The data was obtained in course of performing a CRISPR/Cas9 knock-out in human polarized epithelial cells (CaCo₂). The screen aimed to identify genes relevant for proper epithelial polarization and correct apical transport of the apical transmembrane protein dipeptidyl-peptidase 4. It includes next-generation-sequencing data (raw sgRNA-read-counts) of two experimental (sorted) and corresponding control (ctrl) cell populations. It further contains sequence information on the sgRNAs as represented in the human GeCKOv2-CRISPR library and the corresponding targeted genes.