The dataset contains net stem CH₄ emissions measured in situ during the snow-free period and potential CH₄ production in wood core segments incubated under anoxic conditions. The study was conducted in 2020 and 2021 on five tree species in the Ashiu Experimental Forest of Kyoto University. The study site is located in the upper Yura River watershed around Chojidani (35.34 N, 135.76 E) at an altitude of 630–660 m. Individuals of different sizes were studied at different heights along their stems.

Methane concentrations were measured with a gas analyser (Li 7810, Li-Cor; Lincoln, USA). Stem chambers, covering an area of 1.40 dm², had an internal volume of 2.51 dm³. Incubation of wood was conducted in a 12 ml glass vial, flushed with the incubation mixture (N₂, 10% CO_2, and 1% H₂), and kept at 25 °C in a dark incubator for one week. An air sample (10 µl) was then drawn from each vial through the septum into a syringe and injected through the septum of the small volume sample kit (Li 7800-110) connected in a closed-loop mode to the gas analyser.

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