10X Genomics single-cell RNAseq combined with CRISPR tiling of Dot1l in mouse MLL-AF9 leukemia

High-density single-cell RNAseq and direct-capture Perturb-seq Overall design: 602 sgRNAs targeting the coding exons of mouse Dot1l were cloned into a sgRNA vector with the CS1 capture sequence incorporated into the 3' end of the sgRNA backbone. The sgRNA library was transduced into mouse MLL-AF9 leukemia cells expressing Cas9 endonuclease. Single cells were isolated three days post-transduction using a 10X Chromium and 10X GEM v3.1 kit. Two sequencing libraries were derived from this single-cell sample (1) poly(T) captured mRNA library and (2) CS1 captured sgRNA library. Both libraries were sequenced using an Illumina HiSeq PE150.