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622 results for “Genomic integrity”
FISH datasets used in Zou et al. integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure
<p>This upload contains the FISH datasets used in Zou et al. integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure.</p> <p>If you use the datasets, we would be grateful if you cited the following paper:</p> <p>Zou, C., Zhang, Y., Ouyang, Z. (2016) HSA: integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure. Genome Biology, 17: 40.</p>
DeepAnnotation: A novel interpretable deep learning-based genomic selection model that integrates comprehensive functional annotations
<p>1. Update package, example dataset, and demo code of DeepAnnotation</p> <p>2. Update the transformed genotype data, the phenotype data, the comprehensive functional annotation data for Duroc prepared by RNAfold, DeepSEA, easyMF models, and the four types of input data for training DeepAnnotation model</p> <p>3. Add the conserved functional annotation</p> <p> </p>
VCF files and regression analyses for: Assessing fine-scale pondscape connectivity with amphibian eyes: an integrative approach using genomic and capture-mark-recapture data
<p><span>In the face of habitat loss, preserving functional connectivity is essential to maintain genetic diversity and the demographic dynamics required for the viability of biotic communities. This requires knowledge of the dispersal behavior of target species, which can be modeled as kernels, or probability density functions of dispersal distances at increasing geographic distances. We present an integrative approach to investigate the relationships between genetic connectivity and demographic parameters in organisms with low vagility focusing on five syntopic pond-breeding amphibians. We genotyped 1,056 individuals of two anuran and three urodele species (1,732–3,913 SNPs per species) from populations located in a landscape comprising 64 ponds to characterize fine-scale genetic structure in a comparative framework and combined this genetic data with information obtained in a previous two-year capture-mark-recapture (CMR) study. Specifically, we contrasted graphs reconstructed from genomic data with connectivity graphs based on dispersal kernels and demographic information obtained from CMR data from previous studies and assessed the effects of population size, population density, geographical distances, inverse movement probabilities and the presence of habitat patches potentially functioning as stepping stones on genetic differentiation. Our results suggest a significant influence of local population sizes on patterns of genetic connectivity at small spatial scales. In addition, m</span><span>ovement records and cluster-derived kernels provide robust inferences on most likely dispersal paths that are consistent with </span><span>genomic inferences on genetic connectivity. The integration of genetic and CMR data holds great potential for understanding genetic connectivity at spatial scales relevant to individual organisms, with applications for the implementation of management actions at the landscape level. </span></p>
Data from: Pan-evolutionary and regulatory genome architecture delineated by integrated macro- and microsynteny approach
<p>Based on the published algorithms or tools developed by our and other groups, we introduce a detailed protocol for the most comprehensive and up-to-date genome synteny pipeline (called PanSyn) and provides step-by-step instructions as well as application examples for demonstrating how to use it. PanSyn pipeline includes three major modules (microsynteny analysis, macrosynteny analysis, and integrated micro & macro analysis). PanSyn not only fills a gap of lacking a user-friendly, highly-customized tool for genome macrosynteny analysis but also allows for integrated pan-evolutionary and regulatory analysis of genome microsyntenty and macrosynteny which are not yet available in any public synteny software or tools. PanSyn has been tested under Linux system. PanSyn has multiple subroutines. Users only need to simply modify the configuration file and corresponding command parameters to execute them. Outputs include vector diagrams that are suitable for custom modification. <br> </p>
Integration of genomic and ecologic methods inform management of an undescribed, yet highly exploited, sardine species
