Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic and lipidomic profiling of subcutaneous and visceral adipose tissues in 15 vertebrates

ABSTRACT: The storage of lipids as energy in adipose tissue (AT) has been conserved over the course of evolution. However, substantial differences in ATs physiological activities were reported between species. Hence, establishing the mechanisms shaping evolutionarily divergence in ATs transcriptomes could provide a deeper understanding of AT regulation and its roles in obesity-related diseases. While previous studies performed anatomical, physiological and morphological comparisons between ATs across different species, little is currently understood at the molecular phenotypic levels. Here, we characterized transcriptional and lipidomic profiles of available subcutaneous and visceral ATs samples across 15 vertebrate species, spanning more than 300 million years of evolution, including placental mammals, birds and reptiles. We provide detailed descriptions of the datasets produced in this study and report gene expression and lipid profiles across samples. These resources should provide researchers could insights into the molecular and evolutionary mechanisms underlying functional differences between ATs in vertebrate species.

INSTRUMENT(S): Liquid Chromatography MS - negative - reverse phase, Liquid Chromatography MS - positive - reverse phase

SUBMITTER: Pengliang Liu

PROVIDER: MTBLS5943 | MetaboLights | 2022-11-17

REPOSITORIES: MetaboLights

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	MTBLS5943	Other
	FILES	Other
	a_MTBLS5943_LC-MS_negative_reverse-phase_metabolite_profiling.txt	Txt
	a_MTBLS5943_LC-MS_positive_reverse-phase_metabolite_profiling.txt	Txt
	i_Investigation.txt	Txt

Items per page:

1 - 5 of 8

Similar Datasets

Gene Expression Defines Natural Changes in Mammalian Lifespan

Project description:Mammals differ more than hundred fold in maximum lifespan, which can be altered in either direction during evolution, but the molecular basis for natural changes in longevity is not understood. Divergent evolution of mammals also led to extensive changes in gene expression within and between lineages. To understand the relationship between lifespan and variation in gene expression, we carried out RNA-seq-based gene expression analyses of liver, kidney and brain of 33 diverse species of mammals. Our analysis uncovered parallel evolution of gene expression and lifespan, as well as the associated life history traits, and identified the processes and pathways involved. These findings provide direct insights into how Nature reversibly adjusts lifespan and other traits during adaptive radiation of lineages. RNA-seq gene expression profiling in normal liver, kidney and brain of 33 mammalian species.

2015-02-17 | E-GEOD-43013 | biostudies-arrayexpress

RNA-seq of 6 tissues from 10 species to investigate the evolution of gene expression levels in mammalian organs

Project description:Changes in gene expression are thought to underlie many of the phenotypic differences between species. However, large-scale analyses of gene expression evolution were until recently prevented by technological limitations. Here we report the sequencing of polyadenylated RNA from six organs across ten species that represent all major mammalian lineages (placentals, marsupials and monotremes) and birds (the evolutionary outgroup), with the goal of understanding the dynamics of mammalian transcriptome evolution. We show that the rate of gene expression evolution varies among organs, lineages and chromosomes, owing to differences in selective pressures: transcriptome change was slow in nervous tissues and rapid in testes, slower in rodents than in apes and monotremes, and rapid for the X chromosome right after its formation. Although gene expression evolution in mammals was strongly shaped by purifying selection, we identify numerous potentially selectively driven expression switches, which occurred at different rates across lineages and tissues and which probably contributed to the specific organ biology of various mammals. Our transcriptome data provide a valuable resource for functional and evolutionary analyses of mammalian genomes. To study mammalian transcriptome evolution at high resolution, we generated RNA-Seq data (∼3.2 billion Illumina Genome Analyser IIx reads of 76 base pairs) for the polyadenylated RNA fraction of brain (cerebral cortex or whole brain without cerebellum), cerebellum, heart, kidney, liver and testis (usually from one male and one female per somatic tissue and two males for testis) from nine mammalian species: placental mammals (great apes, including humans; rhesus macaque; mouse), marsupials (gray short-tailed opossum) and monotremes (platypus). Corresponding data (∼0.3 billion reads) were generated for a bird (red jungle fowl, a non-domesticated chicken) and used as an evolutionary outgroup.

2011-10-12 | E-GEOD-30352 | biostudies-arrayexpress

RNA-Seq analysis of gene expression divergence in mammalian liver

Project description:The connection between evolution of regulatory elements and downstream gene expression is incompletely understood in mammals. We carried out a large-scale comparison of matched ChIP-seq and RNA-seq experiments across twenty species of mammals, using liver as a model somatic tissue. Herein we report the RNA-seq dataset, comprising twenty five species of mammals. When analysed alongside our previously reported ChIP-seq experiments, these data reveal a number of insights into how mammalian regulatory evolution propagates into differences in gene expression levels. Please note that all mouse RNA-seq libraries and three out of four human libraries have been previously reported in Array Express submission E-MTAB-4052 and are thus omitted here.

