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We report the use of patient-derived induced pluripotent stem cells (iPSCs) to generate neuronal-like cells similar to those affected in the neurological disorder Ataxia-Telangiectasia (A–T), namely Purkinje and granule cells of the cerebellum. Generation of cerebellar-like cells from murine ESCs and human embryonic stem cells has previously been reported, however isolation and manipulation of discrete sub-populations of cerebellar neuronal cells has proven challenging. Building on these studies, we successfully induce widescale expression of mid–hindbrain markers EN1 and GBX2, and the transcription factors MATH1 and PTF1, which demarcate rhombic lip (granule cell) and ventricular zone (Purkinje, Golgi, and Stellate cell) progenitors, respectively, We then expand these progenitors to produce cells that are morphologically similar to granule cells, which also express markers characteristic of this cell type. To gain insight into the early events that occur during the formation of the cerebellum and how these may be affected in the absence of ATM, RNA sequencing of neuronal progenitors was performed. After 34 days of differentiation, both control and AT samples downregulated pluripotency genes and upregulated neural commitment and anterior/posterior patterning gene programs, including EN1, ISL1, MEIS1, SHH, REELIN, LHX9, WNTLESS, NFIX and members of the HOX gene family. Previously characterized pluripotency-regulating and neurogenesis-associated long non-coding RNAs and small RNA precursors were identified as differentially expressed during development, and novel transcripts with no previous reports of …