Table 2 Zebrafish embryo genotyper-based embryo selection at the BrS locus (n = 43 fish for KI and n = 43 fish for indels).

From: Improved selection of zebrafish CRISPR editing by early next-generation sequencing based genotyping

Editing outcome

N alleles in model

Selection threshold (%)

Average SEF—all fish (%)

Average SEF—excluded fish (%)

Average SEF—selected fish (%)

Fold increase

Significance

KI

1

2

3.02

1.19

7.73

1.56

***

All indels

10

2

1.93

0.88

5.85

2.03

***

Indels < 1%

5

2

0.64

0.48

3.60

4.62

***

Indels 1–5%

3

2

1.38

0.93

3.01

1.18

***

Indels > 5%

2

2

5.96

3.08

7.85

0.32

***

KI

1

5

3.02

1.38

10.20

2.38

***

All indels

10

5

1.93

1.14

8.37

3.34

***

Indels < 1%

5

5

0.64

0.48

7.45

10.62

***

Indels 1–5%

3

5

1.38

1.07

6.17

3.46

***

Indels > 5%

2

5

5.96

3.96

9.03

0.51

***

KI

1

10

3.02

1.44

12.77

3.23

***

All indels

10

10

1.93

1.46

12.56

5.52

***

Indels < 1%

5

10

0.64

0.49

11.51

16.96

***

Indels 1–5%

3

10

1.38

1.14

11.74

7.49

***

Indels > 5%

2

10

5.96

4.82

13.03

1.19

***

  1. KI knock-in, indel insertion/deletion, SEF somatic editing frequency, N number, NS not significant.
  2. ***p-value < 0.001 (based on negative binomial regression with selected and excluded as fixed factors and indel sequence as random factor if > 1 indels were considered in the analysis). The fold increase was calculated as (Average SEF selected fish – average SEF all fish)/average SEF all fish.
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