ls_s5
Euphausia superba
Protocols: Antarctic krill samples (Euphausia superba) were obtained from five different expeditions and from a Norwegian fishing vessel. Sampling was carried out with a Rectangular Midwater Trawl (RMT8+1 for expeditions ANT23-2, ANT23-6 and JR15004, RMT8 for expedition JR260B), an Isaacs-Kidd Midwater Trawl (IKMT, expedition AMLR14) and a continuous pumping system (Norwegian fishing vessel). Snap-frozen Antarctic krill samples stored at -80°C were transferred to the Alfred-Wegener-Institute, Bremerhaven, for molecular analysis.The Antarctic krill originated from three different latitudinal regions: a) Lazarev Sea (62°S -66°S), b) South Orkneys/Bransfield Strait (60°S-63°S), and c) South Georgia (54°S), including summer and winter samples for each region. By visual inspection of the outer sexual organs, male petasma and female thelycum, adult males and females were identified. RNA extraction was performed from frozen krill heads with the RNeasy Midi Kit (QIAGEN, Hilden, Germany). Frozen krill heads were cut on dry ice and moved to 1.5 mL RLT lysis buffer in tissue homogenizing Precellys® tubes (CKMix Tissue Homogenizing Kit, Bertin corp., Rockville, MD, USA). Homogenization was carried out at 4°C in a Precellys® homogenisator with the Cryolys® cooling system (Bertin corp.) with two runs for 15 s at 5000 rpm and 10 s break. Further steps of RNA extraction were carried out according to the manufacturer's protocol of the RNeasy Midi Kit. The quality and quantity of the RNA was inspected using the NanoDrop™2000 UV-Vis Spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and the Agilent 2100 Bioanalyzer system (Agilent technologies, Santa Clara, CA, USA). RNA samples were sent for sequencing to IGA Technology Services, Udine, Italy. Library preparation was performed with 1-2 μg RNA using the TruSeq Stranded mRNA Sample Prep kit (Illumina, San Diego, CA, USA) after manufacturer's instructions. The poly-A mRNA was fragmented 3 minutes at 94°C. 1X Agencourt AMPure XP beads (Agencourt Bioscience Cooperation, Beckman Coulter, Beverly, MA, USA) were used for every purification step. The RNA samples and final libraries were quantified with the Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA) and quality tested by Agilent 2100 Bioanalyzer Nano assay. For cluster generation on the flow cell, libraries were processed with cBot (Illumina, San Diego, CA, USA) following manufacturer's instructions.
ENA-FIRST-PUBLIC
2019-11-16T04:03:16Z
ENA-LAST-UPDATE
2018-12-04T13:44:16Z
External Id
SAMEA5147717
INSDC center name
Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Section Polar Biological Oceanography
INSDC first public
2019-11-16T04:03:16Z
INSDC last update
2018-12-04T13:44:16Z
INSDC status
public
Submitter Id
E-MTAB-7467:ls_s5
broker name
ArrayExpress
collection date
2005-12-23
coordinates
65.51 S 3.03 W
developmental stage
adult
genotype
wild type genotype
geographic location
Lazarev Sea
individual
5
organism part
head
sample name
E-MTAB-7467:ls_s5
scientific_name
Euphausia superba
season
summer
sex
female
strain
wild type