PT  - JOURNAL ARTICLE
AU  - Pamela Milani
AU  - Renan Escalante-Chong
AU  - Brandon C. Shelley
AU  - Natasha L. Patel-Murray
AU  - Xiaofeng Xin
AU  - Miriam Adam
AU  - Berhan Mandefro
AU  - Dhruv Sareen
AU  - Clive N. Svendsen
AU  - Ernest Fraenkel
TI  - Cell freezing protocol optimized for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells
AID  - 10.1101/036798
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 036798
4099  - http://biorxiv.org/content/early/2016/02/10/036798.short
4100  - http://biorxiv.org/content/early/2016/02/10/036798.full
AB  - In recent years, the assay for transposase-accessible chromatin using sequencing (ATAC-Seq) has become a fundamental tool of epigenomic research. However, it has proven difficult to perform this technique on frozen samples because freezing cells before extracting nuclei impairs nuclear integrity and alters chromatin structure. We describe a protocol for freezing cells that is compatible with ATAC-Seq, producing results that compare well with those generated from fresh cells. We found that while flash-frozen samples 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 samples agree quantitatively. 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.