Fecal bacteria
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA375999 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We performed RNAseq, metabolomics and pathway enrichment analysis on cardiac tissue from naked mole-rats (Heterocephalus glaber) and from seven other members of African mole rat genera, Cape mole-rat (Georychus capensis), Cape dune mole-rat (Bathyergus suillus), Common mole-rat (Cryptomys hottentotus hottentotus), Natal mole-rat (C. h. natalenesis), Mahali mole rat (C. h. mahali), Highveld mole-rat (C. h. pretoriae) and Damaraland mole-rats (Fukomys damarensis) representing differing burrow and soil types, degrees of sociality, lifespan and hypoxia tolerance. In addition, we include the evolutionarily highly divergent hottentot golden mole (Ambysomus hottentotus), an Afrotherian subterranean, solitary mammal, and the C57/BL6 laboratory mouse as a standard mammal control. After RNA sequencing, we removed the reads mapped to rRNAs and get rawdata, then we filtered the low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads. These are the data uploaded.
2024-02-20 | E-MTAB-13808 | biostudies-arrayexpress
Project description:One ONT-ULK sequencing run from the kidney of a single male CDMR (Bathyergus suillus) sample used to make the mBatSui1.1.primary genome assembly as an evolutionary comparator to our telomere-to-telomere naked mole-rat genome assembly. Specifically, we assembled a CDMR from a wild-derived sample in South African cape and sequenced in Toronto, Canada, using PacBio HiFi (89 Gb, read N50 = 18 Kb) and ONT-ULK (55 Gb, read N50 = 43 Kb) reads (contig N50 = 33 Mb, Compleasm S = 99%, QV = 71.0). This accession stores the ONT-ULK data for this assembly.
2026-08-05 | E-MTAB-17420 | biostudies-arrayexpress
Project description:One PacBio Hifi sequencing run from the kidney of a single male CDMR (Bathyergus suillus) sample used to make the mBatSui1.1.primary genome assembly as an evolutionary comparator to our telomere-to-telomere naked mole-rat genome assembly. Specifically, we assembled a CDMR from a wild-derived sample in South African cape and sequenced in Toronto, Canada, using PacBio HiFi (89 Gb, read N50 = 18 Kb) and ONT-ULK (55 Gb, read N50 = 43 Kb) reads (contig N50 = 33 Mb, Compleasm S = 99%, QV = 71.0). This accession stores the Pacbio Hifi data for this assembly.
2026-08-05 | E-MTAB-17312 | biostudies-arrayexpress
Project description:Pacbio Hifi sequencing of a male cape dune mole-rat kidney sample
| PRJEB120964 | ENA
Project description:ONT ULK sequencing of a male cape dune mole-rat kidney sample
| PRJEB122994 | ENA
Project description:An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from many tissues of 3 species of mole rats: Cape mole rat (Georychus capensis), Damaraland mole rat (Cryptomys damarensis), Naked mole rat (Heterocephalus glaber). We generated DNA methylation data from n=94 tissues from 3 species: Cryptomys damarensis (n=10), Georychus capensis (n=6), Heterocephalus glaber (n=78). All tissues ewere obtained from frozen tissue collection that were euthanized for other studies. Kidney (n=6), liver (n=61), skin (n=27). The tissues used in this study were obtained from post-mortem specimens from animals free from disease in compliance. Sample collection was from post-mortem material. Tissue samples were snap frozen in liquid nitrogen following dissection and transferred for storage at -80ºC. Genomic DNA was extracted using Qiagen DNeasy Blood and Tissue kit and quantified using Nanodrop and Qubit.als
2021-10-18 | GSE174778 | GEO
Project description:Changes in gene regulation have long been though to underlie most phenotypic differences between species. Subterranean rodents, and in particular the naked mole-rat (NMR), have attracted substantial attention due to their proposed phenotypic adaptations, which include hypoxia tolerance, metabolic changes and cancer resistance. However, it is largely unknown what regulatory changes may associate with these phenotypic traits, and whether these are unique to the NMR, the mole-rat clade or also present in other mammals. Here, we undertook a comparative genomics approach to identify genome-wide promoter and enhancer regions harbouring epigenomic hallmarks of regulatory activity, in heart and liver from two mole-rat species (NMR and DMR) and two rodent outgroups. To identify promoters and enhancers displaying robust shifts in regulatory activity in the mole-rat clade, we adapted and applied a phylogenetic modeling approach to quantitatively compare epigenomic signals at orthologous locations, while accounting for phylogenetic distance and inter-species variation. This method identified thousands of orthologous promoter and enhancer regions with increased activity in ancestral or single-species mole-rat branches, as well as hundreds of promoters and enhancers with reduced activity in mole-rats versus other rodents. These elements underlie both shared tissue-specific changes in gene regulation associated with mole-rat evolution, which include metabolic and functional adaptations in heart and liver. Moreover, by comparing mole-rat specific changes in promoters and enhancers between ancestral and single-species branches, our data revealed a number of candidate pathways with stepwise regulatory changes during mole-rat evolution. Lastly, we analysed the genomic properties of non-alignable promoters and enhancers in mole-rats, and report (i) their overlap with specific repetitive elements and transcription factor binding sites; and (ii) their association with metabolic gene functions. On the whole, these comparative analyses reveal mole-rat specific epigenomic changes across orthologous and non-mappable promoters and enhancers - which inform previously reported mole-rat adaptations from a gene regulation perspective.
2023-08-21 | GSE222972 | GEO
Project description:CAPE has anti-bacterial and viral infection, anti-oxidant, anti-inflammatory, and anti-tumor properties.We found that CAPE suppressed the proliferation and colony-formation ability of NPC cells. We used microarrays to identify differential genes regulated by CAPE in NPC cells and futher analys the potential GO and pathway
2019-02-16 | GSE126608 | GEO
Project description:Analysis of the Naked mole-rat proteome relative to mice
2020-12-18 | MSV000086617 | MassIVE