High-throughput sequencing study of field-collected Neocalanus flemingeri pre-adults (stage CV) and adult females between 2015 and 2022. Dataset includes information and accession numbers of the raw sequence reads. Zooplankton collections were made in the northern Gulf of Alaska in collaboration with the Seward Long-term Monitoring Program and the northern Gulf of Alaska Long-term Ecological Research Program (LTER). Pre-adults were collected during the spring from multiple stations, sorted from ...
Show moreIn 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 N. 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. In September, diapausing N. flemingeri adult females were sorted from collections obtained with a Midi Multinet towed vertically. Individuals were sorted from the 300-700 depth collections. 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). 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).
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.
Lenz, P. H., Roncalli, V., Cieslak, M. C. (2024) Multiyear RNA-Seq of Neocalanus flemingeri stages CV and Adult Female from the R/V Tiglax and R/V Sikuliaq in the Northern Gulf of Alaska from 2015-2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-05-30 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/922330 [access date]
Terms of Use
This dataset is licensed under Creative Commons Attribution 4.0.
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