In recent years, the assay for transposase-accessible chromatin using sequencing (ATAC-Seq) has become a fundamental tool of epigenomic research. However, it is difficult to perform this technique on frozen samples because freezing cells before extracting nuclei can impair nuclear integrity and alter chromatin structure, especially in fragile cells such as neurons. Our aim was to develop a protocol for freezing neuronal cells that is compatible with ATAC-Seq; we focused on a disease-relevant cell type, namely motor neurons differentiated from induced pluripotent stem cells (iMNs) from a patient affected by spinal muscular atrophy. We found that while flash-frozen iMNs are not suitable for ATAC-Seq, the assay is successful with slow-cooled cryopreserved cells. Using this method, we were able to isolate high quality, intact nuclei, and we verified that epigenetic results from fresh and cryopreserved iMNs quantitatively agree.Since its establishment, the assay for transposase-accessible chromatin using sequencing (ATAC-Seq) has revolutionized the study of epigenetics 1,2 . This technique detects open-chromatin regions and maps transcription factor binding events genome-wide by means of direct in vitro transposition of native chromatin. Specifically, hyperactive Tn5 transposase is used to interrogate chromatin accessibility by inserting high-throughput DNA sequencing adapters into open genomic regions, which allows for the preferential amplification of DNA fragments located at sites of active chromatin. Because the DNA sites directly bound by DNA-binding proteins are protected from transposition, this approach enables the inference of transcription factor occupancy at the level of individual functional regulatory regions. Furthermore, ATAC-Seq can be utilized to decode nucleosome occupancy and positioning, by exploiting the fact that the Tn5 transposase cuts DNA with a periodicity of about 150-200 bp, corresponding to the length of the DNA fragments wrapped around histones 3 . This periodicity is maintained up to six nucleosomes and provides information about the spatial organization of nucleosomes within accessible chromatin. ATAC-Seq signals thus allow for the delineation of fine-scale architectures of the regulatory framework by correlating occupancy patterns with other features, such as chromatin remodeling and global gene induction programs. Compared to other epigenetic methodologies, such as FAIRE-Seq and conventional DNase-Seq, ATAC-Seq requires a small number of cells. Therefore, it is suitable for work on precious samples, including differentiated cells derived from induced pluripotent stem cells (iPSCs), primary cell culture, and limited clinical specimens. Recently developed techniques, such as single-cell DNase sequencing (scDNase-seq) 4 , indexing-first ChIP-Seq (iChIP) 5 , ultra-low-input micrococcal nuclease-based native ChIP (ULI-NChIP) 6 , and ChIPmentation 7 , allow for the epigenomic investigation of small number of cells or even single cells without requiring microfluidic devices. However, these ...