RNAseq and quantitative proteomic analysis of Dictyostelium knock-out cells lacking the core autophagy proteins ATG9 and/or ATG16

Purpose: Global survey of the transcriptome and comparison to the proteome in autophagy-deficient strains of D. discoideum. Results: Our RNAseq analysis of ATG9‾, ATG16‾ and ATG9‾/16‾ cells revealed major transcriptional changes in a large number of genes in comparison to AX2. Conclusions: Our study provides the first combined transcriptome and proteome analysis of ATG9‾, ATG16‾ and ATG9‾/16‾ cells and adds to our knowledge of functions of these proteins in Dictyostelium discoideum. Total RNA from vegetative Dictyostelium discoideum cells (AX2 wild-type and ATG9‾, ATG16‾, ATG9‾/16‾ mutant strains) was isolated; sequencing and analysis was as described in Karow et al. Cells, 9(5), E1179. n=9, Illumina Genome Analyzer IIx