Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells

We describe a protocol for freezing neuronal cells that is compatible with ATAC-Seq, producing results that compare well with those generated from fresh cells. We developed our protocol on a disease-relevant cell type, namely motor neurons differentiated from induced pluripotent stem cells from a patient affected by spinal muscular atrophy. We found that while flash-frozen motor neurons are not suitable for ATAC-Seq, the assay is successful with slow-cooled cryopreserved samples. Using this method, we were able to isolate high quality, intact nuclei, and we verified that epigenetic results from fresh and cryopreserved motor neurons agree quantitatively. We quantitatively compare the results from fresh and cryopreserved motor neurons. We generated sequencing data on three technical replicates from both conditions. Submitter declares that reads for the transposed naked DNA used as a control will be made available through dbGaP.