Selective autophagy of the endoplasmic reticulum, known as ER-phagy, is essential to maintain ER homeostasis. We recently showed that members of the autophagy receptor family FAM134 are regulated by phosphorylation-dependent ubiquitination. In an unbiased screen we had identified several kinases downstream of mTOR with profound impact on ER-phagy flux, upon them ATR and CK2. Inhibition of CK2 by SGC-CK2-1 prevented regulatory ubiquitination of FAM134B and FAM134C upon autophagy activation as well as the formation of high-density FAM134B- and FAM134C-clusters. Here we report on additional resource data of global proteomics upon CK2 and ATR inhibition, respectively. Our data suggests that the function of CK2 is mainly limited to the ER / ER-phagy and Golgi, while ATR inhibition by VE-822 affects the vast majority of organelles / selective autophagy pathways.