<p>Assessing genetic diversity within species is key for conservation strategies in the context of human-induced biotic changes. This is important in marine systems where many species remain undescribed while being overfished, and conflicts between resource-users and conservation agencies are common. Combining niche modelling with population genomics can contribute to resolving those conflicts by identifying management units and understanding how past climatic cycles resulted in current patterns of genetic diversity. We addressed these issues on an undescribed but already overexploited species of sardine of the genus <em>Harengula</em>. We find that the species distribution is determined by salinity and depth, with a continuous distribution along the Brazilian mainland and two disconnected oceanic archipelagos. Genomic data indicates that such biogeographic barriers are associated with two divergent intraspecific lineages. Changes in habitat availability during the last glacial cycle led to different demographic histories among stocks. One coastal population experienced a 3.6-fold expansion, whereas an island-associated population contracted 3-fold, relative to the size of the ancestral population. Our results indicate that the island population should be managed separately from the coastal population, and that a Marine Protected Area covering part of the island population distribution can support the viability of this lineage.</p>
Data from: Genomic integrity of Phyciodes butterfly species in a region of contact (Lepidoptera: Nymphalidae)
<p>Crescent butterflies of the <em>Phyciodes tharos </em>group have a long-standing reputation for taxonomic difficulty.<em> </em>We assessed species boundaries in the <em>P. tharos </em>group using genome-wide SNP data, focusing on sampling in western Canada where four species (<em>P. tharos</em>, <em>P. cocyta</em>, <em>P. pulchella,</em> and <em>P. batesii</em>) have classically been recognized. Phylogenetic and cluster-based analyses confirm that there are indeed four species based on the maintenance of genomic integrity in the presence of occasional hybridization and low levels of gene flow. Mitochondrial COI does not consistently distinguish species, with haplotypes extensively shared between species. Here, we provide data matrices and tree files from the phylogenetic and cluster-based analyses.</p>
Recent speciation and hybridization in Icelandic deep-sea isopods: An integrative approach using genomics and proteomics.
<p>The crustacean marine isopod species <i>Haploniscus bicuspis</i> (G.O. Sars, 1877) shows circum-Icelandic distribution in a wide range of environmental conditions and along well-known geographic barriers, such as the Greenland-Iceland-Faroe (GIF) Ridge. We wanted to explore population genetics, phylogeography and cryptic speciation as well as to investigate whether previously described, but unaccepted subspecies have any merit. Using the same set of specimens, we combined mitochondrial COI sequences, thousands of nuclear loci (ddRAD), and proteomic profiles, plus selected morphological characters using Confocal Laser Scanning Microscopy (CLSM). Five divergent genetic lineages were identified by COI and ddRAD, two south and three north of the GIF Ridge. Assignment of populations to the three northern lineages varied and detailed analyses revealed hybridization and gene flow between them, suggesting a single northern species with a complex phylogeographic history. No apparent hybridization was observed among lineages south of the Ridge, inferring the existence of two more species. Differences in proteomic profiles between the three putative species were minimal, implying an ongoing or recent speciation process. Population differentiation was high, even among closely associated populations, and higher in mitochondrial COI than nuclear ddRAD loci. Gene flow is apparently male-biased, leading to hybrid zones and instances of complete exchange of the local nuclear genome through immigrating males. This study did not confirm the existence of subspecies defined by male characters, which probably characterize different male developmental stages.</p>
Supplementary data for: From genomics to integrative taxonomy? The case study of Pocillopora corals
<p><span>With the advent of genomics, sequencing thousands of loci from hundreds of individuals now appears feasible at reasonable costs, allowing complex phylogenies to be resolved. This is particularly relevant for cnidarians, for which insufficient data due to the small number of currently available markers, coupled with difficulties in inferring gene trees and morphological incongruences, encrypts species boundaries, thereby blurring the study and conservation of these organisms. Yet, can genomics alone be used to delimit species in an integrative taxonomic context? Here, focusing on the coral genus <em>Pocillopora</em>, which plays key roles in Indo-Pacific reef ecosystems but has challenged taxonomists for decades, we explored and discussed the usefulness of multiple criteria (genetics, morphology, biogeography and symbiosis ecology) to delimit species of