Table 1.
Distribution of total and unique sequences from human HeLa cells and mouse brain RNP libraries
|
HeLa |
Mouse brain |
|||||
|---|---|---|---|---|---|---|
| Total reads | Unique clusters | Clusters >2 | Total reads | Unique clusters | Clusters >2 | |
| Analysed sequences | 108 518 (100%) | 1636 | 398 | 31 882 (100%) | 1530 | 313 |
| snoRNA | 16 489 (15%) | 141 (9%) | 106 (27%) | 11 701 (37%) | 132 (9%) | 84 (15%) |
| tRNA | 45 818 (42%) | 122 (7%) | 88 (22%) | 4286 (13%) | 89 (6%) | 46 (15%) |
| miRNA | 41 652 (38%) | 252 (15%) | 143 (36%) | 9027 (28%) | 265 (17%) | 106 (15%) |
| rRNA | 1901 (2%) | 4 (<1%) | 4 (1%) | 672 (2%) | 4 (<1%) | 4 (15%) |
| snRNA | 1196 (1%) | 14 (<1%) | 11 (3%) | 4063 (13%) | 14 (<1%) | 14 (15%) |
| Miscellaneous RNA | 1027 (<1%) | 80 (5%) | 29 (7%) | 1279 (4%) | 60 (4%) | 25 (15%) |
| Sense to intron | 494 (<1%) | 313 (19%) | 5 (1%) | 410 (<1%) | 337 (22%) | 10 (3%) |
| Antisense to intron | 439 (<1%) | 275 (16%) | 5 (1%) | 241 (<1%) | 196 (13%) | 7 (2%) |
| Sense to exon | 97 (<1%) | 97 (6%) | 0 | 172 (<1%) | 158 (10%) | 2 (<1%) |
| Antisense to exon | 26 (<1%) | 26 (2%) | 0 | 7 (<1%) | 7 (<1%) | 0 |
| Sense to junction | 9 (<1%) | 9 (<1%) | 0 | 21 (<1%) | 19 (1%) | 0 |
| Antisense to junction | 0 | 0 | 0 | 1 (<1%) | 1 (<1%) | 0 |
| Intergenic | 471 (<1%) | 303 (19%) | 7 (2%) | 397 (1%) | 248 (16%) | 15 (5%) |
After clustering, sequences retrieved from both HeLa and mouse brain libraries were classified into a specific ncRNA family by blasting cDNA sequences against the corresponding genomic nucleotide database (for details see ‘Materials and Methods’ section). Total number of sequences, as well as number of unique sequence clusters, for each ncRNA class, is indicated. The third column in each library indicates the unique sequences represented by at least three cDNA clones. S stands for sense, AS for antisense. Miscellaneous RNA: RNA 7SL, RNA 7SK, piRNAs, vault RNA, RNA Y, RNAse P RNA, RNAse MRP RNA.