{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Dustin Sokolowski"],"organism":["Bathyergus suillus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17420"],"description":["One ONT-ULK sequencing run from the kidney of a single male CDMR (Bathyergus suillus) sample used to make the mBatSui1.1.primary genome assembly as an evolutionary comparator to our telomere-to-telomere naked mole-rat genome assembly. Specifically, we assembled a CDMR from a wild-derived sample in South African cape and sequenced  in Toronto, Canada, using PacBio HiFi (89 Gb, read N50 = 18 Kb) and ONT-ULK (55 Gb, read N50 = 43 Kb) reads (contig N50 = 33 Mb, Compleasm S = 99%, QV = 71.0). This accession stores the ONT-ULK data for this assembly."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Adult Bathyergus suillus were wild-captured in Darling, Western Cape, South Africa using Hickman live traps baited with small pieces of sweet potato. Traps were monitored every 2–3 hours throughout the day and checked again early each morning after being left overnight. Permission to capture animals was obtained from all relevant landowners, and collection permits were issued by the appropriate conservation authorities (Western Cape permit no. CN44-87-13780). All procedures were approved by the University of Pretoria Animal Use and Care Committee (ethics clearance no. NAS022/2021) and conducted under DAFF Section 20 approval (SDAH-Epi-21051907211). Captured animals were transported to the University of Pretoria and housed individually at approximately 23°C, 21% O₂, and ","Nucleic Acid Extraction - Ultra-high molecular weight DNA was extracted from the kidney tissue of a male using a modified phenol/chloroform DNA extraction method.","Library Construction - DNA was extracted using the Monarch HMW tissue extraction kit according to manufacturers recommendations (New England Biolabs).","Sequencing - For ultra-long sequencing, libraries were prepared starting with 80 µg of high molecular weight genomic DNA using the Ultra-Long DNA Sequencing Kit (SQK-ULK114, Oxford Nanopore Technologies, Oxford, UK) according to the manufacturer's protocol. Briefly, DNA diluted in EEB was incubated with a buffer containing fragmentation mix (FRA + FDB). Incubation was carried out at room temperature for 10 mins before being heat inactivated at 75C for 10mins. Following a brief incubation on ice, the fragmented and tagged DNA was incubated with rapid adapter (RA) for 30 mins at room temperature. The resulting fragmented and adapted library was then precipitated using precipitation buffer (PTB). The precipitate was pelleted and resuspended in elution buffer (EB) and allowed to redisolve over"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["PromethION"],"pubmed_abstract":["The naked mole-rat (NMR; <i>Heterocephalus glaber</i>) is a eusocial subterranean rodent with a highly unusual set of physiological traits that has attracted great interest amongst the scientific community. However, the genetic basis of most of these traits has not been elucidated. To facilitate our understanding of the molecular mechanisms underlying NMR physiology and behaviour, we generated a long-read chromosomal-level genome assembly of the NMR. This genome was subsequently annotated and incorporated into multiple whole genome alignments in the Ensembl database. Our long-read assembly identified thousands of repeats and genes that were previously unassembled in the NMR and improved the results of routinely used short-read sequencing-based experiments such as RNA-seq, snRNA-seq, and AT"],"study_type":["DNA-seq"],"species":["Bathyergus suillus"],"pubmed_title":["An updated reference genome sequence and annotation reveals gene losses and gains underlying naked mole-rat biology"],"pubmed_authors":["Daniel Hart","Phillip Zuzarte","Nigel Bennett","Mihai Miclaus","Dustin Sokolowski","Michael Wilson","Jared Simpson","Dustin J Sokolowski, Mihai Miclăuș, Alexander Nater, Daniel Hart, Nigel Bennett, Mariela Faykoo-Martinez, Kendra Hoekzema, Philip Zuzarte, Simon Monis, Sana Akhtar Alvi, Jason Erdmann, Archana Lal Erdmann, Rathnakumar Kumaragurubaran, Jonathan Bayerl, DongAhn Yoo, Nadia Karimpour, Kyra Ungerleider, Huayun Hou, Fergal J Martin, Thibaut Hourlier, Zoe Clarke, Heidi E L Lischer, Dragos V Leordean, Yiyue Jiang, Trevor J Pugh, Ewan St J Smith, Leanne Haggerty, Diana J Laird, Jingtao Lilue, Melissa M Holmes, Evan E Eichler, Rémy Bruggmann, Jared T Simpson, Gabriel Balmus, Michael D Wilson"],"additional_accession":[]},"is_claimable":false,"name":"ONT ULK sequencing of a male cape dune mole-rat kidney sample","description":"One ONT-ULK sequencing run from the kidney of a single male CDMR (Bathyergus suillus) sample used to make the mBatSui1.1.primary genome assembly as an evolutionary comparator to our telomere-to-telomere naked mole-rat genome assembly. Specifically, we assembled a CDMR from a wild-derived sample in South African cape and sequenced  in Toronto, Canada, using PacBio HiFi (89 Gb, read N50 = 18 Kb) and ONT-ULK (55 Gb, read N50 = 43 Kb) reads (contig N50 = 33 Mb, Compleasm S = 99%, QV = 71.0). This accession stores the ONT-ULK data for this assembly.","dates":{"release":"2026-08-05T00:00:00Z","modification":"2026-08-05T01:00:47.067Z","creation":"2026-07-29T12:09:55.468Z"},"accession":"E-MTAB-17420","cross_references":{"pubmed":["39651266"],"ENA":["ERP203003"],"EFO":["EFO_0002944","EFO_0004170","EFO_0002693","EFO_0005518","EFO_0004184"],"doi":["10.1101/2024.11.26.625329"]}}