this genus. Phylogenetic inferences, clustering approaches and species delimitation methods based on genome-wide single-nucleotide polymorphisms (SNPs) were first used to resolve <em>Pocillopora</em> phylogeny and propose genomic species hypotheses from 356 colonies sampled across the Indo-Pacific (western Indian Ocean, tropical southwestern Pacific and south-east Polynesia). These species hypotheses were then compared to previous genetic evidences, as well as to evidences based on morphology, biogeography and symbiosis. Genomics allowed to delimit 21 species hypotheses where only seven are currently recognised based on current taxonomy. Moreover, 13 species were strongly supported by all approaches, either confirming their currently recognised species status, or supporting the presence of new species that need to be formally described. Some of the other genomic species hypotheses were supported by biogeographic or symbiosis evidences, but additional investigations are needed to state on their species status. Altogether, our results support (1) the obsolescence of macromorphology (i.e., overall colony and branches shape) but the relevance of micromorphology (i.e., corallite structures) to refine <em>Pocillopora</em> species limits, (2) the need to identify molecularly species prior to their study, as morphology can blur species identification on the field, (3) the relevance of the mtORF (coupled with other markers in some cases) as a diagnostic marker of most species, and (4) the need for a taxonomical revision in the <em>Pocillopora</em> genus. These results give new insights into the usefulness of multiple criteria for resolving <em>Pocillopora</em> species limits and will ultimately provide helpful insights for the conservation of the species from this scleractinian genus.</span></p>
Data and scripts for the manuscript of svaRetro and svaNUMT: modular packages for annotating retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data
<p>This upload include data and scripts supporting the results described in the manuscript of <em>svaRetro and svaNUMT: modular packages for annotating retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data</em><em>. </em>Detailed description of the contents can be found in README.txt.</p>
Genetic admixture and evolutionary history of Han Chinese in the Shandong Peninsula inferred from integrative modern and ancient genomic resources
<p>The allele frequency data of 264 individuals from Shandong Province and supplementary table.</p>
Concatenated SNP data: Integrative taxonomy of the lizards Cercosaura ocellata species complex (Reptilia: Gymnophthalmidae) based on morphological and genomic data
<p>Concatenated unliked SNP data in phylip format used in 'Integrative taxonomy of the lizards Cercosaura ocellata species complex (Reptilia: Gymnophthalmidae) based on morphological and genomic data' study.</p>
Raw genomic RadSeq data from: Integrative taxonomy of the lizards Cercosaura ocellata species complex (Reptilia: Gymnophthalmidae) based on morphological and genomic data
<p>Raw genomic RadSeq data from individuals used in 'Integrative taxonomy of the lizards Cercosaura ocellata species complex (Reptilia: Gymnophthalmidae) based on morphological and genomic data' study.</p>
RatXcan: A framework for cross-species integration of genome-wide association and gene expression data
<p>Data for paper</p> <p><span>RatXcan: A framework for cross-species integration of genome-wide association and gene expression data</span></p> <p><span>Natasha Santhanam</span><span><span>1</span></span><span><span>†</span></span><span>, Sandra Sanchez-Roige</span><span><span>2,3,4</span></span><span><span>†</span></span><span>, Sabrina Mi</span><span><span>2</span></span><span>, Yanyu Liang</span><span><span>1</span></span><span>, Apurva S. Chitre</span><span><span>2</span></span><span>, Daniel Munro</span><span><span>2</span></span><span>, Denghui Chen</span><span><span>2</span></span><span>, Riyan Cheng</span><span><span>2</span></span><span>, Jianjun Gao</span><span><span>2</span></span><span>, Angel Garcia-Martinez</span><span><span>6</span></span><span>, Anthony M. George</span><span><span>5</span></span><span>, Alexander F. Gileta</span><span><span>2</span></span><span>, Wenyan Han</span><span><span>6</span></span><span>, Katie Holl</span><span><span>7</span></span><span>, Alesa Hughson</span><span><span>8</span></span><span>, Christopher P. King</span><span><span>9</span></span><span>, Alexander C. Lamparelli</span><span><span>9</span></span><span>, Connor D. Martin</span><span><span>5</span></span><span>, Festus Nyasimi</span><span><span>1</span></span><span>, Celine L. St. Pierre</span><span><span>2</span></span><span>, Sarah Sumner</span><span><span>1</span></span><span>, Jordan