Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
72
datasets available to search
ShareScore release 0.9.0
Dataset results
72 results for “Retroelement”
Turnover of retroelements and satellite DNA drives centromere reorganization over short evolutionary timescales in Drosophila
Open the record for dataset details and reuse information.
Data for: Theoretical and practical considerations when using retroelement insertions to estimate species trees in the anomaly zone
<p>A potential shortcoming of concatenation methods for species tree estimation is their failure to account for incomplete lineage sorting. Coalescent methods address this problem but make various assumptions that, if violated, can result in worse performance than concatenation. Given the challenges of analyzing DNA sequences with both concatenation and coalescent methods, retroelement insertions (RIs) have emerged as powerful phylogenomic markers for species tree estimation. Here, we show that two recently proposed quartet-based methods, SDPquartets and ASTRAL_BP, are statistically consistent estimators of the unrooted species tree topology under the coalescent when RIs follow a neutral infinite-sites model of mutation and the expected number of new RIs per generation is constant across the species tree. The accuracy of these (and other) methods for inferring species trees from RIs has yet to be assessed on simulated data sets, where the true species tree topology is known. Therefore, we evaluated eight methods given RIs simulated from four model species trees, all of which have short branches and at least three of which are in the anomaly zone. In our simulation study, ASTRAL_BP and SDPquartets always recovered the correct species tree topology when given a sufficiently large number of RIs, as predicted. A distance-based method (ASTRID_BP) and Dollo parsimony also performed well in recovering the species tree topology. In contrast, unordered, polymorphism, and Camin-Sokal parsimony (as well as an approach based on MDC) typically fail to recover the correct species tree topology in anomaly zone situations with more than four ingroup taxa. Of the methods studied, only ASTRAL_BP automatically estimates internal branch lengths (in coalescent units) and support values (i.e., local posterior probabilities). We examined the accuracy of branch length estimation, finding that estimated lengths were accurate for short branches but upwardly biased otherwise. This led us to derive the maximum likelihood (branch length) estimate for when RIs are given as input instead of binary gene trees; this corrected formula produced accurate estimates of branch lengths in our simulation study, provided that a sufficiently large number of RIs were given as input. Lastly, we evaluated the impact of data quantity on species tree estimation by repeating the above experiments with input sizes varying from 100 to 100,000 parsimony-informative RIs. We found that, when given just 1,000 parsimony-informative RIs as input, ASTRAL_BP successfully reconstructed major clades (i.e clades separated by branches >0.3 CUs) with high support and identified rapid radiations (i.e., shorter connected branches), although not their precise branching order. The local posterior probability was effective for controlling false positive branches in these scenarios.</p>
Data for: Theoretical and practical considerations when using retroelement insertions to estimate species trees in the anomaly zone
Open the record for dataset details and reuse information.
Data from: Islands of retroelements are major components of Drosophila centromeres
Centromeres are essential chromosomal regions that mediate kinetochore assembly and spindle attachments during cell division. Despite their functional conservation, centromeres are amongst the most rapidly evolving genomic regions and can shape karyotype evolution and speciation across taxa. Although significant progress has been made in identifying centromere-associated proteins, the highly repetitive centromeres of metazoans have been refractory to DNA sequencing and assembly, leaving large gaps in our understanding of their functional organization and evolution. Here, we identify the sequence composition and organization of the centromeres of Drosophila melanogaster by combining long-read sequencing, chromatin immunoprecipitation for the centromeric histone CENP-A, and high-resolution chromatin fiber imaging. Contrary to previous models that heralded satellite repeats as the major functional components, we demonstrate that functional centromeres form on islands of complex DNA sequences enriched in retroelements that are flanked by large arrays of satellite repeats. Each centromere displays distinct size and arrangement of its DNA elements but is similar in composition overall. We discover that a specific retroelement, G2/Jockey-3, is the most highly enriched sequence in CENP-A chromatin and is the only element shared among all centromeres. G2/Jockey-3 is also associated with CENP-A in the sister species Drosophila simulans, revealing an unexpected conservation despite the reported turnover of centromeric satellite DNA. Our work reveals the DNA sequence identity of the active centromeres of a premier model organism and implicates retroelements as conserved features of centromeric DNA.
Data from: Islands of retroelements are major components of Drosophila centromeres
Open the record for dataset details and reuse information.
Fig. 2 in Chromosomal distribution of the retroelements Rex1, Rex3 and Rex6 in species of the genus Harttia and Hypostomus (Siluriformes: Loricariidae)
Fig. 2. Metaphases of the Harttia species submitted to FISH with probes of the Rex elements. The numbers indicate chromosomal pairs in highlighted. Bar = 10 μm.
Fig. 1 in Chromosomal distribution of the retroelements Rex1, Rex3 and Rex6 in species of the genus Harttia and Hypostomus (Siluriformes: Loricariidae)
Fig. 1. Metaphases of the Harttia species submitted to FISH with probes of the Rex elements. The numbers indicate chromosomal pairs in highlighted. Bar = 10 μm.
