Table 1.
miRNA and Target Pool Concentrations and iCLIP Coverage Values of Active miRNA Families
| miRNA Family |
Seed Match |
[miRNA] cpc/nM |
8-mer [target] cpc/nM |
7-mer [target] cpc/nM |
6-mer [target] cpc/nM |
Total Ago Occupancy 8-mer Targets |
Total Ago Occupancy 7-mer Targets |
Total Ago Occupancy 6-mer Targets |
|
|---|---|---|---|---|---|---|---|---|---|
| ESC | miR-294 | AGCACTT | 56,700/471 | 1,271/11 | 6,453/54 | 12,077/100 | 2.27 | 1.52 | 1.54 |
| miR-292-5p | GTTTGAG | 13,328/111 | 2,492/21 | 7,664/64 | 40,883/340 | 0.5 | 0.15 | 0.12 | |
| miR-292/467 | GGCACTT | 8,643/72 | 736/6 | 4,185/35 | 12,086/100 | 2.1 | 1.24 | 1.54 | |
| miR-293 | GCGGCAC | 2,644/22 | 360/3 | 1,847/15 | 4,807/40 | 1.53 | 0.63 | 0.53 | |
| miR-15/16 | TGCTGCT | 1,814/15 | 2,484/21 | 24,549/204 | 11,0918/921 | 0.59 | 0.21 | 0.16 | |
| miR-92/25 | GTGCAAT | 1,720/14 | 1,195/10 | 2,653/22 | 17,367/144 | 0.91 | 0.39 | 0.1 | |
| miR-26 | TACTTGA | 1,696/14 | 2,758/23 | 4,784/40 | 28,284/235 | 0.22 | 0.14 | 0.12 | |
| miR-291-5p | CTTTGAT | 584/5 | 1,903/16 | 8,660/72 | 34,740/289 | 0.28 | 0.2 | 0.14 | |
| MSC | let-7 | CTACCTC | 41,748/46.2 | 1,380/1.5 | 2,884/3.2 | 20,414/22.6 | 3.53 | 1.99 | 1.16 |
| miR-125-5p | CTCAGGG | 19,309/21.4 | 1,448/1.6 | 4,442/4.9 | 11,378/12.6 | 1.06 | 0.7 | 0.3 | |
| miR-26 | TACTTGA | 11,624/12.9 | 1,398/1.5 | 2,309/2.6 | 12,612/14.0 | 1.04 | 0.54 | 0.41 | |
| miR-15/16 | TGCTGCT | 6,610/7.3 | 1,450/1.6 | 12,833/14.2 | 56,220/62.3 | 2.72 | 1.08 | 0.71 | |
| miR-21 | ATAAGCT | 5,674/6.3 | 520/0.6 | 1,730/1.9 | 7,694/8.5 | 1.44 | 0.65 | 0.46 | |
| miR-99 | TACGGGT | 4,813/5.3 | 78/0.1 | 399/0.4 | 2,154/2.4 | 1.14 | 1.03 | 0.95 | |
| miR-31 | TCTTGCC | 2,228/2.5 | 1,426/1.6 | 3,603/4.0 | 13,285/14.7 | 1.12 | 0.79 | 0.41 | |
| miR-199 | ACTACTG | 1,226/1.4 | 912/1.0 | 2,827/3.1 | 10,837/12.0 | 0.91 | 0.59 | 0.5 | |
| miR-92/25 | GTGCAAT | 912/1.0 | 787/0.9 | 1,727/1.9 | 8,239/9.1 | 2.27 | 1.01 | 0.43 | |
| miR-27 | ACTGTGA | 849/0.9 | 2,266/2.5 | 6,011/6.7 | 21,091/23.4 | 1.29 | 0.68 | 0.52 | |
| miR-30 | TGTTTAC | 562/0.6 | 2,411/2.7 | 3,296/3.7 | 6,072/6.7 | 1.33 | 1.11 | 0.56 | |
| miR-17/20/93 | GCACTTT | 302/0.3 | 1,018/1.1 | 3,475/3.8 | 14,881/16.5 | 1.91 | 1.08 | 0.57 |
Measured copies per cell (cpc) and converted nM concentrations for all ESC and MSC miRNA families with statistically enriched average iCLIP coverage over random control sites (p < 0.01). Target concentration [target] is the endogenous iCLIP-estimated target abundance per miRNA and site type pair across all genomic regions (corresponding to values graphed in Figures 4C and S7E). Total Ago Occupancy, iCLIP reads per million (RPM) across corresponding sites/site type target pool cpc.