Table 1.
Summary of the chromosomal manipulations induced by the two types of EENs
| No. | Targeted loci in chromosomes and genes in the regiona | EENdb IDb | Distance | Manip.c | Ratio of positive foundersd | Ratio of positive F1e | Average Ratio |
|---|---|---|---|---|---|---|---|
| 1 | Chr. 11: 36.3 Mb | TNT01 + TNT02 | 43.8 kb | Del. | 3/19 | #F3: 5/(10 × 14), 10/296* | 3.7% |
| sema3fb | |||||||
| #F4: 1/(10 × 51) | |||||||
| #M4: 6/(10 × 8) | |||||||
| Inv. | 1/19 | #F6: 2/(10 × 4), 6/41* | 10% | ||||
| 2 | Chr. 8: 12.1 Mb | TNT03 + TNT04 | 0.82 kb | Del. | 2/21 | #M12: 3/14 | 21% |
| dre-mir-126a | #M13: 3/14 | ||||||
| TNT03 + TNT05 | 0.82 kb | Del. | ND | ||||
| TNT03 + TNT06 | 0.70 kb | Del. | ND | ||||
| CNT01 + CNT02 | 0.60 kb | Del. | ND | ||||
| CNT01 + CNT04 | 0.61 kb | Del. | ND | ||||
| CNT03 + CNT02 | 0.60 kb | Del. | ND | ||||
| CNT03 + CNT04 | 0.61 kb | Del. | ND | ||||
| 3 | Chr. 11: 38.5 Mb | TNT07 + TNT08 | 0.19 kb | Del. | 1/9 | #M2: 1/(6 × 7) | 2% |
| dre-mir-126b | |||||||
| 4 | Chr. 1: 2.8 Mb | TNT09 + TNT10 | 1.5 kb | Del. | 5/15 | #M6: 6/14 | 23% |
| dre-mir-17a-1–dre-mir-92a-1 | #M7: 5/(6 × 7) | ||||||
| (miRNA Cluster Chr. 1, including 6 miRNA genes) | #M12: 5/14 | ||||||
| #M14: 5/(6 × 7) | |||||||
| #M15: 2/14 | |||||||
| TNT11 + TNT10 | 2.1 kb | Del. | 1/3 | #M2: 7/(6 × 7) | 20% | ||
| TNT09 + TNT12 | 2.6 kb | Del. | 2/9 | #M1: 2/14 | 21% | ||
| #M9: 4/14 | |||||||
| TNT11 + TNT12 | 3.2 kb | Del. | 2/11 | #M1: 5/28 | 13% | ||
| #M10: 2/28 | |||||||
| 5 | Chr.9: 55.4 Mb | TNT13 + TNT14 | 1.5 kb | Del. | 3/36 | #M19: 2/28 | 16% |
| dre-mir-17a-2–dre-mir-92a-2 | #M25: 2/28 | ||||||
| (miRNA Cluster Chr. 9, including 6 miRNA genes) | #M32: 5/14 | ||||||
| CNT05 + CNT06 | 1.5 kb | Del. | ND | ||||
| CNT05 + CNT08 | 1.5 kb | Del. | ND | ||||
| CNT07 + CNT06 | 1.5 kb | Del. | ND | ||||
| CNT07 + CNT08 | 1.5 kb | Del. | ND | ||||
| 6 | Chr. 11: 18.8 Mb | TNT15 + TNT16 | 30.2 kb | Del. | 2/40 | #M9: 3/(6 × 8), 10/64* | 13% |
| fgd5 and ENSDARG00000070653 | |||||||
| #M43: 5/(6 × 8) | |||||||
| 7 | Chr. 6: 51.7–51.8 Mb | TNT17 + TNT18 | 122 kb | Del. | 5/55 | #M26: 1/(8 × 8) | 14% |
| ENSDARG00000076787 to psmf1 | #M42: 4/16 | ||||||
| (3 coding and 1 miRNA genes) | #M46: 1/(8 × 8) | ||||||
| #M49: 3/16 | |||||||
| #M51: 4/16 | |||||||
| 8 | Chr. 23: 31.3–31.8 Mb | TNT19 + TNT20 | 436 kb | Del. | ND | ||
| tbx18 to tcf21 | |||||||
| (12 coding and 2 snoRNA genes) | |||||||
| 9 | Chr. 25: 15.5–16.5 Mb | TNT21 + TNT22 | 981 kb | Del. | ND | ||
| wt1a to mical2b | |||||||
| (27 coding and 1 miRNA genes) | |||||||
| 10 | Chr. 1: 5.1–5.2 Mb | TNT23 + TNT24 | 73.6 kb | Del. | ND | ||
| gtf3c3 and ENSDARG0000 0063253 | |||||||
| 11 | Chr. 22: 18.9 Mb–Tol2 | TNT25 + TNT26 | 57.5 kb | Del. | 0/40 | ||
| (in a transgenic line) | Inv. | ND | |||||
| midn and eGFP (exogenous) | TNT25 + TNT27 | 55.5 kb | Del. | ND |
aGenome assembly and gene annotation are based on Ensembl Zv9, release 71 (April 2013); ZFIN- or miRBase-approved gene symbols or Ensembl IDs are used.
bEfficiency of individual pair of TALENs and Cas9/gRNA are listed in Supplementary Table S1.
cManip. = manipulation; Del. = deletion; Inv. = inversion.
dND = not determined.
eMosaicism (the ratio of F1 offspring from each founder) was evaluated by different ways and presented in three patterns: (i) a/(b × c): PCR results from c wells of mixed genomic DNA (b F1 embryos per well) were obtained, and a wells were positive (i.e. no less than a F1 embryos were positive); (ii) a/b: PCR results of b single F1 embryos were obtained and a of them were positive; (iii) a/b*: PCR results of single tail clips of b F1 adult fish were obtained, and a of them were positive. In case the data from both embryos and adults are available, the latter are used to calculate the average ratios for the last column.