Tripi</span><span><span>9</span></span><span>, Tengfei Wang</span><span><span>6</span></span><span>, Hao Chen</span><span><span>6</span></span><span>, Shelly Flagel</span><span><span>8</span></span><span>, Keita Ishiwari</span><span><span>5,10</span></span><span>, Paul Meyer</span><span><span>5,9</span></span><span>, Oksana Polesskaya</span><span><span>2</span></span><span>, Laura Saba</span><span><span>11</span></span><span>, Leah C. Solberg Woods</span><span><span>12</span></span><span>, Abraham A. Palmer</span><span><span>2,3</span></span><span>*, Hae Kyung Im</span><span><span>1</span></span><span>*</span></p> <p><span> </span></p> <p><span>[1] Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA</span></p> <p><span>[2] Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA</span></p> <p><span>[3] Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92093, USA</span></p> <p><span>[4] Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA</span></p> <p><span>[5] University at Buffalo, Clinical and Research Institute on Addictions University at Buffalo, Buffalo, NY, 14203, USA</span></p> <p><span>[6] University of Tennessee Health Science Center, Department of Pharmacology, Addiction Science and Toxicology, Memphis, TN, 38120, USA</span></p> <p><span>[7] Medical College of Wisconsin, Department of Pediatrics, Milwaukee, WI, 53226, USA</span></p> <p><span>[8] University of Michigan, Department of Psychiatry, Ann Arbor, MI, 48109, USA</span></p> <p><span>[9] University at Buffalo, Department of Psychology, Buffalo, NY, 14260, USA</span></p> <p><span>[10] University at Buffalo, Pharmacology and Toxicology University at Buffalo, Buffalo, NY, 14203, USA</span></p> <p><span>[11] University of Colorado Anschutz Medical Campus, Department of Pharmaceutical Sciences, Aurora, CO 80045, USA</span></p> <p><span>[12] Wake Forest University School of Medicine, Department of Internal Medicine, Winston-Salem, NC, 27157, USA</span></p>
Data from: Integrating Bayesian genomic cline analyses and association mapping of morphological and ecological traits to dissect reproductive isolation and introgression in a Louisiana Iris hybrid zone
Hybrid zones provide unique opportunities to examine reproductive isolation and introgression in nature. We utilized 45,384 Single Nucleotide Polymorphism (SNP) loci to perform association mapping of 14 floral, vegetative, and ecological traits that differ between Iris hexagona and Iris fulva, and to investigate, using a Bayesian Genomic Cline (BGC) framework, patterns of genomic introgression in a large and phenotypically diverse hybrid zone in southern Louisiana. Many loci of small effect-size were consistently found to be associated with phenotypic variation across all traits, and several individual loci were revealed to influence phenotypic variation across multiple traits. Patterns of genomic introgression were quite heterogeneous throughout the Louisiana Iris genome, with I. hexagona alleles tending to be favored over those of I. fulva. Loci that were found to have exceptional patterns of introgression were also found to be significantly associated with phenotypic variation in a small number of morphological traits. However, this was the exception rather than the rule, as most loci that were associated with morphological trait variation were not significantly associated with excess ancestry. These findings provide insights into the complexity of the genomic architecture of phenotypic differences and are a first step towards identifying loci that are associated with both trait variation and reproductive isolation in nature.
Integrated genome-wide investigations of the housefly, a global vector of diseases reveal unique dispersal patterns and bacterial communities across farms
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Data from: Local adaptation in mainland anole lizards: Integrating population history and genome-environment associations
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Phenomic data-driven biological prediction of maize through field-based high throughput phenotyping integration with genomic data
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Supplementary data for: From genomics to integrative taxonomy? The case study of Pocillopora corals
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Integrative genomics of the mammalian alveolar macrophage response to intracellular mycobacteria: RNA-seq statistics and results
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Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of genetic maps and conserved synteny
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Allen Brain Atlas
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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.