Global analysis of enhancer targets: Mosaic-seq

Single-cell perturbation assays such as Mosaic-seq enable highly multiplexed functional assessment of enhancers in their endogenous genomic context. By introducing a few computational and experimental improvements, we expanded the Mosaic-seq analysis to capture the secondary gene targets of enhancers. Our analysis of >500 putative enhancers in K562 cells demonstrates that many secondary hits are shared among enhancers targeting different transcriptional factors, which reveals an interwoven enhancer-driven gene regulatory network. Together, our data underscore the flexibility of manipulating gene transcription by modifying enhancer activity. We performed Mosaic-seq on 518 enhancers in K562 cells. We used 10X genomics 3’ V2 kit to prepare the single-cell transcriptome libraries. The sgRNA is expressed by using the CROP-seq design, and a sgRNA enrichment library was also prepared for each single-cell library. In total, we performed ten 10X runs for five different batches, with a total number of > 100K cells sequenced. For the processed data, we uploaded the gene expression matrix (HDF5 format) from 10X cellranger pipeline in together with the sgRNA information of each cell.