Cell-type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening
In silico genetic screen at 2-Mb windows
. Briefly, for each chromatin remodeling gene, we designed on average 6–8 single guide RNAs , for a total of2,500 sgRNAs. The sgRNA sequences were synthesized by Twist Bioscience, and cloned into a lentivirus-based sgRNA vector tagged with GFP . Cas9-expressing T-ALL cell lines were transduced with sgRNA library virus at a low multiplicity of infection , followed by infection efficiency assessment through GFP percentage on Day 4 posttransduction.
. For pooled CRISPR screening analysis, samples of each time-point were normalized as sgRNA read count/total read count × 100,000. Subsequently, normalized reads were then used to calculate logfc for each gRNA. The fold changes between Day 4 and Day 20 for each gene were averaged from all CRISPR gRNA targets.-test comparing the fold changes of all gRNA targets of the same gene with fold change of 1.was used to compute the interactions of each selected viewpoint in a roll-window fashion.
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