Dataset: metatranscriptomics - Niskin vs. in situ
Deployment: Urania-2012-09

Water was collected using 12L Niskin bottles mounted on a General Oceanics rosette sampler equipped with conductivity-temperature and depth (CTD) and pressure sensors. After transferring water from Niskin bottles to a large sterile carboy, 30 liters of water were pumped through a 0.22µm Sterivex filter cartridge using a peristaltic pump operating around 125 ml/min containing a Durapore filter (Millipore, Millford, MA, USA), which was immediately filled with RNAlater (Life Technologies Inc., Grand Island, NY, USA) and frozen at -80°C until extraction. Water samples from the same depth and on the same day were also collected and preserved in situ using the MS-SID in situ microbial sampler equipped with a CTD, two turbidity sensors, and an oxygen optode. Three MS-SID samples were filtered in situ at 125 ml/min through a 47mm 0.2 µm Durapore (Millipore, USA) filter that, upon cessation of filtration was within 10-20 seconds flooded with the preservative RNAlater following filtration. The three filters collected 4L, 3L and 3.4L of water, respectively. Upon retrieval of the instrument to the ship’s deck, the Fixation Filter Units were disassembled, and the filters and associated RNAlater solutions were transferred aseptically to three separate sterile cryovials, and frozen at -80°C until extraction. The Sterivex capsule (from Niskin bottle collection) was also stored at -80°C until extraction. RNA preps performed as in Edgcomb et al. 2014 DSR II.