{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Michael Wilson"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["ATAC-seq"],"organism":["Heterocephalus glaber"],"species":["Heterocephalus glaber"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14649"],"description":["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. To complement gene annotation and ascertain the organization of an NMR epigenome, we generated a chromatin state map of the female subordinate hypothalamus hypothalamus that included long-range promoter-enhancer interactions. This repository stores the ATAC-seq data used in the chromatin state map. Specifically, this dataset contains female subordinates, male subordinates, female exsubordinates 1 week after colony removal, and male exsubordinates 1 week after colony removal (N=3 per sex and pubertal stage)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Libraries were sequenced on Illumina NOVAseq S4 flowcell with a 150-bp run to obtain 50-100 million paired-end reads per sample.","Nucleic Acid Extraction - Tissue was homogenised in a dounce homogenizer in PBS, then washed 2x with ice-cold PBS. Cells were counted with a CountessTM using 1:1 dilution of Trypan Blue. ATAC-Seq was performed according to Buenrostro, et al. (2015). Briefly, 100000 cells were used for each sample and resuspended in 50uL of lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Cells were spun for 10 mins at 600xg and 4C to prepare a crude nuclei extract. Nuclear pellets were then resuspended in transposition mix (25uL 2X TD buffer, 2.5uL TD [Illumina #20034198], and 23uL nuclease-free water) and incubated in a thermomixer at 37C for 30 mins shaking at 800rpm. DNA was isolated using the DNA Clean & Concentrator-5 kit (Zymo  #D4013) and eluted in 11.5uL of 10mM Tris-HCl, pH 8.0.","Library Construction - Libraries were prepared using 10uL of each sample. To generate libraries 50uL PCR reactions were made using 25uL NEBNext® High-Fidelity 2X PCR Master Mix(NEB #M0541L) , 2.5uL of universal Ad1_noMx primer, 2.5uL of Ad2.x barcoded primer and 10uL nuclease-free water. Reactions were run according to recommended conditions with an annealing temperature of 63C and amplified for a total of 5 cycles. qPCR was subsequently run using 5uL of each 50uL PCR reaction to determine the number of additional cycles choosing a cycle number which provided ⅓ maximum fluorescence value. After subsequent PCR cycles, libraries were cleaned using a two-sided AMPureXP bead clean up using 0.5X then 1.3X beads. Libraries were eluted in a final volume of 21uL of 10mM Tris-HCl, pH 8.0, and quantified with the DNA-HS Qubit assay.","Sample Collection - Naked mole-rats were bred in-house and maintained in stable colonies (i.e. established breeders were present) housed in large (45.75 cm L × 24 cm W × 15.25 cm H) and small (30 cm L × 18 cm W × 13 cm H) polycarbonate cages connected by plastic tubes (25 cm L × 5 cm D). Animals were fed sweet potato ad libitum supplemented with wet 19% protein mash (Envigo RMS, Inc.) and kept on a 12:12 light/dark cycle at 28–30 C. All procedures were approved by the University Animal Care Committee and performed in accordance with federal and institutional guidelines.  Twelve NMR hypothalamus samples between two and four years of age were collected using the same method as in Hi-C and ChIP-sequencing. These twelve NMRs were divided into subordinates (SUB), and subordinates were removed from the colony for one week (EXSUB-wk1), in both males, and females (N=3 per developmental stage/sex). NMR hypothalamus were dissected, flash frozen and stored at -80C for up to four months."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Simon Monis","Michael Wilson","Dustin Sokolowski","Mariela Martinez","Sana Alvi","Melissa Holmes"],"additional_accession":[]},"is_claimable":false,"name":"Chromatin accessibility in the adult male and female naked mole rat hypothalamus before and during colony removal","description":"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. To complement gene annotation and ascertain the organization of an NMR epigenome, we generated a chromatin state map of the female subordinate hypothalamus hypothalamus that included long-range promoter-enhancer interactions. This repository stores the ATAC-seq data used in the chromatin state map. Specifically, this dataset contains female subordinates, male subordinates, female exsubordinates 1 week after colony removal, and male exsubordinates 1 week after colony removal (N=3 per sex and pubertal stage).","dates":{"release":"2025-11-22T00:00:00Z","modification":"2025-11-22T02:02:33.381Z","creation":"2024-11-28T17:30:31.963Z"},"accession":"E-MTAB-14649","cross_references":{"ENA":["ERP166636"],"Biostudies":["E-MTAB-14648"],"EFO":["EFO_0002944","EFO_0007045","EFO_0004170","EFO_0005518","EFO_0004184"]}}