ISH-guided freeze-matrix assisted punches: Technique for extracting punches from thin slide-mounted tissues for DNA methylation analysis

Molecular and Behavioral Neuroscience Institute, Department of Psychiatry, and Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA.
BioTechniques (Impact Factor: 2.95). 09/2012; 53(3):175-80. DOI: 10.2144/0000113912
Source: PubMed


Dissection of discrete brain regions for molecular analysis is complicated by trade-offs between accuracy, flexibility, and costs. We developed a flexible and cost-effective method, in situ hybridization (ISH) guided freeze-matrix assisted punches (IFAP), for extracting nanogram quantities of DNA from slide-mounted sections as thin as 12 μm. Using ISH to localize regions of interest, tissue is targeted by applying a small bead of M-1 embedding matrix onto cryosections, snap-freezing, and collecting the beads for nucleic acid purification. The method quantitatively recovers RNA and DNA usable for PCR and DNA methylation analysis.

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