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. Overall design: 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