Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
30
datasets available to search
ShareScore release 0.9.0
Dataset results
30 results for “Naked mole-rat”
Genome, repeat, and functional annotation associated with the naked mole-rat genome assembly, mHetGlaV3 (GCA_964261345.1)
<p>The naked mole-rat (NMR; Heterocephalus glaber) is a eusocial subterranean rodent with a highly unusual set of physiological traits, such as extreme longevity, 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, mHetGlaV2, was subsequently annotated and incorporated into a “91 eutherian mammals” multiple whole genome alignment in Ensembl. </p> <p>We identified intra-chromosomal misassemblies within mHetGlaV2. We fixed these misassemblies by comparing syntenic blocks between this assembly and the Canadian Porcupine (EreDor) genome assembly (https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_028451465.1/) and a FISH-Karyotype of the naked mole-rat completed by Romanenko et al., 2023 (PMID: 380307020) to address any misassemblies and place centromeres. Chromosome numbering was identified from a composite karyogram of karyotypes from over 350 cells. This scaffold-corrected assembly is labelled mHetGlaV3 (https://www.ebi.ac.uk/ena/browser/view/GCA_964261345.1).</p> <p>This repository stores the repeat, genome, and epigenome annotations for HetGlaV3.</p> <p>mHetGlaV3.primary.gtf.gz. Gene structures and gene symbols are transferred from ENSEMBL annotations of mHetGlaV2 using liftOff with default parameters. Additional gene symbols were identified using TOGA and manual curation.</p> <p>mHetGlaV3.primary.gtf.gz. Simple repetitive regions and transposable elements were annotated using EarlGrey (https://github.com/TobyBaril/EarlGrey) using "Rodentia" annotations for RepeatMasker.</p> <p>mHetGlaV3.primary.genesymbol_table.txt.txt.gz. A tab-delimited file where rows are gene IDs and columns are gene symbols generated with each method. "Consensus" shows the best matching gene symbol for each gene ID.</p> <p>mHetGlaV3.primary_annotated_blacklist.bed.gz. Provides an assembly "blacklist" for mHetGlaV3. This blacklist is a bed file annotating assembly breakpoints between HetGlaV2 and HetGlaV3. This blacklist contains additional columns (e.g., closest gene, overlapping TE etc.) and should therefore be filtered to the first column before being incorporated into traditional genomic pipelines.</p> <p>mHetGlaV3.primary_hypothalamus_ABC_enhancer.bedpe.gz. Activity-By-Contact enhancers (https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction) generated in the female subordinate naked mole-rat hypothalamus using Hi-C-seq, ChIP-seq of H3K27Ac data, ATAC-seq, and RNA-seq information.</p> <p>mHetGlaV3.primary_hypothalamus_chromHMM.bed.gz. Chromatin states (using Chromhmm) annotating the female subordinate naked mole-rat hypothalamus using H3K4me3 (promoter), H4K4me2 (promoter-enhancer), H3K27Ac (active enhancer), H3K36me3 (elongated), H3K27me3 (polycomb repressed), H3K9me3 (heterochromatin), and CTCF (whole brain) ChIP-seq data, as well as ATAC-seq and RNA-seq data.</p> <p>mHetGlaV3.primary.fa.gz. Genome assembly fasta file for the naked mole-rat (V3, primary assembly). This assembly matches the primary assembly stored on ENA, however the chromosome names match these files, rather than have chromosome names processed by ENA (e.g. chr 1 instead of "OZ179169.1 Heterocephalus glaber genome assembly, chromosome: 1").</p> <p> </p> <p>UPDATES:</p> <p>* The 1.2 update fixed unscaffolded contig names from those used in-lab to those compatible with ENA.</p> <p>* The 1.3 update added small (50~100kbp) contigs onto mHetGlaV3.primary.fa.gz that were filtered before the ENA submission.</p> <p>* The 1.4 update fixed a small chromosome naming inconsistency spotted in the 1.3 update.</p>
Auditory brainstem development of Naked Mole-Rats (Heterocephalus glaber)
<p>Life underground often leads to animals having specialized auditory systems to accommodate the constraints of acoustic transmission in tunnels. Despite living underground, naked mole-rats use a highly vocal communication system, implying that they rely on central auditory processing. However, little is known about these animals' central auditory system, and whether it follows a similar developmental time course as other rodents. Naked mole-rats show slowed development in the hippocampus suggesting they have altered brain development compared to other rodents. Here, we measured morphological characteristics and voltage-gated potassium channel Kv3.3 expression and protein levels at different key developmental time points (postnatal days 9, 14, 21, and adulthood) to determine whether the auditory brainstem (lateral superior olive (LSO) and medial nucleus of the trapezoid body (MNTB)), develops similarly to two common auditory rodent model species: gerbils and mice. Additionally, we measured the hearing onset of naked mole-rats using auditory brainstem response (ABR) recordings at the same developmental timepoints. In contrast to other work in naked mole-rats showing that they are highly divergent in many aspects of their physiology, we show that naked mole-rats have a similar hearing onset, between P9-P14, to many other rodents. On the other hand, we show some developmental differences, such as a unique morphology and Kv3.3 protein levels in the brainstem.</p>
Auditory brainstem development of Naked Mole-Rats (Heterocephalus glaber)
Open the record for dataset details and reuse information.
