CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation

We investigated the transcriptional consequences of Chd7 and Runx1 loss in 416B cells, a myeloid progenitor cell line. We engineered the cell line to express Cas9 protein and targeted endogenous Chd7 and Runx1 loci with sgRNAs introduced with lentiviral constructs. We read out the transcriptomes of control and perturbed cells using RNA-Seq following an established SMART-Seq2 protocol (Picelli et al. 2014). Overall design: 416B cells were transduced with sgRNAs targeting either Chd7 gene (3 different sgRNAs), Runx1 gene (one sgRNA) or GFP (control). Each condition was performed in quadruplicate. Transcriptional changes were assessed using differential expression between treated and the control cells