Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

H3K27Ac and CENPA ChIP-seq experiments for the naked mole-rat liver

ABSTRACT: This 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. These experiments included an Input control, and a H3K27Ac ChIP-seq experiment to annotate active enhancers and ensure hat the ChIP-seq experiment with antibodies performed as expected.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Heterocephalus glaber

SUBMITTER: Dustin Sokolowski

PROVIDER: E-MTAB-17296 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

An updated reference genome sequence and annotation reveals gene losses and gains underlying naked mole-rat biology.

Sokolowski Dustin J DJ Miclăuș Mihai M Nater Alexander A Faykoo-Martinez Mariela M Hoekzema Kendra K Zuzarte Philip P Monis Simon S Alvi Sana Akhtar SA Erdmann Jason J Erdmann Archana Lal AL Kumaragurubaran Rathnakumar R Bayerl Jonathan J Yoo DongAhn D Karimpour Nadia N Ungerleider Kyra K Hou Huayun H J Martin Fergal F Hourlier Thibaut T Clarke Zoe Z Lischer Heidi E L HEL Leordean Dragos V DV Jiang Yiyue Y Pugh Trevor J TJ Smith Ewan St J ESJ Haggerty Leanne L Laird Diana J DJ Lilue Jingtao J Holmes Melissa M MM Eichler Evan E EE Bruggmann Rémy R Simpson Jared T JT Balmus Gabriel G Wilson Michael D MD

bioRxiv : the preprint server for biology 20241128

The 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 in ...[more]

PMID: 39651266

Similar Datasets

Project description:Circulating tumour cells in women with advanced oestrogen-receptor (ER)-positive/human epidermal growth factor receptor 2 (HER2)-negative breast cancer acquire a HER2-positive subpopulation after multiple courses of therapy. In contrast to HER2-amplified primary breast cancer, which is highly sensitive to HER2-targeted therapy, the clinical significance of acquired HER2 heterogeneity during the evolution of metastatic breast cancer is unknown. Here we analyse circulating tumour cells from 19 women with ER+/HER2- primary tumours, 84% of whom had acquired circulating tumour cells expressing HER2. Cultured circulating tumour cells maintain discrete HER2+ and HER2- subpopulations: HER2+ circulating tumour cells are more proliferative but not addicted to HER2, consistent with activation of multiple signalling pathways; HER2- circulating tumour cells show activation of Notch and DNA damage pathways, exhibiting resistance to cytotoxic chemotherapy, but sensitivity to Notch inhibition. HER2+ and HER2- circulating tumour cells interconvert spontaneously, with cells of one phenotype producing daughters of the opposite within four cell doublings. Although HER2+ and HER2- circulating tumour cells have comparable tumour initiating potential, differential proliferation favours the HER2+ state, while oxidative stress or cytotoxic chemotherapy enhances transition to the HER2- phenotype. Simultaneous treatment with paclitaxel and Notch inhibitors achieves sustained suppression of tumorigenesis in orthotopic circulating tumour cell-derived tumour models. Together, these results point to distinct yet interconverting phenotypes within patient-derived circulating tumour cells, contributing to progression of breast cancer and acquisition of drug resistance. Seventy-four single candidate CTCs from two representative ER+/HER2- patients (BRx-42 and BRx-82) and 14 triple negative patients were isolated via micromanipulation and subjected to single-cell RNA-sequencing. Thirteen candidate CTCs expressed PTPRC at a level higher than 10 reads-per-million, so were deemed potential White Blood Cells and therefore dropped from further consideration. Expression profiles of CTCs expressing ERBB2 at a level greater than 10 RPM were compared with those expressing ERBB2 at a level less than 10 RPM.

Dataset Information

H3K27Ac and CENPA ChIP-seq experiments for the naked mole-rat liver

Publications

An updated reference genome sequence and annotation reveals gene losses and gains underlying naked mole-rat biology.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets