Ontology highlight
ABSTRACT:
PROVIDER: PRJNA415283 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6201763_1.fastq.gz | Fastqsanger.gz | |||
| SRR6201763_2.fastq.gz | Fastqsanger.gz | |||
| SRR6201764_1.fastq.gz | Fastqsanger.gz | |||
| SRR6201764_2.fastq.gz | Fastqsanger.gz | |||
| SRR6201765_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 8 |
Similar Datasets
Project description:Evolutionary alterations to cis-regulatory sequences are likely to cause adaptive phenotypic complexity, through orchestrating changes in cellular proliferation, identity and communication. For non-model organisms with adaptive key-innovations, patterns of regulatory evolution have been predominantly limited to targeted sequence-based analyses. Chromatin-immunoprecipitation with high-throughput sequencing (ChIP-seq) is a technology that has only been used in genetic model systems and is a powerful experimental tool to screen for active cis-regulatory elements. Here, we show that it can also be used in ecological model systems and permits genome-wide functional exploration of cis-regulatory elements. As a proof of concept, we use ChIP-seq technology in adult fin tissue of the cichlid fish Oreochromis niloticus to map active promoter elements, as indicated by occupancy of trimethylated Histone H3 Lysine 4 (H3K4me3). The fact that cichlids are one of the most phenotypically diverse and species-rich families of vertebrates could make them a perfect model system for the further in-depth analysis of the evolution of transcriptional regulation. examination of H3K4me3 in adult fin tissue of the Nile tilapia (Oreochromis niloticus)
2015-07-07 | E-GEOD-62791 | biostudies-arrayexpress
Project description:Adaptive immunity and the five vertebrate NF-kB/Rel family members first appeared in cartilaginous fish, suggesting that NF-kB family expansion allowed the acquisition of new functions to regulate adaptive immune responses. Transcriptome profiling revealed that, even in macrophages, the NF-kB family member, c-Rel, most potently regulates a cytokine gene linked to adaptive immunity, Il12b, with limiting roles at key regulators of innate immunity. Neofunctionalization of c-Rel to regulate Il12b depends on its unique DNA-binding properties, which we examined using structural, biochemical, functional, and genomic approaches. Among our findings was functional c-Rel homodimer binding to motifs with little resemblance to canonical NF-kB motifs. To determine whether c-Rel’s unique binding properties drove c-Rel-RelA divergence, we compared binding properties in various vertebrate species. c-Rel-RelA binding properties diverged in mammals and amphibians but were comparable in earlier vertebrates, suggesting that divergent DNA binding emerged relatively late during vertebrate evolution to support increasing complexity of adaptive immune regulation.
2023-11-29 | GSE243010 | GEO
Project description:This experiment set contains the arrays referenced in Ferea, TL, et al. titled "Systematic changes in gene expression patterns following adaptive evolution in yeast"(Proc Natl Acad Sci USA 1999 96(17):9721-6). A Saccharomyces cerevisiae population was cultured for many generations under conditions to which it is not optimally adapted. These experiments were designed to investigate adaptive evolution under natural selection.
2005-06-16 | E-SMDB-98 | biostudies-arrayexpress
Project description:Evolution of transcriptional regulation is thought to be a major cause of the evolution of phenotypic traits. We compared DNase I Hypersensitive sites in fibroblast cells from five primates (human, chimpanzee, gorilla, orangutan, and macaque). We identified approximately 90,000 DHS sites, of which 59% are not significantly different between species, 27% are differential and likely due to a single evolutionary change, and 14% are differential and likely due to multiple changes. We found that including additional closely related species allows us to better distinguish between accessibility changes that are specific to a single species and those that have experienced changes in chromatin accessibility across multiple species during evolution.
2019-10-11 | GSE129034 | GEO
Project description:Transcription Factor binding evolution in five mouse species
| PRJEB1247 | ENA
Project description:Purpose: High-altitude adaptive evolution of transcription, and the convergence and divergence of transcriptional alteration across species in response to high-altitude environments, is an important topic of broad interest to the general biology community. Our study aims to answer this important biological question. Methods: We generated deep transcriptome data of high- and low- altitude populations across four species: chicken, pig, goat and sheep, as well as high-altitude yak and low-altitude cattle, from six tissues (heart, kidney, liver, lung, skeletal muscle and spleen). Results: Here we provide a comprehensive comparative transcriptome landscape of expression and alternative splicing variation between low- and high-altitude populations across multiple species for distinct tissues. Conclusions: Our data serves a valuable resource for further study on adaptive transcription evolution and identification of candidate adaptive genes.
2017-09-06 | GSE93855 | GEO
Project description:Evolutionary alterations to cis-regulatory sequences are likely to cause adaptive phenotypic complexity, through orchestrating changes in cellular proliferation, identity and communication. For non-model organisms with adaptive key-innovations, patterns of regulatory evolution have been predominantly limited to targeted sequence-based analyses. Chromatin-immunoprecipitation with high-throughput sequencing (ChIP-seq) is a technology that has only been used in genetic model systems and is a powerful experimental tool to screen for active cis-regulatory elements. Here, we show that it can also be used in ecological model systems and permits genome-wide functional exploration of cis-regulatory elements. As a proof of concept, we use ChIP-seq technology in adult fin tissue of the cichlid fish Oreochromis niloticus to map active promoter elements, as indicated by occupancy of trimethylated Histone H3 Lysine 4 (H3K4me3). The fact that cichlids are one of the most phenotypically diverse and species-rich families of vertebrates could make them a perfect model system for the further in-depth analysis of the evolution of transcriptional regulation.
2015-07-07 | GSE62791 | GEO
Project description:Elucidating patterns of adaptive evolution in genome-reduced Escherichia coli
| PRJDB13224 | ENA
Project description:Elucidating patterns of adaptive evolution in genome-reduced Escherichia coli
| PRJDB13225 | ENA
Project description:Adaptive immunity and the five vertebrate NF-kB/Rel family members first appeared in cartilaginous fish, suggesting that NF-kB family expansion allowed the acquisition of new functions to regulate adaptive immune responses. Transcriptome profiling revealed that, even in macrophages, the NF-kB family member, c-Rel, most potently regulates a cytokine gene linked to adaptive immunity, Il12b, with limiting roles at key regulators of innate immunity. Neofunctionalization of c-Rel to regulate Il12b depends on its unique DNA-binding properties, which we examined using structural, biochemical, functional, and genomic approaches. Among our findings was functional c-Rel homodimer binding to motifs with little resemblance to canonical NF-kB motifs. To determine whether c-Rel’s unique binding properties drove c-Rel-RelA divergence, we compared binding properties in various vertebrate species. c-Rel-RelA binding properties diverged in mammals and amphibians but were comparable in earlier vertebrates, suggesting that divergent DNA binding emerged relatively late during vertebrate evolution to support increasing complexity of adaptive immune regulation.
2024-03-11 | GSE243011 | GEO