In collaboration with the Seward Long-Term Observation Program (LTOP) (http://www.sfos.uaf.edu/sewardline/) and the NGA LTER Program (https://nga.lternet.edu/), we obtained Neocalanus flemingeri individuals during the annual April-May and September oceanographic cruises. During the spring cruises stage CV individuals were collected from four to six locations: spanning the inner shelf to outer shelf gradient along the Seward Line in the northern Gulf of Alaska and at least one station in adjoining Prince William Sound. Samples were collected using a CalVET net (53-µm mesh) towed vertically from 100 m depth to surface. Mixed plankton samples were immediately diluted with surface seawater, and maintained at ~5ºC prior to and during sorting. From each station actively swimming (healthy) N. flemingeri CVs were rapidly sorted under the microscope and preserved within 15 minutes to 1hr of the tow in RNALater Stabilization Reagent (QIAGEN). The rapid sorting of live plankton can lead to misidentifications given the presence of closely related congeners, thus species verification is recommended using the RNA-seq data to check the cytochrome c oxidase subunit 1 (mtCOI) sequence. In September, diapausing N. flemingeri adult females were sorted from collections obtained with a Midi Multinet towed vertically. Collections were diluted with seawater upon net retrieval. Individuals were sorted under the microscope from the 300-700 depth collections and either preserved immediately in RNALater or separated into holding containers for incubation experiments. In three years (2015, 2016, 2017) additional adult females were incubated for different lengths of time and preserved after a specified interval as indicated in the sample information. In July, 2019 we participated in a ship of opportunity cruise to the Gulf of Alaska Seamounts (SKQ201916S) and preserved diapausing adult females collected between 1000-2000 meters from two offshore stations (GAK19 and DeepQuinn).

RNA extraction, gene library preparation and RNA-seq

Total RNA was extracted from individual CV from each station using QIAGEN RNeasy Plus Mini Kit (catalog # 74134) in combination with a Qiashredder column (catalog # 79654) following the instructions of the manufacturer and stored at -80ºC. Total RNA concentration and quality were checked using an Agilent Model 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA). For each station, total RNA from three of the ten individuals with high quality RNA yields were selected for RNA-seq and shipped on dry ice to the University of Georgia Genomics Facility (dna.uga.edu). There, double-stranded cDNA libraries were prepared from total RNA extracted using the Kapa Stranded mRNA-seq kit (KK8420) following manufacturer’s instructions. Briefly, RNA samples were first purified with two oligo-dT selection (polyA enrichment using oligodT beds), and then fragmented and reverse transcribed into double-stranded complementary DNA. Each sample was tagged with an indexed adapter and they were simultaneously paired-end sequenced (PE150 or PE75 bp) using an Illumina NextSeq 500 instrument using High-Output Flow Cell. Data in NCBI are the raw sequence reads.