Data from: Challenging the inbreeding hypothesis in a eusocial mammal: population genetics of the naked mole-rat, Heterocephalus glaber.
Open the record for dataset details and reuse information.
Naked Mole-rat in Heterocephalidae
Naked Mole-rat
Increased hyaluronan by naked mole-rat HAS2 improves healthspan in mice [microbiome]
GEO Series GSE234286. Mus musculus. 39 samples. Type: Other.
Droplet-based single-cell RNA-sequencing of mouse and naked mole-rat spleen and circulating immune cells, in natural conditions, following lipopolysaccharide (LPS) challanege, and saline control
GEO Series GSE132642. Heterocephalus glaber; Mus musculus. 63 samples. Type: Expression profiling by high throughput sequencing.
An autochthonous model of lung cancer in the Naked Mole-Rat (Heterocephalus glaber)
GEO Series GSE305565. Heterocephalus glaber. 3 samples. Type: Expression profiling by high throughput sequencing.
RNA sequencing reveals differential expression of mitochondrial and oxidation reduction genes in the long-lived naked mole-rat when compared to mice.
GEO Series GSE30764. Mus musculus; Heterocephalus glaber. 2 samples. Type: Expression profiling by high throughput sequencing.
An autochthonous model of lung cancer in the Naked Mole-Rat (Heterocephalus glaber)
GEO Series GSE305802. Heterocephalus glaber. 52 samples. Type: Other.
RNA sequencing of the spleen of naked mole-rat and mouse
GEO Series GSE179350. Heterocephalus glaber; Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
DNA methylation clocks as a predictor for ageing and age estimation in naked mole-rats, Heterocephalus glaber
GEO Series GSE137957. Heterocephalus glaber. 39 samples. Type: Methylation profiling by high throughput sequencing.
The evolution of the naked mole-rat T cells
GEO Series GSE214390. Mus musculus; Heterocephalus glaber. 66 samples. Type: Expression profiling by high throughput sequencing.
Increased hyaluronan by naked mole-rat HAS2 extends healthspan in mice
GEO Series GSE234563. Mus musculus. 144 samples. Type: Expression profiling by high throughput sequencing.
The rate of ageing-associated DNA methylation dynamics is a molecular readout of lifespan variation amongst mammalian species [Bis-PCR: naked mole-rat]
GEO Series GSE104215. Heterocephalus glaber. 24 samples. Type: Methylation profiling by high throughput sequencing.
Epigenetic aging of the demographically non-aging naked mole-rat [RRBS]
GEO Series GSE179039. Heterocephalus glaber. 107 samples. Type: Methylation profiling by high throughput sequencing.
RNA-seq of breeding and non-breeding naked mole-rats and guinea pigs
GEO Series GSE98719. Heterocephalus glaber; Cavia porcellus. 476 samples. Type: Expression profiling by high throughput sequencing.
Increased hyaluronan by naked mole-rat HAS2 extends healthspan in mice
GEO Series GSE234154. Homo sapiens; Mus musculus; Rattus norvegicus. 19 samples. Type: Expression profiling by array; Methylation profiling by array.
Single-cell RNA-Sequencing maps the hematopoietic landscape in naked mole-rats [unfractionated BM]
GEO Series GSE185720. Heterocephalus glaber; Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
Single-cell RNA-Sequencing maps the hematopoietic landscape in naked mole-rats [unfractionated PB]
GEO Series GSE202903. Heterocephalus glaber. 7 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.