biostudies-arrayexpressDustin SokolowskiHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17311This data contributes to a telomere-to-telomere genome assembly and annotation of the naked mole-rat, Heterocephalus glaber. To epigenetically annotate centromeres, we performed CENPA ChIP-seq experiments in the male subordinate NMR livers. To ensure antibody quality, as this was the first time CENPA ChIP-seq was performed in the NMR, we performed H3K27Ac and CENPA ChIP-seq experiments on a TeloHAOEC cell line.biostudies-arrayexpressSequencing - Libraries were sequenced on IlluminaNOVAseq S4 flowcell with a 150-bp run to obtain 50 million reads paired-end per sample.Sample Collection - Human TeloHAECs were grown in cell cultureLibrary Construction - 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]. The amplified and barcoded library was then purified and selected for 200–350-bp fragments using AMPure XP beads (BECKMAN COULTER #A63881)Nucleic Acid Extraction - Cells were 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 centrifuged 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) or anti-CENPA (ThermoFisher MA1-20832) antibodies and incubated overnight rotating at 4C.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Paired-end FASTQ files were initially visualized with fastqc. TruSeq3-PE adaptors were trimmed with trimmomatic/0.32, and paired-end reads with a minimum read length of 36bp were kept131. Reads were aligned to each assembly using the paired-end module of bwa-mem13,116. For the CENPA ChIP-seq and input, we used bwa and samtools parameters previously described to work with CENPA ChIP-seq data 13,116 to better resolve multi-mapping reads “(from their study: k = 19, w = 100, d = 100, r = 1.5, c = 10000, A = 1, B = 4, O = 6, E = 1, L = 5, U = 9, T = 30, v = 3)” (Arora et al. 2023).Sequence Alignment - Paired-end FASTQ files were initially visualized with fastqc126. TruSeq3-PE adaptors were trimmed with trimmomatic/0.32, and paired-end reads with a minimum read length of 36bp were kept131. Reads were aligned to each assembly using the paired-end module of bwa-mem13,116. For the CENPA ChIP-seq and input, we used bwa and samtools parameters previously described to work with CENPA ChIP-seq data 13,116 to better resolve multi-mapping reads “(from their study: k = 19, w = 100, d = 100, r = 1.5, c = 10000, A = 1, B = 4, O = 6, E = 1, L = 5, U = 9, T = 30, v = 3)”MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000The naked mole-rat (NMR; <i>Heterocephalus glaber</i>) is a eusocial subterranean rodent with a highly unusual set of physiological traits 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 was subsequently annotated and incorporated into multiple whole genome alignments in the Ensembl database. Our long-read assembly identified thousands of repeats and genes that were previously unassembled in the NMR and improved the results of routinely used short-read sequencing-based experiments such as RNA-seq, snRNA-seq, and ATAC-seq. We identified several spermatozoa related gene losses that may underlie the unique degenerative sperm phenotype in NMRs (<i>IRGC</i>, <i>FSCB</i>, <i>AKAP3</i>, <i>MROH2B</i>, <i>CATSPER1</i>, <i>DCDC2C</i>, <i>ATP1A4</i>, <i>TEKT5, and ZAN</i>), and an additional gene loss related to the established NK-cell absence in NMRs (<i>PILRB</i>). We resolved several tandem duplications in genes related to pathways underlying unique NMR adaptations including hypoxia tolerance, oxidative stress, and nervous system protection (<i>TINF2</i>, <i>TCP1</i>, <i>KYAT1</i>). Lastly, we describe our ongoing efforts to generate a reference telomere-to-telomere assembly in the NMR which includes the resolution of complex gene families. This new reference genome should accelerate the discovery of the genetic underpinnings of NMR physiology and adaptation.ChIP-seqHomo sapiensAn updated reference genome sequence and annotation reveals gene losses and gains underlying naked mole-rat biologyMihai MiclausSimon MonisDustin SokolowskiMichael WilsonJared SimpsonSana Akhtar AlviDustin J Sokolowski, Mihai Miclăuș, Alexander Nater, Mariela Faykoo-Martinez, Kendra Hoekzema, Philip Zuzarte, Simon Monis, Sana Akhtar Alvi, Odei Barreñada, Miguel Brieño-Enríquez, Jason Erdmann, Archana Lal Erdmann, Rathnakumar Kumaragurubaran, Jonathan Bayerl, DongAhn Yoo, Nadia Karimpour, Kyra Ungerleider, Huayun Hou, Fergal J Martin, Thibaut Hourlier, Zoe Clarke, Heidi E L Lischer, Dragos V Leordean, Yiyue Jiang, Trevor J Pugh, Ewan St J Smith, Leanne Haggerty, Diana J Laird, Jingtao Lilue, Melissa M Holmes, Evan E Eichler, Rémy Bruggmann, Jared T Simpson, Gabriel Balmus, Michael D WilsonfalseH3K27Ac and CENPA ChIP-seq experiments for human TeloHAEC cellsThis data contributes to a telomere-to-telomere genome assembly and annotation of the naked mole-rat, Heterocephalus glaber. To epigenetically annotate centromeres, we performed CENPA ChIP-seq experiments in the male subordinate NMR livers. To ensure antibody quality, as this was the first time CENPA ChIP-seq was performed in the NMR, we performed H3K27Ac and CENPA ChIP-seq experiments on a TeloHAOEC cell line.2026-08-05T00:00:00Z2026-08-05T01:00:49.079Z2026-07-03T19:54:45.805ZE-MTAB-1731139651266ERP196156EFO_0002944EFO_0004170EFO_0002692EFO_0004917EFO_0005518EFO_0003816EFO_000418410.1101/2024.11.26.625329