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665 results for “Exons”
Mimicry and mitonuclear discordance in nudibranchs: new insights from exon capture phylogenomics
<p>Phylogenetic inference and species delimitation can be challenging in taxonomic groups that have recently radiated and where introgression produces conflicting gene trees, especially when species delimitation has traditionally relied on mitochondrial data and colour pattern. <i>Chromodoris</i>, a genus of colourful and toxic nudibranch in the Indo-Pacific, has been shown to have extraordinary cryptic diversity and mimicry, and has recently radiated, ultimately complicating species delimitation. In these cases, additional genome-wide data can help improve phylogenetic resolution and provide important insights about evolutionary history. Here, we employ a transcriptome-based exon capture approach to resolve <i>Chromodoris</i> phylogeny with data from 2,925 exons and 1,630 genes, derived from 15 nudibranch transcriptomes. We show that some previously identified mimics instead show mitonuclear discordance, likely deriving from introgression or mitochondrial capture, but we confirm one 'pure' mimic in Western Australia. Sister-species relationships and species-level entities were recovered with high support in both concatenated Maximum Likelihood (ML) and summary coalescent phylogenies, but the ML topologies were highly variable while the coalescent topologies were consistent across datasets. Our work also demonstrates the broad phylogenetic utility of 149 genes that were previously identified from eupulmonate gastropods. This study is one of the first to i) demonstrate the efficacy of exon capture for recovering relationships among recently radiated invertebrate taxa, ii) employ genome-wide nuclear markers to test mimicry hypotheses in nudibranchs and iii) provide evidence for introgression and mitochondrial capture in nudibranchs.</p>
Data from: Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes
Mosses are a highly diverse lineage of land plants, whose diversification, spanning at least 400 million years, remains phylogenetically ambiguous due to the lack of fossils, massive early extinctions, late radiations, limited morphological variation, and conflicting signal among previously used markers. Here, we present phylogenetic reconstructions based on complete organellar exomes and a comparable set of nuclear genes for this major lineage of land plants. Our analysis of 142 species representing 29 of the 30 moss orders reveals that relative average rates of non-synonymous substitutions in nuclear versus plastid genes are much higher in mosses than in seed plants, consistent with the emerging concept of evolutionary dynamism in mosses. Our results highlight the evolutionary significance of taxa with reduced morphologies, shed light on the relative tempo and mechanisms underlying major cladogenic events, and suggest hypotheses for the relationships and delineation of moss orders.
Data from: Lineage-specific sequence evolution and exon edge conservation partially explain the relationship of evolutionary rate and expression level in A. thaliana
Rapidly evolving proteins can aid the identification of genes underlying phenotypic adaptation across taxa, but functional and structural elements of genes can also affect evolutionary rates. In plants, the 'edges' of exons, flanking intron junctions, are known to contain splice enhancers and to have a higher degree of conservation compared to the remainder of the coding region. However, the extent to which these regions may be masking indicators of positive selection or account for the relationship between dN/dS and other genomic parameters is unclear. We investigate the effects of exon edge conservation on the relationship of dN/dS to various sequence characteristics and gene expression parameters in the model plant Arabidopsis thaliana. We also obtain lineage-specific dN/dS estimates, making use of the recently sequenced genome of Thellungiella parvula, the second closest sequenced relative after the sister species Arabidopsis lyrata. Overall, we find that the effect of exon edge conservation, as well as the use of lineage-specific substitution estimates, upon dN/dS ratios partly explains the relationship between the rates of protein evolution and expression level. Furthermore, the removal of exon edges shifts dN/dS estimates upwards, increasing the proportion of genes potentially under adaptive selection. We conclude that lineage-specific substitutions and exon edge conservation have an important effect on dN/dS ratios and should be considered when assessing their relationship with other genomic parameters..
