Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic evolution across bilaterian tissues

ABSTRACT: Transcriptomic evolution across bilaterian tissues

PROVIDER: PRJNA846095 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR19548800_1.fastq.gz	Fastqsanger.gz
	SRR19548800_2.fastq.gz	Fastqsanger.gz
	SRR19548801_1.fastq.gz	Fastqsanger.gz
	SRR19548801_2.fastq.gz	Fastqsanger.gz
	SRR19548802_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 178

Similar Datasets

Transcriptomic evolution across bilaterian tissues

Project description:We investigate tissue transcriptomic evolution across bilaterian animals by analyzing RNA-seq data from eight different tissues across twenty species.

2022-10-12 | GSE205498 | GEO

The Genetic and Transcriptomic Evolution of Melanoma

Project description:<p>The overarching goal of the study was to better understand the evolution of melanoma. To do this, we collected archival tissue of melanomas adjacent to their intact, remnant precursor lesions. We also collected archival tissue of primary melanomas and their matching metastases. From the formalin-fixed paraffin-embedded (FFPE) blocks, we microdissected non-neoplastic (normal), precursor, and descendent portions of tissue. Both RNA and DNA were extracted from the microdissected tissues and subjected to next generation sequencing. In summary, we performed matched DNA/RNA sequencing of melanoma/precursor/normal trios, allowing us to trace the genetic and transcriptomic evolution of melanoma.</p>

| phs001550 | dbGaP

Evolutionary conservation of the eumetazoan gene regulatory landscape

Project description:Bilaterian animals differ from other metazoans in their apparent bilateral symmetry and the development of a third germ layer. Both might have facilitated the evolution of the diverse and complex bilaterian body plans. The first cnidarian genome sequence revealed that despite their morphological simplicity, this sister group to all bilaterians shares an immense genomic complexity with vertebrates. This suggested that it might have been the complexity of gene regulation which increased during the evolution of bilaterians. We compared the gene regulatory landscape of cnidarians and bilaterians. To this end we generated the first genome-wide prediction of gene regulatory elements and profiled five epigenetic marks in a non-bilaterian animal, the cnidarian Nematostella vectensis. We found that the location of chromatin modifications relative to genes and distal enhancers is conserved among eumetazoans. Surprisingly, the genomic landscape of gene regulatory elements is highly similar between Nematostella and bilaterian model organisms. This suggests that complex regulation of developmental gene expression evolved in eumetazoans without a major increase in complexity in bilaterians. ChIP-seq of p300, RNA Pol2, and five histone modifications in Nematostella vectensis.

2013-12-02 | E-GEOD-46488 | biostudies-arrayexpress

Transcriptomic profiling of sea anemone tissues

Project description:Transcriptomic profiling of sea anemone tissues

| PRJNA646454 | ENA

Origin and evolution of neural microexons

Project description:The mechanisms by which entire programs of gene regulation emerged during evolution are poorly understood. Neuronal microexons represent the most conserved class of alternative splicing in vertebrates and are critical for proper brain development and function. Here, we discover neural microexon programs in non-vertebrate species and trace their origin to bilaterian ancestors through the emergence of a previously uncharacterized ‘enhancer of microexons' (eMIC) protein domain. The eMIC domain originated as an alternative, neural-enriched splice isoform of the pan-eukaryotic Srrm2/SRm300 splicing factor gene, and subsequently became fixed in the vertebrate and neuronal-specific splicing regulator Srrm4/nSR100 and its paralog Srrm3. Remarkably, the eMIC domain is necessary and sufficient for microexon splicing, and functions by interacting with the earliest components required for exon recognition. The emergence of a novel domain with restricted expression in the nervous system thus resulted in the evolution of splicing programs that contributed to qualitatively expand neuronal molecular complexity in bilaterians.

2019-03-12 | PXD010034 | Pride

The brain regulatory program predates central nervous system evolution

Project description:Understanding how brains evolved is critical to determine the origin(s) of centralized nervous systems. Brains are patterned along their anteroposterior axis by stripes of gene expression that appear to be conserved, suggesting brains are homologous. However, the striped expression is also part of the deeply conserved anteroposterior axial program. An emerging hypothesis is that similarities in brain patterning are convergent, arising through the repeated co-option of axial programs. To resolve whether shared brain neurogenic programs likely reflect convergence or homology, we investigated the evolution of axial programs in neurogenesis. We show that the bilaterian anteroposterior program patterns the nerve net of the cnidarian Nematostella along the oral-aboral axis arguing that anteroposterior programs regionalized developing nervous systems in the cnidarian-bilaterian common ancestor prior to the emergence of brains. This finding rejects shared patterning as sufficient evidence to support brain homology and provides functional support for the plausibility that axial programs could be co-opted if nervous systems centralized in multiple lineages

2022-11-22 | GSE218419 | GEO

Pervasive concerted evolution in gene expression shapes cell type transcriptomes

Project description:Complex multicellular organisms have evolved numerous cell types with many different functions. Comparative transcriptomic data yields valuable insights into cell type, tissue, and organ evolution. However, interpreting this data requires understanding how transcriptomes evolve. A particularly difficult problem is that cell type transcriptomes may not evolve independently, a key assumption of most evolutionary analyses. Non-independence of cell types can occur when cell types share regulatory mechanisms. This leads to concerted evolution in gene expression across different cell types, confounding efforts to unravel the history of cell type evolution, and identify cell type-specific patterns of expression. Here we present a statistical model to estimate the level of concerted transcriptome evolution and apply it to published and new data. The results indicate that tissues undergo pervasive concerted evolution in gene expression. Tissues related by morphology or developmental lineage exhibit higher levels of concerted evolution. Concerted evolution also causes tissues from the same species to be more similar in gene expression to each other than to homologous tissues in another species. This result may explain why some tissue transcriptomes cluster by species rather than homology. Our analysis of bird skin appendages data suggests levels of concerted evolution also varies with phylogenetic age of the tissue. Our study illustrates the importance of accounting for concerted evolution when interpreting comparative transcriptome data, and should serve as a foundation for future investigations of cell type evolution.

2017-10-13 | GSE89040 | GEO

Epigenomic profiling and transcriptomic profiling of LUAD patients tumor tissues and tumor adjacent tissues

Project description:To provide an in-depth understanding of the epigenomic heterogeneity of LUAD, we here investigated the H3K27ac histone modification profiles of tumors and adjacent normal lung tissues from 42 LUAD patients and explored the role of epigenetic alterations in LUAD progression. We also investigated transcriptomic alterations among 36 patients tumor tissues.

| EGAS00001005132 | EGA

Pronounced expression of extracellular matrix proteoglycans regulated by Wnt pathway underlies the parallel evolution of lip hypertrophy in East African cichlids

Project description:Proteome analysis of East African chiclid lip tissues to evaluate the parallel evolution of lip hypertrhophy.

2025-04-09 | PXD051571 | JPOST Repository

Single Cell Transcriptomic Profiling of Cardiac Tissues and Surrounding Tissues During Early Cardiac Development

Project description:Single Cell Transcriptomic Profiling of Cardiac Tissues and Surrounding Tissues During Early Cardiac Development

| PRJNA848405 | ENA