11.3 Glossary

A

adjacent break A break located within 1 base pair (bp) of another break.

B

break A single break observed by the INDUCE-seq Pipeline resulting from a Double-Stranded Break (DSB).

break site The chromosomal location where one or more breaks were observed.

break site probability score A percentage representing the probability that a site resulted from the treatment applied to the samples, rather than from an endogenous process present in the control untreated samples.

BSB INDUCE-seq Analysis Workspace The LatchBio environment dedicated to INDUCE-seq.

C

condition All information that distinguishes a sample (other than it being a technical replicate) from the experiment.

E

endogenous break A break occurring as a result of the cell's natural processes. Endogenous breaks typically occur at lower recurrency than breaks induced by a nuclease mechanism. The majority of breaks detected are caused by these processes.

I

INDUCE-seq Analysis The analysis workflow used to identify and visualise breaks captured by the On-Demand INDUCE-seq Solution assay.

induced break A break occurring as a result of the editing process.

L

LatchBio A web-based, cloud platform used for handling and analysing sequencing data.

M

manifest A tabular format for storing nuclease or sample metadata.

N

nuclease mechanism All information regarding the nuclease treatment applied to the cell samples.

normalised sample to control ratio For each break site in an edited/treated sample, the break count and the count in the equivalent genomic interval in the untreated control are recorded. After normalisation per million total breaks in each respective sample, the treated-to-control ratio is calculated.

R

recurrency class A collection of break sites with the same recurrency. For example, a recurrency class of 5 represents a set of recurrent break sites each observed 5 times.

recurrent break Multiple breaks at the same break site. Adjacent breaks are merged to represent breaks forming part of the same break site. For some nuclease mechanisms, breaks are induced over a wider window (e.g. Cas12a at HPRT1), making a wider merge distance appropriate.

S

sample An individual well of the cell plate described in the sequencing input sample sheet. Multiple cell samples that have undergone the same treatment are considered replicates.