Data from: Distribution of MICB diversity in the Zhejiang Han population: PCR sequence-based typing for exons 2–6 and identification of five novel MICB alleles
The polymorphism of major histocompatibility complex class I chain-related gene B (MICB) and variations in MICB alleles in a variety of populations have been characterized using several genotyping approaches. In the present study, a novel polymerase chain reaction sequence-based typing (PCR-SBT) method was established for the genotyping of MICB exons 2–6, and the allelic frequency of MICB in the Zhejiang Han population was investigated. Among 400 unrelated healthy Han individuals from Zhejiang Province, China, a total of 20 MICB alleles were identified, of which MICB*005:02:01, MICB*002:01:01, and MICB*004:01:01 were the most predominant alleles, with frequencies of 0.57375, 0.1225, and 0.08375, respectively. Nine MICB alleles were detected on only one occasion, giving a frequency of 0.00125. Of the 118 distinct MICB ∼ HLA-B haplotypes identified, 42 showed significant linkage disequilibrium (P < 0.05). Haplotypes MICB*005:02:01 ∼ B*46:01, MICB*005:02:01 ∼ B*40:01, and MICB*008 ∼ B*58:01 were the most common haplotypes, with frequencies of 0.0978, 0.0761, and 0.0616, respectively. Five novel alleles, MICB*005:07, MICB*005:08, MICB*027, MICB*028, and MICB*029 were identified. Compared with the MICB*005:02:01 sequence, a G > A substitution was observed at nucleotide position 210 in MICB*005:07, and a 1,134 T > C substitution in MICB*005:08 and an 862 G > A substitution in MICB*027 were detected. In addition, it appears that MICB*028 probably arose from MICB*004:01:01 with an A to G substitution at position 1,147 in exon 6. MICB*029 had a G > T transversion at nucleotide position 730 in exon 4, compared with that of MICB*002:01:01. On the basis of the new PCR-SBT assay, these observed results demonstrated MICB allelic variations in the Zhejiang Han population.
A new mechanism for a familiar mutation – bovine DGAT1 K232A modulates gene expression through multi-junction exon splice enhancement
<p>The <i>DGAT1</i> gene encodes an enzyme responsible for catalysing the terminal reaction in mammary triglyceride synthesis, and underpins a well-known pleiotropic quantitative trait locus (QTL) with a large influence on milk composition phenotypes. Since first described over 15 years ago, a protein-coding variant K232A has been assumed as the causative variant underlying these effects, following <i>in-vitro</i> studies that demonstrated differing levels of triglyceride synthesis between the two protein isoforms. In the current study, we used a large RNAseq dataset to re-examine the underlying mechanisms of this large milk production QTL, and hereby report novel expression-based functions of the chr14 g.1802265AA>GC variant that encodes the <i>DGAT1 </i>K232A substitution. Using expression QTL (eQTL) mapping, we demonstrate a highly-significant mammary eQTL for <i>DGAT1, </i>where the K232A mutation appears as one of the top associated variants for this effect. By conducting <i>in vitro</i> expression and splicing experiments in bovine mammary cell culture, we further show modulation of splicing efficiency by this mutation, likely through disruption of an exon splice enhancer as a consequence of the allele encoding the 232A variant. Although the relative contributions of the enzymatic and transcription-based mechanisms now attributed to K232A remain unclear, these results suggest that transcriptional impacts contribute to the diversity of lactation effects observed at this locus.</p>
Data from: An evaluation of transcriptome-based exon capture for frog phylogenomics across multiple scales of divergence (Class: Amphibia, Order: Anura)
Custom sequence capture experiments are becoming an efficient approach for gathering large sets of orthologous markers in nonmodel organisms. Transcriptome-based exon capture utilizes transcript sequences to design capture probes, typically using a reference genome to identify intron–exon boundaries to exclude shorter exons (<200 bp). Here, we test directly using transcript sequences for probe design, which are often composed of multiple exons of varying lengths. Using 1260 orthologous transcripts, we conducted sequence captures across multiple phylogenetic scales for frogs, including outgroups ~100 Myr divergent from the ingroup. We recovered a large phylogenomic data set consisting of sequence alignments for 1047 of the 1260 transcriptome-based loci (~561 000 bp) and a large quantity of highly variable regions flanking the exons in transcripts (~70 000 bp), the latter improving substantially by only including ingroup species (~797 000 bp). We recovered both shorter (<100 bp) and longer exons (>200 bp), with no major reduction in coverage towards the ends of exons. We observed significant differences in the performance of blocking oligos for target enrichment and nontarget depletion during captures, and differences in PCR duplication rates resulting from the number of individuals pooled for capture reactions. We explicitly tested the effects of phylogenetic distance on capture sensitivity, specificity, and missing data, and provide a baseline estimate of expectations for these metrics based on a priori knowledge of nuclear pairwise differences among samples. We provide recommendations for transcriptome-based exon capture design based on our results, cost estimates and offer multiple pipelines for data assembly and analysis.
