RT Journal Article
SR Electronic
T1 Cell freezing protocol optimized for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 036798
DO 10.1101/036798
A1 Pamela Milani
A1 Renan A. Escalante-Chong
A1 Brandon C. Shelley
A1 Natasha L. Patel-Murray
A1 Xiaofeng Xin
A1 Miriam Adam
A1 Berhan Mandefro
A1 Dhruv Sareen
A1 Clive N. Svendsen
A1 Ernest Fraenkel
YR 2016
UL http://biorxiv.org/content/early/2016/01/15/036798.abstract
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.