characteristics.text: 2025-11-22
characteristics.characteristic: ENA first public
characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
characteristics.characteristic: INSDC center name
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS22467256
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-14648:WL3028
characteristics.characteristic: Submitter Id
characteristics.text: 2 to 5
characteristics.unit: year
characteristics.characteristic: age
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: not collected
characteristics.characteristic: collection date
characteristics.text: naked mole-rat
characteristics.characteristic: common name
characteristics.text: Protocols: 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. 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 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].
characteristics.characteristic: description
characteristics.text: Subordinate
characteristics.characteristic: developmental stage
characteristics.text: wild type genotype
characteristics.characteristic: genotype
characteristics.text: not collected
characteristics.characteristic: geographic location (country and/or sea)
characteristics.text: WL3028
characteristics.characteristic: individual
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Heterocephalus glaber
characteristics.characteristic: organism
characteristics.text: Heterocephalus glaber
characteristics.characteristic: organism
characteristics.text: hypothalamus
characteristics.characteristic: organism part
characteristics.text: Heterocephalus glaber
characteristics.characteristic: scientific_name
characteristics.text: male
characteristics.characteristic: sex
characteristics.text: wild type
characteristics.characteristic: strain
characteristics.text: WL3028
characteristics.characteristic: title