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Chunk #49 — Online Methods — Single-cell Multiome Assay — Nuclei Isolation for Single-cell Multiome

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Integrated Single-Cell Multiomic Profiling of Caudate Nucleus Suggests Key Mechanisms in Alcohol Use Disorder.
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183 fresh-frozen post-mortem caudate brain samples were utilized in the assay. The 183 specimens were divided into 23 pools, with 8 in each pool. The donors in each pool were both condition (with or without AUD) and sex balanced. For each pool, around 20 mg tissue from each donor specimen was collected and combined into a sterilized 2 ml Dounce homogenizer. 2 ml chilled NP40 lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Nonidet P40 Substitute, 1mM DTT, 1 U/μl RNase inhibitor) was added to the Dounce homogenizer before the tissues were thawed. The tissues were homogenized 15x using pestle A, and 10x using pestle B, and were transferred into a centrifuge tube to incubate for 2 minutes on ice. After that, 2 ml wash buffer containing PBS, 1% BSA and 1 U/μl RNase inhibitor was added and mixed well. The lysed tissue was centrifuged at 500 rcf for 5 minutes at 4°C, then washed twice more with wash buffer and filtered through 70 μm and then 40 μm cell strainer separately. The pellet