Supplement: Analyzing CRISPR Editing Results

Source: Supplement: Analyzing CRISPR Editing Results

Overview of ICE Editing Analysis

Once the analysis is complete, a new window appears with a graphical representation of the results and a list of the analyzed samples (Figure 1).

If the sample run had no issues, the analysis window shows a green checked circle in front of the sample name. If there was a minor error during processing, the window shows a yellow checked circle. If there are no results or there was a processing error, you will see a red exclamation point in front of that sample. You can hover over the yellow or red circles to gather details on the issues associated with each sample.

Successfully analyzed samples will display the following parameters:

• Sample—The unique label name for each sample.

• Guide Target—The 17–23-nucleotide sequence of the DNA-targeting region of the guide RNA, excluding the PAM sequence.

• PAM Sequence—The Protospacer Adjacent Motif (PAM) sequence for the nuclease used. Currently, ICE is configured for the Cas9 nuclease from Streptococcus
pyogenes (SpCas9).

• ICE—The editing efficiency (percentage of the pool with non-wild-type sequence) as determined by comparing the edited trace to the control trace. In the ICE algorithm, potential editing outcomes are proposed and fitted to the observed data using linear regression.

• R²—When the ICE linear regression is computed during generation of the ICE Score, the Pearson correlation coefficient (R²) is also computed and reported. The higher the R² value, the more confident you can be in the ICE score.

• KO-Score—Represents the proportion of cells that have either a frameshift or 21 + bp indel likely to result in a functional KO of the targeted gene.

You can perform more in-depth analyses on each sample by clicking on the sample name or on its corresponding bar graph entry. Clicking to initiate the in-depth analysis will open a new window with three tabs. Each of the three tabs (Contributions, lndel Distribution, and Traces) provides particular details about the indel profile of the edited sample.

Published at Thu, 31 May 2018 18:45:49 +0000