total sequences | Percentage (%) | |
| Total Unique small RNA Reads | 2323170 | 100 | 45161406 | 100 | 629751 | 100 | 12160105 | 100 | 415452 | 100 | 10012888 | 100 | 1164049 | 100 | 11549959 | 100 | 536995 | 100 | 11438454 | 100 |
| Total Perfect Matched small RNA reads | 720862 | 31.0 | 31590053 | 69.9 | 201875 | 32.1 | 8682951 | 71.4 | 120695 | 29.1 | 7266543 | 72.6 | 373224 | 32.1 | 7502137 | 65.0 | 152674 | 28.4 | 8138422 | 71.1 |
| miRNAs a | 7530 | 1.0 | 15068478 | 47.7 | 3365 | 1.7 | 4451386 | 51.3 | 2684 | 2.2 | 4041090 | 55.6 | 3967 | 1.1 | 2454320 | 32.7 | 3164 | 2.1 | 4121682 | 50.6 |
| Non-Coding RNA b | 71131 | 9.9 | 6443708 | 20.4 | 39956 | 19.8 | 1556064 | 17.9 | 27417 | 22.7 | 709223 | 9.8 | 47132 | 12.6 | 2798792 | 37.3 | 29197 | 19.1 | 1379629 | 17.0 |
| rRNA | 39273 | 5.4 | 5495818 | 17.4 | 25585 | 12.7 | 1311512 | 15.1 | 18091 | 15.0 | 539528 | 7.4 | 31298 | 8.4 | 2452251 | 32.7 | 20826 | 13.6 | 1192527 | 14.7 |
| tRNA | 18189 | 2.5 | 244828 | 0.8 | 7063 | 3.5 | 54006 | 0.6 | 3977 | 3.3 | 36283 | 0.5 | 7954 | 2.1 | 112091 | 1.5 | 3540 | 2.3 | 42448 | 0.5 |
| snoRNA | 2360 | 0.3 | 36480 | 0.1 | 1030 | 0.5 | 9531 | 0.1 | 660 | 0.5 | 5882 | 0.1 | 1280 | 0.3 | 13861 | 0.2 | 729 | 0.5 | 7206 | 0.1 |
| snRNA | 454 | 0.1 | 7249 | 0.0 | 214 | 0.1 | 1107 | 0.0 | 130 | 0.1 | 614 | 0.0 | 309 | 0.1 | 4669 | 0.1 | 107 | 0.1 | 859 | 0.0 |
| other ncRNA | 10855 | 1.5 | 659333 | 2.1 | 6064 | 3.0 | 179908 | 2.1 | 4559 | 3.8 | 126916 | 1.7 | 6291 | 1.7 | 215920 | 2.9 | 3995 | 2.6 | 136589 | 1.7 |
| Transcript-derived reads | 289993 | 40.2 | 873840 | 2.8 | 52157 | 25.8 | 173709 | 2.0 | 31598 | 26.2 | 105720 | 1.5 | 173270 | 46.4 | 445779 | 5.9 | 52878 | 34.6 | 148632 | 1.8 |
| Genomic repeat-derived reads | 67509 | 9.4 | 732080 | 2.3 | 24669 | 12.2 | 66751 | 0.8 | 11222 | 9.3 | 47251 | 0.7 | 25197 | 6.8 | 91641 | 1.2 | 10348 | 6.8 | 526437 | 6.5 |
| LINE | 33783 | 50.0 | 124881 | 17.1 | 12312 | 49.9 | 36423 | 54.6 | 5312 | 47.3 | 26188 | 55.4 | 13129 | 52.1 | 32850 | 35.8 | 4622 | 44.7 | 29420 | 5.6 |
| SINE | 5681 | 8.4 | 512264 | 70.0 | 1830 | 7.4 | 8885 | 13.3 | 941 | 8.4 | 10160 | 21.5 | 2178 | 8.6 | 26692 | 29.1 | 1016 | 9.8 | 466527 | 88.6 |
| LTR | 10571 | 15.7 | 35643 | 4.9 | 3637 | 14.7 | 10730 | 16.1 | 1797 | 16.0 | 5286 | 11.2 | 4007 | 15.9 | 13374 | 14.6 | 1751 | 16.9 | 6253 | 1.2 |
| DNA | 8644 | 12.8 | 19283 | 2.6 | 2881 | 11.7 | 5062 | 7.6 | 1674 | 14.9 | 2877 | 6.1 | 3398 | 13.5 | 8261 | 9.0 | 1444 | 14.0 | 3083 | 0.6 |
| SSR | 2293 | 3.4 | 3002 | 0.4 | 1012 | 4.1 | 1216 | 1.8 | 372 | 3.3 | 427 | 0.9 | 658 | 2.6 | 868 | 0.9 | 316 | 3.1 | 491 | 0.1 |
| Low | 2524 | 3.7 | 3194 | 0.4 | 1895 | 7.7 | 2287 | 3.4 | 178 | 1.6 | 196 | 0.4 | 338 | 1.3 | 483 | 0.5 | 173 | 1.7 | 228 | 0.0 |
| Unknown Repeats | 4013 | 5.9 | 33813 | 4.6 | 1102 | 4.5 | 2148 | 3.2 | 948 | 8.4 | 2117 | 4.5 | 1489 | 5.9 | 9113 | 9.9 | 1026 | 9.9 | 20435 | 3.9 |
| Unknown | 284699 | 39.5 | 8471947 | 26.8 | 81728 | 40.5 | 2435041 | 28.0 | 47774 | 39.6 | 2363259 | 32.5 | 123658 | 33.1 | 1711605 | 22.8 | 57087 | 37.4 | 1962042 | 24.1 |
HB: hibernating state brain; AB: active state brain; HA: hibernating state adipose tissue; AA: active state adipose tissue. rRNA, ribosomal RNA; tRNA, transfer RNA; snoRNA, small nucleolar RNA; snRNA, small nuclear RNA; LINE, Long INterspersed Elements; SINE, Short INterspersed Elements; LTR, Transposable elements with Long Terminal Repeats; DNA, DNA transposons; SSR, Simple Sequence Repeats; Low, Low Complexity Sequences; unknown, derived from unannotated/intergenic regions.
a miRNA reads identified by miCheck, searched against the Sanger miRBase (Release 19) and manually inspected for canonical structure from 24656421 total potential reads (S2 Fig and S5 Table).
b Screening against non-coding RNA databases (Release 10) to filter ncRNAs (tRNA, rRNA, snoRNA and other ncRNA) by Bowtie.