Fig. 3 in Chromosomal distribution of the retroelements Rex1, Rex3 and Rex6 in species of the genus Harttia and Hypostomus (Siluriformes: Loricariidae)
Fig. 3. Metaphases of the Hypostomus species submitted to FISH with probes of the Rex elements. The numbers indicate chromosomal pairs in highlighted. Bar = 10 μm.
Supplementary material 5 from: Suntronpong A, Thapana W, Twilprawat P, Prakhongcheep O, Somyong S, Muangmai N, Peyachoknagul S, Srikulnath K (2017) Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus). Comparative Cytogenetics 11(3): 435-462. https://doi.org/10.3897/compcytogen.v11i3.11739
Supplementary Table 5 : Data type: Table
Supplementary material 4 from: Suntronpong A, Thapana W, Twilprawat P, Prakhongcheep O, Somyong S, Muangmai N, Peyachoknagul S, Srikulnath K (2017) Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus). Comparative Cytogenetics 11(3): 435-462. https://doi.org/10.3897/compcytogen.v11i3.11739
Supplementary Table 4 : Data type: Table
Supplementary material 1 from: Suntronpong A, Thapana W, Twilprawat P, Prakhongcheep O, Somyong S, Muangmai N, Peyachoknagul S, Srikulnath K (2017) Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus). Comparative Cytogenetics 11(3): 435-462. https://doi.org/10.3897/compcytogen.v11i3.11739
Supplementary Table 1 : Data type: Table
Supplementary material 3 from: Suntronpong A, Thapana W, Twilprawat P, Prakhongcheep O, Somyong S, Muangmai N, Peyachoknagul S, Srikulnath K (2017) Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus). Comparative Cytogenetics 11(3): 435-462. https://doi.org/10.3897/compcytogen.v11i3.11739
Supplementary Table 3 : Data type: Table
Supplementary material 7 from: Suntronpong A, Thapana W, Twilprawat P, Prakhongcheep O, Somyong S, Muangmai N, Peyachoknagul S, Srikulnath K (2017) Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus). Comparative Cytogenetics 11(3): 435-462. https://doi.org/10.3897/compcytogen.v11i3.11739
Supplementary Figure 2 : Data type: Image
Supplementary material 2 from: Suntronpong A, Thapana W, Twilprawat P, Prakhongcheep O, Somyong S, Muangmai N, Peyachoknagul S, Srikulnath K (2017) Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus). Comparative Cytogenetics 11(3): 435-462. https://doi.org/10.3897/compcytogen.v11i3.11739
Supplementary Table 2 : Data type: Table
Supplementary material 6 from: Suntronpong A, Thapana W, Twilprawat P, Prakhongcheep O, Somyong S, Muangmai N, Peyachoknagul S, Srikulnath K (2017) Karyological characterization and identification of four repetitive element groups (the 18S – 28S rRNA gene, telomeric sequences, microsatellite repeat motifs, Rex retroelements) of the Asian swamp eel (Monopterus albus). Comparative Cytogenetics 11(3): 435-462. https://doi.org/10.3897/compcytogen.v11i3.11739
Supplementary Figure 1 : Data type: Image
Retroelement-Age
<p><span>Reactivation of retroelements in the human genome has been linked to aging. However, whether the epigenetic state of specific retroelements can predict chronological age remains unknown. We provide evidence that locus-specific retroelement DNA methylation can be used to create retroelement-based epigenetic clocks that accurately measure chronological age in the immune system, across human tissues, and pan-mammalian species. We also developed a highly accurate retroelement epigenetic clock compatible with EPICv.2.0 data that was constructed from CpGs that did not overlap with existing first and second-generation epigenetic clocks, suggesting a unique signal for epigenetic clocks not previously captured. We found retroelement-based epigenetic clocks were reversed during transient epigenetic reprogramming, accelerated in people living with HIV-1, and responsive to antiretroviral therapy. Our findings highlight the utility of retroelement-based biomarkers of aging and support a <span>renewed emphasis on the role of retroelements in geroscience.</span></span></p>
DUX4 activates germline genes, retroelements and immune-mediators: Implications for facioscapulohumeral dystrophy
GEO Series GSE33799. Homo sapiens. 36 samples. Type: Expression profiling by array.
Retroelements and DUX4 Create Primate-specific Promoters for Germline Genes
GEO Series GSE45883. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Dnmt1 binds and represses genomic retroelements via DNA methylation in mouse early embryos (DELP-seq)
GEO Series GSE104437. Mus musculus. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Targeted protein evolution in the gut microbiome by diversity-generating retroelements
GEO Series GSE282133. Bacteroides thetaiotaomicron VPI-5482; Bacteroides ovatus ATCC 8483; Bacteroides finegoldii CL09T03C10; Bacteroides uniformis ATCC 8492; Bacteroides fragilis 638R. 20 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.