Data from: Association between the dopamine D4 receptor gene exon III variable number of tandem repeats and political attitudes in female Han Chinese
Twin and family studies suggest that political attitudes are partially determined by an individual's genotype. The dopamine D4 receptor gene (DRD4) exon III repeat region that has been extensively studied in connection with human behaviour, is a plausible candidate to contribute to individual differences in political attitudes. A first United States study provisionally identified this gene with political attitude along a liberal–conservative axis albeit contingent upon number of friends. In a large sample of 1771 Han Chinese university students in Singapore, we observed a significant main effect of association between the DRD4 exon III variable number of tandem repeats and political attitude. Subjects with two copies of the 4-repeat allele (4R/4R) were significantly more conservative. Our results provided evidence for a role of the DRD4 gene variants in contributing to individual differences in political attitude particularly in females and more generally suggested that associations between individual genes, and neurochemical pathways, contributing to traits relevant to the social sciences can be provisionally identified.
Data from: Identification and qualification of 500 nuclear, single-copy, orthologous genes for the Eupulmonata (Gastropoda) using transcriptome sequencing and exon capture
The qualification of orthology is a significant challenge when developing large, multiloci phylogenetic data sets from assembled transcripts. Transcriptome assemblies have various attributes, such as fragmentation, frameshifts and mis-indexing, which pose problems to automated methods of orthology assessment. Here, we identify a set of orthologous single-copy genes from transcriptome assemblies for the land snails and slugs (Eupulmonata) using a thorough approach to orthology determination involving manual alignment curation, gene tree assessment and sequencing from genomic DNA. We qualified the orthology of 500 nuclear, protein-coding genes from the transcriptome assemblies of 21 eupulmonate species to produce the most complete phylogenetic data matrix for a major molluscan lineage to date, both in terms of taxon and character completeness. Exon capture targeting 490 of the 500 genes (those with at least one exon >120 bp) from 22 species of Australian Camaenidae successfully captured sequences of 2825 exons (representing all targeted genes), with only a 3.7% reduction in the data matrix due to the presence of putative paralogs or pseudogenes. The automated pipeline Agalma retrieved the majority of the manually qualified 500 single-copy gene set and identified a further 375 putative single-copy genes, although it failed to account for fragmented transcripts resulting in lower data matrix completeness when considering the original 500 genes. This could potentially explain the minor inconsistencies we observed in the supported topologies for the 21 eupulmonate species between the manually curated and 'Agalma-equivalent' data set (sharing 458 genes). Overall, our study confirms the utility of the 500 gene set to resolve phylogenetic relationships at a range of evolutionary depths and highlights the importance of addressing fragmentation at the homolog alignment stage for probe design.
Figure 3 from: Gómez-Sánchez EF, Ochoa-Díaz-López H, Espinoza-Medinilla EE, Velázquez-Ramírez DD, Santos-Hernandez NG, Ruiz-Castillejos C, Vidal-López DG, Moreno-Rodríguez A, Flores-Villegas AL, López-Argueta E, De Fuentes-Vicente JA (2022) Mini-exon gene reveals circulation of TcI Trypanosoma cruzi (Chagas, 1909) (Kinetoplastida, Trypanosomatidae) in bats and small mammals in an ecological reserve in southeastern Mexico. ZooKeys 1084: 139-150. https://doi.org/10.3897/zookeys.1084.78664
Figure 3 PCR products of the mini-exon gene in blood of smalls mammals from the "El Zapotal" Ecological Reserve. Amplification resulted in a PCR product of 350 bp and this confirms that these parasites belong to the TCI group. L: ladder; samples: Q positive control (Qro. strain); 1–6 D. marsupialis; 7–10 P. mexicanus; 11 H. desmarestianus; 12 D. mexicana.
