To generate this dataset, fluorescence-activated cell sorting (FACS) was used to enrich neuronal nuclei with and without TDP-43 from postmortem brain tissue from patients with FTD and ALS (FTD–ALS); RNA-seq was performed to compare the transcriptomic profiles of TDP-43-positive and TDP-43-negative neuronal nuclei. The gene discussed is TARDBP; the disease is frontotemporal dementia.