Table 1 Rates and flow estimates for the 3-state model of DSB Repair for the 72 h time course

From: Uncovering the dynamics of precise repair at CRISPR/Cas9-induced double-strand breaks

Target

Process

Ratea (proportion of total event/hour)

CI [1–99%]c

Flowb after 72 h (proportion of total molecules)

CI [1–99%]c

P-value

Psy1

Cutting

0.0092

0.0064-0.5434

0.5755

0.4031−31.0895

<0.01

Repair-error

0.0335

0.0276-0.0419

0.1518

0.1364-0.1683

<0.01

Precise Repair

0.0791

0.0373-7.2711

0.3581

0.1812-30.6583

<0.01

e (processed DSB)

0.2052

0.1659-0.2392

/

/

<0.01

U (uncut fraction)

0

0–0.0001

/

/

0.98

r (induction speed)

9402.089

2.5443-20909.0328

/

/

<0.01

d (induction decay)

0

0–0

/

/

<0.01

Repair accuracy

/

/

0.7024

0.5478-0.9951

<0.01

CRTISO

Cutting

0.0175

0.0129-0.029

0.8815

0.5429-1.2973

<0.01

Repair-error

0.0777

0.0611-0.0976

0.4375

0.3604-0.5178

<0.01

Precise Repair

0.0675

0–0.1563

0.3799

0–0.8654

0.1

e (processed DSB)

0.32

0.2332-0.3908

/

/

<0.01

U (uncut fraction)

0

0–0.1179

/

/

0.92

r (induction speed)

48.8311

5.3069-24293.2738

/

/

<0.01

d (induction decay)

0

0–0.0048

/

/

<0.01

Repair accuracy

/

/

0.4648

0–0.7

0.1

PhyB2

Cutting

0.0718

0.0434-0.9763

0.9113

0.5786-26.7611

<0.01

Repair-error

0.0864

0.0741-0.122

0.5282

0.4966-0.579

<0.01

Precise Repair

0.0583

0.0036-5.5634

0.3567

0.0229-26.0203

<0.01

e (processed DSB)

0.0817

0.048-0.1353

/

/

<0.01

U (uncut fraction)

0.4047

0–0.4395

/

/

0.04

r (induction speed)

8.0297

2.9301-1079.26

/

/

<0.01

d (induction decay)

0

0–0.0073

/

/

<0.01

Repair accuracy

/

/

0.4031

0.0414-0.9784

<0.01

  1. aRates are reported as the number of events per molecule per hour.
  2. bThe flow is reported as the proportion of molecules that experienced that event at the end of the experiment.
  3. cConfidence intervals (CI) are reported as the 1% and 99% percentiles of the estimates obtained from 100 stratified bootstraps of the data, while p-values as the proportion of bootstraps with value smaller or equal than 0 (one-sided test). When none of the 100 bootstraps had value equal to 0 we reported p-values as <0.01. The induction curve is modeled as a logistic increase in activity of the RNPs with speed r, a fraction U of cells upon which the RNPs do not cut DNA, and a decay. d An error parameter. Describes the proportion of DSBs which show DSB ends not coinciding with the expected position (see Methods: Determining the parameters of the induction curve). Repair accuracy is computed as the proportion of DSBs repaired precisely over all repaired DSBs (precise and error repair) at the end of the time course.
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