{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Michael Wilson"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["ChIP-seq"],"organism":["Heterocephalus glaber"],"species":["Heterocephalus glaber"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14648"],"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 ChIP-seq data used in the chromatin state map (H3K4me3, H3K4me2, H3K27Ac, H3K27me3, H3K36me3, H3K9me3, CTCF-whole-brain), and promoter and enhancer mapping of male subordinate hypothalamus samples (H3K4me3, H3K4me2)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Tissue was dounced in freshly prepared solution A ( 1% formaldehyde, 50mM Hepes-KOH, 100mM NaCl, 1mM EDTA, 0.5mM EGTA) and incubated for 20 mins at room temperature. The formaldehyde was then quenched with 1/20 volume of 2.5M glycine and incubated for 5 min. Tissue was then rinsed with ice cold PBS twice and centrifuge at 4 C at 2500 x rcf for 5 min. Crosslinked tissue was then lysed using Chromatin Easy Shear Low SDS Kit (Diagenode #C01020013). Chromatin was sheared into 100–500 bp DNA fragments by sonication (Diagenode Bioruptor Pico) for 8 cycles of 30s ON and 30s OFF. Approximately 1.5% of chromatin was used for input DNA extraction","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. The hypothalamus for eighteen NMR subordinates (14 female, 4 male) were collected for ChIP-sequencing using the same approach as in Hi-C sequencing. For ChIP-seq of CTCF, we collected the whole brain of two NMRs.","Library Construction - For each ChIP, chromatin lysates  were combined with 10ug of anti-H3K27ac (Active Motif #39133), anti-H3K4me2 (Millipore # 07-030), H3K27me3 (Millipore #07-449), H3K36me3 (Abcam #ab9050) and H3K9me2 (Abcam #ab8898) antibodies and incubated overnight rotating at 4C. For library preparation, all the ChIP DNA and input DNA were mixed with reagents from NEBNext Ultra II Library Prep Kit (NEBNext #E7645S) according to the manufacturer's protocol.This DNA was then amplified with barcoded primers for Illumina sequencing (NEBNext® Multiplex Oligos for Illumina® #E7335S). PCR amplifications were carried out as [98 °C 30 s, (98 °C 10 s, 65 °C 75s) ×9cycles, 65 °C 5 min, 4 °C hold].","Sequencing - The amplified and barcoded library was then purified and selected for 200–350-bp fragments using AMPure XP beads (BECKMAN COULTER #A63881) and sequenced on IlluminaNOVAseq S4 flowcell with a 150-bp run to obtain 50 million reads paired-end per sample."],"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":"Naked mole rat hypothalamus chromatin state map","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 ChIP-seq data used in the chromatin state map (H3K4me3, H3K4me2, H3K27Ac, H3K27me3, H3K36me3, H3K9me3, CTCF-whole-brain), and promoter and enhancer mapping of male subordinate hypothalamus samples (H3K4me3, H3K4me2).","dates":{"release":"2025-11-22T00:00:00Z","modification":"2025-11-22T02:02:33.368Z","creation":"2024-11-28T17:30:04.194Z"},"accession":"E-MTAB-14648","cross_references":{"ENA":["ERP166635"],"EFO":["EFO_0002944","EFO_0004170","EFO_0002692","EFO_0005518","EFO_0004184"]}}