GEO DataSets

(Submitter supplied) The brain requires complex mechanisms of genome regulation to encode and store behavioural information. In mammals, DNA methylation deposited at non-CG dinucleotides characterises brain epigenomes. However, it is unclear to what extent this non-canonical form of DNA methylation is evolutionarily conserved. To test this we profile brain cytosine methylation across the major vertebrate lineages, amphioxus, honeybee and octopus, finding that non-CG methylation in adult brain methylomes is restricted to vertebrates. more...

Organism:

Apis mellifera; Callorhinchus milii; Octopus bimaculoides; Branchiostoma lanceolatum; Danio rerio; Monodelphis domestica; Gallus gallus; Ornithorhynchus anatinus; Lethenteron camtschaticum

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

9 related Platforms

11 Samples

Download data: CGMAP, TSV

(Submitter supplied) In order to study the green anole dosage compensation mechanism we generated strand-specific RNA-seq libraries for a total of 186 samples from the green anole and other representative amniotes (human, mouse, opossum, platypus, chicken and xenopus). Moreover, in order to understand the dosage compensation mechanism of A. carolinensis, we generated ChIP-Seq data for the histone modification H4K16ac and compared levels of acetylation between males and females. more...

Organism:

Monodelphis domestica; Xenopus tropicalis; Gallus gallus; Ornithorhynchus anatinus; Mus musculus; Homo sapiens; Anolis carolinensis

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

8 related Platforms

197 Samples

Download data: BW, TXT

(Submitter supplied) A major challenge in biology is to determine how evolutionarily novel characters originate, however, mechanistic explanations for the origin of novelties are almost completely unknown. The evolution of mammalian pregnancy is an excellent system in which to study the origin of novelties because extant mammals preserve major stages in the transition from egg-laying to live-birth. To determine the molecular bases of this transition, we characterized the pregnant/gravid uterine transcriptome from tetrapods, including species in the three major mammalian lineages, and used ancestral transcriptome reconstruction to trace the evolutionary history of uterine gene expression. more...

Organism:

Dasypus novemcinctus; Canis lupus familiaris; Ornithorhynchus anatinus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18702 GPL18701 GPL13923

3 Samples

Download data: TXT

(Submitter supplied) Only a minuscule fraction of long non-coding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into their functionality, but comparative analyses have been precluded by our ignorance of lncRNAs in non-model organisms. Here, we use RNA sequencing to identify lncRNAs in eleven tetrapod species and we present the first large-scale evolutionary study of lncRNA repertoires and expression patterns. more...

Organism:

Monodelphis domestica; Gallus gallus; Ornithorhynchus anatinus; Xenopus tropicalis; Macaca mulatta; Gorilla gorilla; Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

15 related Platforms

55 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Two-thirds of gene promoters in mammals are associated with regions of non-methylated DNA, called CpG islands (CGIs), which counteract the repressive effects of DNA methylation. In lower vertebrates, computational CGI predictions often reside away from gene promoters, suggesting a major divergence in gene promoter architecture across vertebrates. By experimentally identifying non-methylated DNA in the genomes of seven diverse vertebrates, we instead reveal that non-methylated islands (NMIs) of DNA are a central feature of vertebrate gene promoters. more...

Organism:

Xenopus tropicalis; Homo sapiens; Mus musculus; Anolis carolinensis; Danio rerio; Gallus gallus; Ornithorhynchus anatinus

Type:

Methylation profiling by high throughput sequencing

10 related Platforms

24 Samples

Download data: BED

(Submitter supplied) MicroRNAs (miRNAs) are major post-transcriptional regulators of gene expression, yet their origins and functional evolution in mammals remain little understood due to the lack of appropriate comparative data. Using RNA sequencing, we have generated extensive and comparable miRNA data for five organs in six species that represent all main mammalian lineages and birds (the evolutionary outgroup), with the aim to unravel the evolution of mammalian miRNAs. more...

Organism:

Macaca mulatta; Homo sapiens; Monodelphis domestica; Gallus gallus; Ornithorhynchus anatinus; Didelphis virginiana; Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

7 related Platforms

38 Samples

Download data: TXT

(Submitter supplied) As a result of sex chromosome differentiation from ancestral autosomes, male mammalian cells only contain one X chromosome. It has long been hypothesized that X-linked gene expression levels have become doubled in males to restore dosage balance between the X and autosomes, and that the resulting X overexpression in females then drove the evolution of X inactivation (XCI). However, this model has never been directly tested and patterns and mechanisms of dosage compensation across different mammals and birds generally remain little understood. more...

