Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: How to Make an Elephant

PROVIDER: PRJNA622303 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	SRR11458313_1.fastq.gz	Fastqsanger.gz
	SRR11458313_2.fastq.gz	Fastqsanger.gz
	SRR11458314_1.fastq.gz	Fastqsanger.gz
	SRR11458314_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 31

Similar Datasets

DNA Damage Response in Elephant Cells

Project description:The identity of most functional elements in the mammalian genome and the phenotypes they impact are unclear. Here, we perform a genome-wide comparative analysis of patterns of accelerated evolution in species with highly distinctive traits to discover candidate functional elements for clinically important phenotypes. We identify accelerated regions (ARs) in the elephant, hibernating bat, orca, dolphin, naked mole rat and thirteen-lined ground squirrel lineages in mammalian conserved regions, uncovering ~33,000 elements that bind hundreds of different regulatory proteins in humans and mice. ARs in the elephant, the largest land mammal, are uniquely enriched at elephant DNA damage response genes and changed conserved regulatory sites. The genomic hotspot for elephant ARs is the E3 ligase subunit of the Fanconi Anemia Complex, a master regulator of DNA repair. Additionally, ARs in the six species are associated with specific human clinical phenotypes that have apparent concordance with overt traits in each species.

2018-01-01 | GSE107117 | GEO

How to Make an Elephant: Functional Genomic Divergence and the Evolution of Cancer Suppression

Project description:How to Make an Elephant: Functional Genomic Divergence and the Evolution of Cancer Suppression

| PRJNA623216 | ENA

The methylome of a cartilaginous fish, Callorhinchus milii, reveals conservation of epigenetic regulation across jawed vertebrates

Project description:Background Methylation of CG dinucleotides constitutes a critical system of epigenetic memory in bony vertebrates, where it modulates gene expression and suppresses transposon activity. The genomes of studied vertebrates are pervasively hypermethylated, with the exception of regulatory elements such as transcription start sites (TSSs), where the presence of methylation is associated with gene silencing. This system is not found in the sparsely methylated genomes of invertebrates, and establishing how it arose during early vertebrate evolution is impeded by a paucity of epigenetic data from basal vertebrates. Methods We perform whole-genome bisulfite sequencing to generate the first genome-wide methylation profiles of a cartilaginous fish, the elephant shark Callorhinchus milii. Employing these to determine the elephant shark methylome structure and its relationship with expression, we compare this with higher vertebrates and an invertebrate chordate using published methylation and transcriptome data. Results Like higher vertebrates, the majority of elephant shark CG sites are highly methylated, and methylation is abundant across the genome rather than patterned in the mosaic configuration of invertebrates. This global hypermethylation includes transposable elements and the bodies of genes at all expression levels. Significantly, we document an inverse relationship between TSS methylation and expression in the elephant shark, supporting the presence of the repressive regulatory architecture shared by higher vertebrates. Conclusions Our demonstration that methylation patterns in a cartilaginous fish are characteristic of higher vertebrates imply the conservation of this epigenetic modification system across jawed vertebrates separated by 465 million years of evolution. In addition, these findings position the elephant shark as a valuable model to explore the evolutionary history and function of vertebrate methylation.

2017-03-24 | GSE96683 | GEO

Differentially represented proteins in response to tuberculosis identified by quantitative serum proteomics in Asian elephants

Project description:The study reported here is the first characterization of elephant serum proteome in response to TB. These results advance our understanding of elephant immune response to M. tuberculosis and provide potential biomarkers for diagnosis and control of TB in this endangered species.

2022-10-15 | PXD033830 | Pride

Characterisation of eggshell proteomes from the extinct Madagascar elephant bird

Project description:Characterisation of eggshell proteomes from the extinct Madagascar elephant bird

2023-01-20 | PXD035725 | Pride

Project description:Transcriptome sequencing of elephant grass, purple elephant grass and Guiminyin elephant grass

| PRJNA1150492 | ENA

Loxodonta africana

Project description:African elephant

| PRJNA12568 | ENA

Elephas maximus

Project description:Asian elephant

| PRJNA43705 | ENA

Project description:Small RNA sequencing of elephant grass, purple elephant grass and Guiminyin elephant grass

| PRJNA1150346 | ENA

Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample

Project description:Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides, and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) which died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding twenty-eight chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive-X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth’s death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.

2024-05-22 | GSE268050 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data