Figure 1 from: Gómez-Sánchez EF, Ochoa-Díaz-López H, Espinoza-Medinilla EE, Velázquez-Ramírez DD, Santos-Hernandez NG, Ruiz-Castillejos C, Vidal-López DG, Moreno-Rodríguez A, Flores-Villegas AL, López-Argueta E, De Fuentes-Vicente JA (2022) Mini-exon gene reveals circulation of TcI Trypanosoma cruzi (Chagas, 1909) (Kinetoplastida, Trypanosomatidae) in bats and small mammals in an ecological reserve in southeastern Mexico. ZooKeys 1084: 139-150. https://doi.org/10.3897/zookeys.1084.78664
Figure 1 Location of the "El Zapotal" Ecological Reserve in southeastern Mexico, note the border of the reserve with the urban area.
Figure 2 from: Gómez-Sánchez EF, Ochoa-Díaz-López H, Espinoza-Medinilla EE, Velázquez-Ramírez DD, Santos-Hernandez NG, Ruiz-Castillejos C, Vidal-López DG, Moreno-Rodríguez A, Flores-Villegas AL, López-Argueta E, De Fuentes-Vicente JA (2022) Mini-exon gene reveals circulation of TcI Trypanosoma cruzi (Chagas, 1909) (Kinetoplastida, Trypanosomatidae) in bats and small mammals in an ecological reserve in southeastern Mexico. ZooKeys 1084: 139-150. https://doi.org/10.3897/zookeys.1084.78664
Figure 2 PCR products of the mini-exon gene in blood of bats from the "El Zapotal" Ecological Reserve. Amplification resulted in a PCR product of 350 bp and this confirms that these parasites belong to the TCI group. L: Ladder; Samples: 1 positive control (Qro. strain); 2–11 A. jamaicensis; 12–14 A. lituratus; 15–16 C. perspicillata; 17–18 S. lilium; 19 G. soricina.
Alternatively spliced exon regulates context-dependent MEF2D higher-order assembly during myogenesis
<p>Molecular dynamics data on four MEF2D beta-domain peptide constructs.</p>
A Spanish Medical Record Review of Clinical Characteristics and Outcomes in Non-small Cell Lung Cancer Participants With EGFR Exon 20 Insertion
ClinicalTrials.gov study NCT05419700. IPD Sharing: YES. Countries: 1. Publications: 0.
Study Of Zelboraf (Vemurafenib) in Patients With Locally-Advanced, Unresectable, Stage IIIc Or Metastatic Melanoma and Activating Exon 15 BRAF Mutations Other Than V600E
ClinicalTrials.gov study NCT01586195. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Study to Evaluate the Efficacy Safety and Tolerability of Ultevursen in Subjects With RP Due to Mutations in Exon 13 of the USH2A Gene (Sirius)
ClinicalTrials.gov study NCT05158296. IPD Sharing: NO. Countries: 4. Publications: 0.
Study to Evaluate the Efficacy Safety and Tolerability of QR-421a in Subjects With RP Due to Mutations in Exon 13 of the USH2A Gene With Early to Moderate Vision Loss (Celeste)
ClinicalTrials.gov study NCT05176717. IPD Sharing: NO. Countries: 2. Publications: 0.
Study of Capmatinib in Indian Patients With MET Exon 14 Skipping Mutation Positive Advanced NSCLC.
ClinicalTrials.gov study NCT05110196. IPD Sharing: YES. Countries: 1. Publications: 0.
A Study of Capmatinib (INC280) in NSCLC Patients With MET Exon 14 Alterations Who Have Received Prior MET Inhibitor
ClinicalTrials.gov study NCT02750215. IPD Sharing: NO. Countries: 1. Publications: 0.
Testing Crizotinib as Potentially Targeted Treatment in Cancers With MET Exon 14 Deletion Genetic Changes (MATCH - Subprotocol C2)
ClinicalTrials.gov study NCT06360575. IPD Sharing: YES. Countries: 1. Publications: 0.
Data from: A targeted next-generation sequencing toolkit for exon-based cichlid phylogenomics
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