{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Dustin Sokolowski"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17270"],"description":["Naked mole-rat show a strong phenotype of sperm hypo-motility and abnormal morphology. Comparative genomic analyses in our study presenting the telomere-to-telomere genome for the naked mole-rat identified several sperm-gene relaxation and sperm-gene loss events in the NMR. To test the transcriptomic impacts of these gene-loss events, we performed RNA-seq between the sperm of NMR subordinates, ex-subordinates released from suppressive colony cues, and mice. Briefly, only 5-15% of NMR sperm have typical morphology, and only ~7% of those sperm were motile, whereas over 70% of M. musculus sperm are intact and motile There was insufficient motile sperm in the NMR to separate sperm based on motility before RNA-seq. This study was sequenced with sufficient depth to allow for improved sperm-gene "],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Libraries were sequenced and sequenced on IlluminaNOVAseq S4 flowcell with a 150-bp run to obtain 50 million reads paired-end per sample.","Library Construction - The E3330S- Nebnext ultra express RNA library prep kit was used following the manufacturers protocol.","Sample Collection - Naked Mole rat: All experimental procedures followed federal and institutional guidelines and were approved by the Magee-Womens Research Institute, University of Pittsburgh (IACUC protocol# IS00024112). Naked mole-rat colonies were housed in polycarbonate cages of three sizes (large: 65 cm L × 45 cm W × 23 cm H; medium: 46 cm L × 24 cm W × 15 cm H; small: 30 cm L × 18 cm W × 13 cm H) connected by tubes (25 cm L × 18 cm D) and lined with corn cob bedding. Naked mole-rats were kept on a 12:12 light/dark cycle at 28–30 °C, humidity 40-55%, and fed ad libitum with a diet consisting of sweet potato, grapes, celery, apples, corn, bananas, yams, and Pronutro (Bokomo, South Africa). Ex-subordinate males were coupled with a single female during a year; NMR were euthanized using ","Nucleic Acid Extraction - Total RNA was extracted from each tissue sample using the NucleoSpin miRNA Kit (Macherey-Nagel) according to the manufacturer's instructions. Tissue samples were lysed in NucleoZOL (Macherey-Nagel) and transferred to bead mill tubes containing six 2.8 mm ceramic beads (Fisher Scientific, Cat. No. 19-628-3). Samples were homogenized using an Omni Bead Ruptor 24 bead mill at 5m/sec for one cycle of 30 seconds seconds at 4°C. RNA concentration and purity were assessed using a NanoDrop spectrophotometer, and RNA integrity was evaluated using an Agilent 2100 Bioanalyzer."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Unpaired reads were filtered and average base pair quality (q) < 30 using trim_galore/0.4.4133. Paired reads were aligned to the corresponding existing NMR assembly, depending on the analysis with hisat2 in paired end mode using default parameters (Kim et al. 2019), and filtered for properly paired reads with an alignment quality > 20 using using samtools view (-bSq 20 -f 0x2) (Li et al. 2009).  Reads were counted to exon features using featureCounts. One-to-one orthologs were mapped between the mouse and naked mole-rat using Orthofinder, with human and cape-dune mole-rat annotations as an additional species for ortholog mapping."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"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":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_title":["An updated reference genome sequence and annotation reveals gene losses and gains underlying naked mole-rat biology"],"pubmed_authors":["Miguel Brieño-Enríquez","Mihai Miclaus","Simon Monis","Dustin Sokolowski","Odei Barreñada","Michael Wilson","Jared Simpson","Sana Akhtar Alvi","Dustin J Sokolowski, Mihai Miclăuș, Alexander Nater, Mariela Faykoo-Martinez, Kendra Hoekzema, Philip Zuzarte, Simon Monis, Sana Akhtar Alvi, Odei Barreñada, Miguel Brieño-Enríquez, 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":"RNA sequencing of sperm extracted from the epididymis in naked mole-rat subordinates, naked mole-rat ex-subordinates, and mice","description":"Naked mole-rat show a strong phenotype of sperm hypo-motility and abnormal morphology. Comparative genomic analyses in our study presenting the telomere-to-telomere genome for the naked mole-rat identified several sperm-gene relaxation and sperm-gene loss events in the NMR. To test the transcriptomic impacts of these gene-loss events, we performed RNA-seq between the sperm of NMR subordinates, ex-subordinates released from suppressive colony cues, and mice. Briefly, only 5-15% of NMR sperm have typical morphology, and only ~7% of those sperm were motile, whereas over 70% of M. musculus sperm are intact and motile There was insufficient motile sperm in the NMR to separate sperm based on motility before RNA-seq. This study was sequenced with sufficient depth to allow for improved sperm-gene ","dates":{"release":"2026-07-31T00:00:00Z","modification":"2026-07-31T13:26:43.912Z","creation":"2026-06-24T23:40:58.307Z"},"accession":"E-MTAB-17270","cross_references":{"pubmed":["39651266"],"ENA":["ERP195692"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"],"doi":["10.1101/2024.11.26.625329"]}}