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The Sonne transit cruise SO226-3 DipFIP took place from March 4th (Wellington, New Zealand) to March 28th (Kaohsiung, Taiwan) in 2013. CTD data for 16 stations along the cruise track were recorded using the onboard a SEABIRD SBE 9 plus CTD down to depth of 800m. Obtained hydrographic data were binned to 1 m intervals with the available SBE software. Obvious outliers in the readings of the oxygen sensor close to the sea surface have been manually removed. Fluorospectrometer (bbe Moldaenke) pigment data measured for 24 depth intervals are available for 10 stations. Measurements were conducted in the shipboard laboratory on water samples from the CTD rosette. Data are averages of a least 30 readings per sample.