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Chunk #47 — STAR★METHODS — METHOD DETAILS — FISH stain and imaging

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Transcriptional and anatomical diversity of medium spiny neurons in the primate striatum.
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We embedded brains in optimal cutting temperature (OCT) and stored them at −80°C until cutting. We cut floating sections at 15 and 30 μm, in monkey B and K, respectively, mounted tissue on 2x3” pre-treated slides, and preserved the slides in a freezer at −80°C. We used the Advanced Cell Diagnostics (ACD) RNAscope platform and Multiplex Fluorescent Detection Reagents v2 (ACD, Cat# 323110) to perform FISH with slight modifications for monkey brain tissue. We air dried slides for 30 min after removal from −80°C freezer and baked them at 60°C for 20 min. We treated the brain sections with hydrogen peroxide (ACD, Cat# 322335) for 10 min at room temperature and then with RNAscope Target Retrieval Reagents (ACD, Cat# 322000) for 8 min at 99°C. We incubated the slides in 100% alcohol for 3 min and then dried them in 60°C for 10 min. We treated the samples with protease III (ACD, Cat# 322337) for 30 min at 40°C and incubated them with probes for 2 hr. After hybridization with AMP 1, 2 and 3, we incubated the slides with