An article published in GenomeBiology presents INSERT-seq: a simple, cheap and robust method to quantitatively characterise DNA integration in diverse ex vivo and in vivo samples.
In order to assess the impact of read length in the detection of insertions, we performed a simulation of data using different read lengths. Reads of 250 and 1000 bases were generated for a total of 1000 random genomic locations with R scripting and Biostrings []. We performed 10 replicates, simulating 100 insertions for each condition. A normal distribution was applied to read length, setting the standard deviation to 10 for short reads and 25 for long reads .
An insertion is considered to fall in a repetitive region if the insertion site or 20 base pairs surrounding it contained a repetitive region from Dfam database. The same procedure was repeated for read lengths of 100, 350 and 5000 bases for further comparisons., and Dulbecco’s modified eagle medium high glucose , 10% FBS, 2 mM glutamine, 0.1 mg/mLpenicillin and streptomycin, was used. K-562 cells [ATCC® ACS-CCL-243™] were grown in RPMI 1640 supplemented with 10% FBS.
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