2017-10-11 | E-MTAB-4550 | biostudies-arrayexpress

The evolution of gene expression levels in mammalian organs

2011-10-13 | GSE30352 | GEO

Transcription profiling of human, chimp and mouse brain

Project description:Microarray technologies allow the identification of large numbers of expression differences within and between species. Although environmental and physiological stimuli are clearly responsible for changes in the expression levels of many genes, it is not known whether the majority of changes of gene expression fixed during evolution between species and between various tissues within a species are caused by Darwinian selection or by stochastic processes. We find the following: (1) expression differences between species accumulate approximately linearly with time; (2) gene expression variation among individuals within a species correlates positively with expression divergence between species; (3) rates of expression divergence between species do not differ significantly between intact genes and expressed pseudogenes; (4) expression differences between brain regions within a species have accumulated approximately linearly with time since these regions emerged during evolution. These results suggest that the majority of expression differences observed between species are selectively neutral or nearly neutral and likely to be of little or no functional significance. Therefore, the identification of gene expression differences between species fixed by selection should be based on null hypotheses assuming functional neutrality. Furthermore, it may be possible to apply a molecular clock based on expression differences to infer the evolutionary history of tissues.

2022-11-20 | E-AFMX-1 | biostudies-arrayexpress

Gene Expression Defines Natural Changes in Mammalian Lifespan

2015-02-17 | GSE43013 | GEO

Transcriptome profiling by array of visceral and subcutaneous adipose tissue from colorectal cancer patients

Project description:Transcriptomes of visceral and subcutaneous adipose tissue from colorectal cancer patients were profiled to investigate differences between depots. Samples were collected at time-point of primary surgery.

2019-06-22 | E-MTAB-8013 | biostudies-arrayexpress

The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans

Project description:This set of arrays contains all microarray experiments done involving comparisons among C. elegans natural isolates and mutation-accumulation lines. Abstract: The evolutionary importance of gene-expression divergence is unclear: some studies suggest that it is an important mechanism for evolution by natural selection, whereas others claim that most between-species regulatory changes are neutral or nearly neutral. We examined global transcriptional divergence patterns in a set of Caenorhabditis elegans mutation-accumulation lines and natural isolate lines to provide insights into the evolutionary importance of transcriptional variation and to discriminate between the forces of mutation and natural selection in shaping the evolution of gene expression. We detected the effects of selection on transcriptional divergence patterns and characterized them with respect to coexpressed gene sets, chromosomal clustering of expression changes and functional gene categories. We directly compared observed transcriptional variation patterns in the mutation-accumulation and natural isolate lines to a neutral model of transcriptome evolution to show that strong stabilizing selection dominates the evolution of transcriptional change for thousands of C. elegans expressed sequences. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. Computed

2006-01-31 | E-GEOD-4123 | biostudies-arrayexpress

Rapid evolution of the embryonically-expressed homeobox gene LEUTX within primates

Project description:LEUTX is a homeodomain transcription factor expressed in the very early embryo with a function around embryonic genome activation. The LEUTX gene is found only in eutherian mammals, including humans, but unlike the majority of homeobox genes, the encoded amino acid sequence is very different between divergent mammalian species. However, whether dynamic evolution has also occurred between closely related mammalian species remains unclear. In this work, we perform a comparative genomics study of LEUTX within the primates, revealing dramatic evolutionary sequence change between closely related species. Positive selection has acted on sites in the LEUTX protein, including six sites within the homeodomain; this suggests that selection may have driven changes in the set of downstream targets. Transfection into cell culture followed by transcriptomic analysis reveals small functional differences between human and marmoset LEUTX, suggesting rapid sequence evolution has fine-tuned the role of this homeodomain protein within the primates.

2023-02-06 | GSE224384 | GEO

Cis- and trans- regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids

Project description:Gene-expression divergence between species shapes morphological evolution, but the molecular basis is largely unknown. Here we show cis- and trans-regulatory elements and chromatin modifications on gene-expression diversity in genetically tractable Arabidopsis allotetraploids. In Arabidopsis thaliana and Arabidopsis arenosa, both cis and trans with predominant cis-regulatory effects mediate gene-expression divergence. The majority of genes with both cis- and trans-effects are subjected to compensating interactions and stabilizing selection. Interestingly, chromatin modifications correlate with cis - and trans -regulation. In F1 allotetraploids, Arabidopsis arenosa trans factors predominately affect allelic expression divergence. Arabidopsis arenosa trans factors tend to upregulate Arabidopsis thaliana alleles, whereas Arabidopsis thaliana trans factors up- or down-regulate Arabidopsis arenosa alleles. In resynthesized and natural allotetraploids, trans effects drive expression of both homoeologous loci into the same direction. We provide evidence for natural selection and chromatin regulation in shaping gene-expression diversity during plant evolution and speciation. Examination of gene expression in 5 tetraploid Arabidopsis using mRNA-seq

2012-05-31 | E-GEOD-29687 | biostudies-arrayexpress

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