Ontology highlight
ABSTRACT:
PROVIDER: PRJNA849615 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Vesper bats (family Vespertilionidae) experienced a rapid adaptive radiation beginning around 36 mya that resulted in the second most species rich mammalian family. Coincident with that radiation was an initial burst of DNA transposon activity that has continued into the present. Deep sequencing of small RNAs from the vespertilionid, Eptesicus fuscus, as well as dog and horse revealed that substantial numbers of novel bat miRNAs are derived from DNA transposons unique to vespertilionids. In fact, 35.9% of Eptesicus-specific miRNAs derive from DNA transposons compared to 2.2 and 5.9% of dog- and horse-specific miRNAs, respectively and targets of several miRNAs are identifiable. Timing of the DNA transposon expansion and the introduction of novel miRNAs coincides remarkably well with the rapid diversification of the family Vespertilionidae. We suggest that the rapid and repeated perturbation of regulatory networks by the introduction of many novel miRNA loci was a factor in the rapid radiation.
2014-05-19 | GSE47593 | GEO
Project description:Phylogenomics resolves the ancient and rapid radiation of banded newts (genus Ommatotriton)
| PRJNA1096730 | ENA
Project description:Vesper bats (family Vespertilionidae) experienced a rapid adaptive radiation beginning around 36 mya that resulted in the second most species rich mammalian family. Coincident with that radiation was an initial burst of DNA transposon activity that has continued into the present. Deep sequencing of small RNAs from the vespertilionid, Eptesicus fuscus, as well as dog and horse revealed that substantial numbers of novel bat miRNAs are derived from DNA transposons unique to vespertilionids. In fact, 35.9% of Eptesicus-specific miRNAs derive from DNA transposons compared to 2.2 and 5.9% of dog- and horse-specific miRNAs, respectively and targets of several miRNAs are identifiable. Timing of the DNA transposon expansion and the introduction of novel miRNAs coincides remarkably well with the rapid diversification of the family Vespertilionidae. We suggest that the rapid and repeated perturbation of regulatory networks by the introduction of many novel miRNA loci was a factor in the rapid radiation. A testicular tissue sample from dog, horse, and two different Eptesicus fuscus individuals. Four samples total.
2014-05-19 | E-GEOD-47593 | biostudies-arrayexpress
Project description:Ionizing radiation exposure from a potential nuclear energy plant leak or detonation of a nuclear weapon can cause massive casualties to both warfighters and civilians. Biomarkers in biological specimens like blood and tissue, such as RNA, proteins, and metabolites, have shown potential to determine radiation dose levels. However, these biomarkers in blood and urine are short-lived, typically detectable only within hours or a few days. To address the need for stable, long-term radiation exposure biomarkers, we developed two LC-MS-based methods using non-invasive hair samples to identify radiation-induced biomarkers
2024-10-14 | MSV000096086 | GNPS
Project description:Mammalian interphase chromosomes interact with the nuclear lamina (NL) through hundreds of large Lamina Associated Domains (LADs). We report a method to map NL contacts genome-wide in single human cells. Analysis of ~400 maps reveals a core architecture of gene-poor LADs that contact the NL with high cell-to-cell consistency, interspersed by LADs with more variable NL interactions. The variable contacts are more sensitive to a change in genome ploidy than the consistent contacts. Single-cell maps indicate that NL contacts involve multivalent interactions over hundreds of kilobases. Moreover, we observe extensive intra-chromosomal coordination of NL contacts, even over tens of megabases. Such coordinated loci exhibit preferential interactions as detected by Hi-C. Finally, single-cell gene expression and chromatin accessibility analysis shows that loci with consistent NL contacts are expressed at lower levels and are more consistently inaccessible than loci with lower contact frequencies. These results highlight fundamental principles of single cell chromatin organization. Hi-C Data
2015-09-24 | E-GEOD-69841 | biostudies-arrayexpress
Project description:Intragenomic polymorphisms among high-copy loci: A genus-wide study of nuclear ribosomal DNA in Asclepias (Apocynaceae)
| PRJNA261980 | ENA
Project description:Homologous vertebrate tissues express a highly conserved set of transcribed genes; paradoxically, expression of tRNAs that are required to translate mRNAs into proteins have been reported to be divergent. To resolve this paradox, we mapped the genome-wide occupancy of pol III in primary tissues isolated from six mammals. We confirmed that the specific tRNA genes bound by pol III, as well as the extent and stability of binding, can vary substantially among mammalian tissues, and we discovered that this divergence is far greater between species. We combined pol III occupancy from genomically discrete tRNA loci into collective binding into isoacceptor classes and then into amino acid-based isotype classes, and at each step we found increasing conservation. At the level of amino acid isotypes, pol III binding is almost invariant among all the tissues and species profiled. Thus, the basal transcriptional machinery is constrained collectively in its synthesis of functional tRNA isotypes, despite rapid divergence of polymerase binding to specific tRNA genes. Part of experiment series: RNA-Seq E-MTAB-424, ChIP-Seq E-MTAB-957
2011-07-29 | E-MTAB-958 | biostudies-arrayexpress