Illumina HiSeq 4000 paired end sequencing; Chromosome-length, trio-binned, diploid genome assembly of the naked mole-rat (Heterocephalus glaber) by integrating Nanopore long-read genome sequencing, 10X short read genome sequencing, and Hi-C sequencing - 10X short reads
Chromosome-length, trio-binned, diploid genome assembly of the naked mole-rat (Heterocephalus glaber) by integrating Nanopore long-read genome sequencing, 10X short read genome sequencing, and Hi-C sequencing - 10X short reads
A female breeder (approximately 4 years of age), male breeder (approximately 5.5 years of age) naked-mole-rat and a female and male subordinate (offspring of the breeders; approximately 1 year of age) were selected. Animals were anesthetized with isoflurane and rapidly decapitated. A gonad was removed for each animal and flash frozen in isopentane on dry ice. Tissue for DNA extraction was homogenized in cell lysis buffer [10mM TRIS(pH8.0), 25mM EDTA, 100mM NaCl, 0.5% SDS, RNase A] and digested with proteinase K overnight at 37C. The resulting lysate was extracted twice with TRIS saturated phenol (pH8.0) followed by a single extraction with chloroform. DNA was precipitated from solution by adding 1/10th volume 3M Sodium Acetate and 2.5 volumes of 95% ethanol followed by gentle inversion. Precipitated DNA was spooled onto a glass rod and washed with excess 70% ethanol and allowed to partially air dry before being resuspended in an appropriate volume of EB [10mM TRIS (pH8.0)] The Genome Reagent Kits v2 User Guide, Protocol Step 4 (https://support.10xgenomics.com/genome-exome/index/doc/user-guide-chromium-genome-reagent-kit-v2-chemistry) library construction protocol was followed exactly with no changes.