biostudies-arrayexpressMelody ClarkHarpagifer antarcticushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17028This project aimed to identify the transcriptomic response of a gill primary cell line derived from the Antarctic plunderfish Harpagifer antarcticus which were cultured at 0°C and 6°Cbiostudies-arrayexpressSequencing - Sequencing platform: NovaSeq X Plus Paired end 150bpNucleic Acid Extraction - Total RNA was extracted using TRI Reagent (cat no T9424 Merck) according to the manufacturer's protocol.Sample Collection - Harpagifer antarcticus (Nybelin, 1947) were collected by divers from a depth of 12 m from Ryder Bay (67°34’07”S, 68°07’30”W), close to the Rothera research station run by the British Antarctic Survey on the Antarctic Peninsula. They were transported to the British Antarctic Survey Cambridge aquarium where they were maintained in recirculating sea water aquaria at 0°C. : Three H. antarcticus were Schedule 1 killed and the organs rapidly dissected. Gill samples were added to tissue culture media and placed on ice. The tissues were chopped up in culture media (100ml of media = 90ml Leibovitz’s L-15 media, no phenol, cat no 21083027 Life Technologies, 10ml foetal bovine serum, cat no F9665 Sigma Aldrich, 1ml P/S/N (Penicillin/Streptomycin/Neomycin) antibiotic, cat no 15640055 Life Technologies, 1ml amphotericin B antibiotic, cat no A2942 Sigma Aldrich, 500µl gentamycin antibiotic, cat no G1272 Sigma Aldrich) and the resultant cell suspensions of each sample added to individual wells in 6-well Nunclon™ tissue culture plates. For each fish, one of the of gill samples was incubated at 0°C with the paired sample incubated at 6°C for 6 days. After six days, the cell suspensions were added to 2ml microcentrifuge tubes and briefly spun to lightly pellet any cell debris. The cell suspensions were then removed to a clean 2ml microcentrifuge tube and centrifuged at 4,000 rpm for 5 minutes. Centrifugation was performed at the relevant incubation temperature (0°C or 6°C). The majority of the supernatant was removed and the cell pellet resuspended by flicking the tube manually. At all times during processing, in between centrifugation, the cells were kept on ice. 500µl of TRI Reagent (cat no T9424 Merck) was added to each resuspended cell pellet. Each tube was briefly flicked to ensure full mixing and rapidly frozen on dry ice. The samples were stored at -80°C until further processing.Library Construction - 1 ug of RNA was used with the KAPA RNA HyperPrep Kit (KR1350) to make strand-specific RNA-seq libraries, after RNA depletion. RNA was fragmented using heat and magnesium and a first strand cDNA synthesis performed random priming. This was followed by a combined 2nd strand synthesis and A-tailing, which converted the cDNA:RNA hybrid to double-stranded cDNA (dscDNA), incorporating dUTP into the second cDNA strand and adding dAMP to the 3' ends of the resulting dscDNA. Adapter ligation, where dsDNA adapters with 3' dTMP overhangs were ligated to library insert fragments was performed, followed by library amplification, to amplify library fragments carrying appropriate adapter sequences at both ends using high-fidelity, low-bias PCR. The strand marked with dUTP is not amplified.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesMetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq XRNA-seq of coding RNAHarpagifer antarcticusA new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiationMelody ClarkMartelossi J, Krasheninnikova K, Denton A, Mathers T, Wood J, Durbin R, Fong N, Bentley DL, Clark MS, Bista I. falseRNA-seq of a primary cell line derived from the gill tissue of the Antarctic plunderfish Harpagifer antarcticusThis project aimed to identify the transcriptomic response of a gill primary cell line derived from the Antarctic plunderfish Harpagifer antarcticus which were cultured at 0°C and 6°C2026-09-01T00:00:00Z2026-09-01T13:35:33.012Z2026-05-06T16:24:11.092ZE-MTAB-17028publ-0-ll6r-removableERP193103EFO_0002944EFO_0004170EFO_0005518EFO_0003738EFO_0004184