{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Dustin Sokolowski"],"organism":["Heterocephalus glaber"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17313"],"description":["Two PacBio Hifi sequencing runs from the kidney of a single male NMR sample used to make the mHetGla4.1.primary genome assembly. Specifically, we assembled a second NMR genome from an unrelated male of a separate captive colony in Toronto, Canada, using PacBio HiFi (155.8 Gb, read N50 = 11.45 Kb) and ONT-LSK (299.6 Gb, read N50 = 10.1 Kb) reads (contig N50 = 75.7 Mb, Compleasm S = 98%). This accession stores the Pacbio Hifi data for this independent assembly."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - High molecular weight DNA was extracted from frozen liver with the NEB Monarch cells and tissue kit, following the manufacturer's instructions.","Sample Collection - A single 1 year old male naked mole-rat was harvested for mHetGla4, where a liver was harvested and flash-frozen in isopentane on dry ice.","Sequencing - The polymerase-bind library was then loaded on PacBio Revio with 24 hours movie capture time.","Library Construction - Long-read whole genome sequencing was performed at Network Biology Collaborative Center (NBCC), at Mount Sinai Hospital in Toronto, Ontario. The gDNA quality was accessed by Agilent Fragment Analyzer 5200.The high-quality gDNA with GQN > 7.0 was first cleaned up with PacBio Short Read Eliminator (cat#102-208-300) according to the manufacturer protocol. It was then sheared with Covaris g-TUBE (cat# 520079) and the SMRTbell HiFi library was prepared using PacBio SMRTBell Prep Kit 3.0 (cat#102-182-700). The quality and quantity of the SMRTbell HiFi Library were measured by Agilent Fragment Analyzer and Qubit 2.0 (Thermo Fisher Scientific), respectively. The final polymerase-bind library was prepared with ABC (annealing, binding, and cleanup) procedure according to the S"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["PacBio RS II"],"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":["Heterocephalus glaber"],"pubmed_title":["An updated reference genome sequence and annotation reveals gene losses and gains underlying naked mole-rat biology"],"pubmed_authors":["Phillip Zuzarte","Mihai Miclaus","Dustin Sokolowski","Michael Wilson","Mariela Faykoo-Martinez","Jared Simpson","Kin Chan","Melissa Holmes","Dustin J Sokolowski, Mihai Miclăuș, Alexander Nater, 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":"Pacbio Hifi sequencing of a naked mole-rat male subordinate kidney sample","description":"Two PacBio Hifi sequencing runs from the kidney of a single male NMR sample used to make the mHetGla4.1.primary genome assembly. Specifically, we assembled a second NMR genome from an unrelated male of a separate captive colony in Toronto, Canada, using PacBio HiFi (155.8 Gb, read N50 = 11.45 Kb) and ONT-LSK (299.6 Gb, read N50 = 10.1 Kb) reads (contig N50 = 75.7 Mb, Compleasm S = 98%). This accession stores the Pacbio Hifi data for this independent assembly.","dates":{"release":"2026-08-05T00:00:00Z","modification":"2026-08-05T01:00:48.955Z","creation":"2026-07-06T08:22:57.157Z"},"accession":"E-MTAB-17313","cross_references":{"pubmed":["39651266"],"ENA":["ERP196192"],"EFO":["EFO_0002944","EFO_0004170","EFO_0002693","EFO_0005518","EFO_0004184"],"doi":["10.1101/2024.11.26.625329"]}}