DeepxCas9:
How to interpret the result table
-Location: The location of the selected 30 bp target sequence within the whole input sequence
The location is indicated using the following format.
Starting base pair from the beginning of the whole input sequence: ending base pair from the beginning of the whole input sequence
Example 1. 59:88 (Interpretation) The 30 bp target sequence spans from the 59th to the 88th bp of the input sequence, counting from the beginning of the whole input sequence.
Example 2. 96:67 (Interpretation) The 30 bp target sequence spans from the 96th to the 67th bp of the input sequence, counting from the beginning of the whole input sequence. Thus, the target sequence containing the PAM is the reverse complement of the input sequence.
-Input Sequence: The 30 bp region in the input sequence containing the target sequence. If the PAM is in the input sequence, the input sequence is identical to the target sequence. If the PAM is on the opposite strand of the input sequence, the input sequence is reverse complementary to the target sequence. The PAM sequence or the reverse complementary sequence of the PAM is indicated in red.
-Target sequence: The 30 bp target sequence including the PAM, which is indicated in red.
-Guide RNA sequence: 20 nt guide RNA sequence.
-GC content: GC content of the 20 bp protospacer sequence (guide RNA sequence)
-DeepxCas9 or DeepSpCas9-NG score: A DeepxCas9 or DeepSpCas9-NG score is the expected indel frequency (expressed as a percentage) at the target sequence when the sgRNA and Cas9 variants are lentivirally delivered into HEK293T cells for three days. For example, if the DeepxCas9 score at a certain target sequence is 10, then the expected indel frequency at the target sequence at three days after lentiviral delivery of xCas9 and sgRNA is 10%. For users’ information, we provide the actual relations between the measured indel frequency and the DeepxCas9 or DeepSpCas9-NG score; the following plot shows an almost linear y = x relationship between the predicted score and measured indel frequency at lentivirally integrated target sequences three days after lentiviral delivery of either xCas9 or SpCas9-NG and the corresponding sgRNAs in HEK293T cells.
-Note: If there is polyT within the guide RNA sequence, the presence of polyT would be described here.
-Percentile rank of the DeepxCas9 or DeepSpCas9-NG score: The percentile rank was calculated based on the large data sets of DeepxCas9 scores at 4,956 target sequences and DeepSpCas9-NG scores at 4,641 target sequences. These 4,956 and 4,641 target sequences were randomly selected from the human genome without any prior information about the activity of the corresponding sgRNAs (21 and 7 target sequences were chosen per 5-nt PAM for xCas9 and SpCas9-NG, respectively). A percentile rank of 100 represents the highest Cas9 activity, whereas a percentile rank of 0 represents the lowest activity. The relations between the percentile rank of the score and the actual score in DeepxCas9 and DeepSpCas9-NG are shown below for users’ information.