Organism:

Ornithorhynchus anatinus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13798

3 Samples

Download data: TXT

(Submitter supplied) MicroRNAs are small non-coding RNAs that regulate a variety of biological processes. In the last version of the miRBase database (Release 17), 720 mouse microRNAs are accompanied by only 408 rat microRNAs. Given the importance of rat as a model organism, we used next generation sequencing and microarray technologies to discover novel microRNAs in rat kidneys.

Organism:

Oryzias latipes; Pan troglodytes; Pongo pygmaeus; Ovis aries; Taeniopygia guttata; Xenopus laevis; Macaca nemestrina; Canis lupus familiaris; Rattus norvegicus; Takifugu rubripes; Rhinopithecus bieti; Saguinus labiatus; Danio rerio; Gallus gallus; Ornithorhynchus anatinus; Macaca mulatta; Pan paniscus; Equus caballus; Petromyzon marinus; Xenopus tropicalis; Ateles geoffroyi; Symphalangus syndactylus; Homo sapiens; Sus scrofa; Bos taurus; Mus musculus; Tetraodon nigroviridis

Type:

Non-coding RNA profiling by array

Platform:

GPL14819

6 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Pan troglodytes; Pongo pygmaeus; Monodelphis domestica; Gallus gallus; Ornithorhynchus anatinus; Macaca mulatta; Pan paniscus; Gorilla gorilla; Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

10 related Platforms

131 Samples

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(Submitter supplied) Small RNA pathways play evolutionarily conserved roles in gene regulation and in defense from pathogenic and parasitic nucleic acids. The character and expression patterns of small RNAs show conservation throughout animal lineages, but specific animal clades also show variations on these recurring themes, including species-specific small RNAs. The monotremes, with only platypus and four species of echidna as extant members, represent the basal branch of the mammalian lineage. more...

Organism:

Ornithorhynchus anatinus; Tachyglossus aculeatus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL11057 GPL11058

3 Samples

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(Submitter supplied) Platform table annotations based on miRBase release version 17 catalog number : MRA-1033 http://www.lcsciences.com/applications/transcriptomics/mirna-profiling/mirna/mirna-available-arrays/vertebrates-array-content/ Protocol: Arrays are made based µParaflo microfluidic technology.

Organism:

Petromyzon marinus; Danio rerio; Oryzias latipes; Xenopus laevis; Xenopus tropicalis; Gallus gallus; Ornithorhynchus anatinus; Ateles geoffroyi; Macaca mulatta; Macaca nemestrina; Symphalangus syndactylus; Pan paniscus; Pan troglodytes; Pongo pygmaeus; Homo sapiens; Canis lupus familiaris; Equus caballus; Sus scrofa; Bos taurus; Ovis aries; Mus musculus; Rattus norvegicus; Takifugu rubripes; Taeniopygia guttata; Rhinopithecus bieti; Saguinus labiatus; Tetraodon nigroviridis

1 Series

6 Samples

Download data: TXT

(Submitter supplied) Microarray assay was performed by LC Science Company. The microfluidic PicoArray reactor is made from silicon using standard microelectronic fabrication procedures. The reactor contains three topographical features: pico- reaction chambers, fluid microchannels, and inlet/outlet through holes. The chip contains 128 x 31 (total 3698) individual reaction chambers, each with an internal volume of 270 pl. more...

Organism:

Ornithorhynchus anatinus; Lemur catta; Saguinus imperator; Ateles sp.; Lagothrix; Macaca mulatta; Macaca nemestrina; Symphalangus syndactylus; Gorilla gorilla; Pan paniscus; Pan troglodytes; Pongo; Homo sapiens; Canis lupus familiaris; Equus caballus; Sus scrofa; Bos taurus; Ovis aries; Cricetulus griseus; Mus musculus; Rattus norvegicus; Monodelphis domestica; Rhinopithecus bieti

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(Submitter supplied) n/a

Organism:

Ornithorhynchus anatinus

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