The database includes the raw data of the article “HDAC6 and TDP-43 promote autophagy impairment in Amyotrophic Lateral Sclerosis”. Aim of this work was to investigate how TDP-43 and HDAC6 interacts, leading to the impairment of the autophagy pathway. The work was performed in both PBMCs and in transfected SH-SY5Y cells. The database contains the data obtained by the following evaluations: a) western blot (WB) analysis in healthy control and sporadic ALS patients PBMCs b) western blot analysis of protein involved in autophagy pathway after transfection with TDP-43 WT plasmid c) western blot analysis of protein involved in autophagy pathway after silencing of HDAC6. This work provides solid evidence supporting the hypothesis that dysregulation of HDAC6 is a key factor in the disruption of the autophagy pathway previously detected in sALS PBMCs. To the best of our knowledge, we demonstrated for the first time that both excessive reduction in acetylated α-tubulin levels, due to HDAC6 overexpression, and excessive increase in acetylated α-tubulin levels, resulting from HDAC6 downregulation, lead to impairments in autophagy. These findings could be exploited as possible therapeutic target.