GEO DataSets

(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) We collected small RNA sequencing data from brain and heart of an adult Xenopus tropicalis individual to investigate the conservation of site-specific miRNA editing events identified in mammals.

Organism:

Xenopus tropicalis

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18470

2 Samples

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

Type:

Expression profiling by high throughput sequencing

10 related Platforms

131 Samples

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(Submitter supplied) microRNAs (miRNAs) are important post-transcriptional regulators of gene expression. However, comprehensive expression profiles of miRNAs during spermatogenesis in mammals is lacking. In the present study, we sequenced small RNAs in highly purified spermatogonial stem cells (SSCs), spermatocytes in the pre-leptotene, leptotene, zygotene and pachytene stages, haploid round spermatids and spermatozoa. more...

Organism:

Sus scrofa; Mus musculus; Oryctolagus cuniculus; Rattus norvegicus

Type:

Non-coding RNA profiling by high throughput sequencing

4 related Platforms

20 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) are endogenous RNA molecules that contribute to the regulation of gene expression post-transcriptionally. Recently, patterns of sequence evolution and evolutionary emergence of miRNAs have been analyzed in detail. However, the extent to which miRNA expression levels vary within and between species, the role of stabilizing selection versus other evolutionary mechanisms in shaping the temporal dynamics of these changes, and how this variation might unveil the interplay between miRNAs and mRNAs remain poorly understood. more...

Organism:

Drosophila simulans; Drosophila melanogaster; Drosophila yakuba

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL9394 GPL11000 GPL9058

12 Samples

Download data: TXT, XLS

(Submitter supplied) We found two lines of evidence suggesting that miRNA abundance has been shaped by different evolutionary regimes at the two developmental stages. Attributed to functional constraints, which points to mechanisms more subtle and diverse than previously thought.

Organism:

Drosophila melanogaster; Drosophila simulans; Drosophila yakuba

Type:

Non-coding RNA profiling by array

Platform:

GPL18365

72 Samples

Download data: TXT

(Submitter supplied) We found two lines of evidence suggesting that miRNA abundance has been shaped by different evolutionary regimes at the two developmental stages attributed to functional constraints, which points to mechanisms more subtle and diverse than previously thought.

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL14007

24 Samples

Download data: PAIR

(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) This SuperSeries is composed of the SubSeries listed below.

Organism:

Arabidopsis thaliana; Capsella rubella; Arabidopsis lyrata

Type:

Non-coding RNA profiling by high throughput sequencing

4 related Platforms

12 Samples

Download data: FNA, GFF3, QUAL

(Submitter supplied) Deep sequencing of small RNA from three closely related brassicaceae A. thaliana, A. lyrata and Capsella rubella was done to systematically analyze the evolution of MIRNA genes and their targets.

Organism:

Arabidopsis thaliana; Arabidopsis lyrata

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL9062 GPL9180

4 Samples

Download data: GFF3, TXT

(Submitter supplied) Deep sequencing of small RNA from three closely related brassicaceae A. thaliana, A. lyrata and Capsella rubella was done to systematically analyze the evolution of MIRNA genes and their targets.

Organism:

Arabidopsis lyrata; Capsella rubella

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL10143 GPL10142

8 Samples

Download data: FNA, GFF3, QUAL, TXT

(Submitter supplied) Characterization of miRNAs in red flour beetle Tribolium castaneum by deep sequencing of two different RNA libraries.

Organism:

Tribolium castaneum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11311

2 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:

Tachyglossus aculeatus; Ornithorhynchus anatinus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL11057 GPL11058

3 Samples

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(Submitter supplied) MicroRNAs (miRNA) are small, endogenous RNAs that regulate the expression of mRNAs posttranscriptionally. Evolutionarily new miRNAs, like new protein-coding genes, are dominantly expressed in reproductive organs. To dissect the evolutionary dynamics of new miRNAs in Drosophila spp, we sequenced small RNAs from two species of Drosophila, including four samples from reproductive organs and one sample from imaginal discs / CNS. more...

Organism:

Drosophila simulans; Drosophila pseudoobscura

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL13306 GPL13310

5 Samples

Download data: TXT