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537
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ShareScore release 0.9.0
Dataset results
537 results for “genome structure”
Unbiased, Genome-wide in vivo Mapping of Transcriptional Regulatory Elements Reveals Sex Differences in Chromatin Structure Associated with Sex-specific Liver Gene Expression
GEO Series GSE21777. Mus musculus. 10 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations
GEO Series GSE32674. Homo sapiens. 5 samples. Type: Genome variation profiling by high throughput sequencing.
Isolation and genome-wide characterization of cellular DNA:RNA triplex structures II
GEO Series GSE120846. Homo sapiens. 9 samples. Type: Other.
An analysis of genomic structural alteration in three human ES cell lines.
GEO Series GSE54576. Homo sapiens. 11 samples. Type: SNP genotyping by SNP array.
Three-dimensional genome structures of single mammalian sperm [scHi-C]
GEO Series GSE276999. Homo sapiens; Mus musculus. 717 samples. Type: Other.
N3-Kethoxal-seq for genome-wide RNA structure mapping in vivo
GEO Series GSE122096. Homo sapiens; Mus musculus. 26 samples. Type: Other; Expression profiling by high throughput sequencing.
Three-dimensional genomic structure and cohesin occupancy correlates with transcriptional activity during spermatogenesis
GEO Series GSE132054. Mus musculus. 18 samples. Type: Expression profiling by high throughput sequencing; Other; Genome binding/occupancy profiling by high throughput sequencing.
A map of cis-regulatory elements and 3D genome structures in zebrafish
GEO Series GSE134055. Danio rerio. 204 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
Burkitt Lymphoma Pathogenesis and Therapeutic Targets from Structural and Functional Genomics
GEO Series GSE35163. Homo sapiens. 32 samples. Type: Expression profiling by array.
The Genome Wide Structure of the Jewish People
GEO Series GSE21478. Homo sapiens. 466 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
An integrated peach genome structural variation map uncovers genes associated with fruit traits
<p>The VCF files generated from 336 peach accessions, including SVs (>50bp), SNPs and indels (<50bp).</p>
Genomic structure of the Sicklefin Barb, Puntioplites falcifer (Cyprinidae), in the lower Mekong River basin reveals patterns of both migration and population partitioning
<p>Effective management of the Sicklefin Barb, <i>Puntioplites falcifer</i>, with the planned construction of several dams in the Mekong River Basin depends upon disentangling conflicting reports of isolated populations and highly migratory behavior. We investigated patterns of population genomic structure, relatedness, and inferred connectivity among three locations on the Mekong and a fourth at Attapeu on the Sekong tributary. The results supported both isolation of populations and migratory behavior. STRUCTURE, AMOVA, and PCA revealed three distinct nDNA clusters. The most divergent nDNA cluster (pairwise <i>F</i><sub>ST</sub> ≥ 0.43, <i>p < </i>0.0001) exhibited negligible inferred relative migration rates with the other samples (<i>m</i> ≤ 0.02), including those from common sampling locations, and was likely a different species - putatively <i>P. proctozysron </i>(Ppr). However, mtDNA barcoding suggested differentiation between Ppr and a published mtDNA genome for this species. Most of the fish from the Sekong tributary belonged to a second distinct nDNA cluster and the sample from that location was differentiated from the Mekong sites (pairwise <i>F</i><sub>ST</sub> = 0.02 - 0.03, <i>p</i> < 0.0001). Supporting migration, a third nDNA cluster exhibited high rates of migration among the Mekong locations (<i>m</i> = 0.6 - 1) and was found in small numbers at the Sekong location which was characterized by intermediate migration rates with the Mekong (<i>m</i> = 0.3 - 0.4). Mitochondrial DNA barcoding indicated that the fish comprising the Mekong and Sekong nDNA clusters were differentiated from a <i>P. falcifer </i>mtDNA genome sampled well upstream of the Mekong locations in this study. Estimates of <i>N</i><sub>e</sub> by both location and nDNA cluster were near or below the minimal sustainable size (173-1651), suggesting susceptibility to over-exploitation or population fragmentation. Together, these results suggest that proposed hydropower dams could subdivide connected Mekong populations, isolate and split the Sekong population, and further drive down <i>N</i><sub>e</sub> if accommodations are not made to facilitate connectivity. Additionally, the combined pattern of nDNA and mtDNA diversity is consistent with substantial cryptic diversity and a <i>P. falcifer</i> – <i>P. proctozysron</i> species complex that could be further described with rigorous population genomic surveys and expanded geographic sampling.</p>
Data from: A genome-wide assessment of genetic diversity and population structure of Korean native cattle breeds
Background: The native cattle breeds are an important genetic resource for meat and milk production throughout Asia. In Asia cattle were domesticated around 10,000 years ago and in Korea cattle are being raised since 2000 B.C. There are three native breeds of cattle in Korea viz. Brown Hanwoo, Brindle Hanwoo and Jeju Black. While one of these breeds, Brown Hanwoo, is a part of a Food and Agricultural Organization and national genetic evaluation plans, others get little attention. This study is an effort to understand and provide a detailed insight into the population structure and genetic variability of the Korean cattle breeds along with other Asian breeds using various methods. In this study we report the genetic variation and structure of the Korean cattle breeds and their comparison with five other Asian cattle breeds along with a panel of animals from European taurine, African taurine and indicine cattle breeds. Results: Asian cattle were found to be least differentiated which reflects their recent history. Amongst the Asian breeds Hainan, which is an indicine breed, had the lowest gene diversity while Yanbian had the highest followed by Mongolian and Korean cattle. Amongst the Korean breeds Brown Hanwoo had the highest diversity followed by Brindle Hanwoo and Jeju Black. The genetic diversity in Asian cattle breeds was found comparable to the European taurines and more than the African taurines and Zebu cattle. Korean cattle breed, Brown Hanwoo was consistently found to be closer to Yanbian, a Chinese cattle breed. We found low divergence and moderate levels of genetic diversity among the native Korean breeds. Indicine introgression from Hainan was seen in other Asian breeds. From Europe, Limousin, Holstein and Hereford introgression was found in Asian breeds. Conclusions: In this study we provide a genome-wide insight into the genetic history of the native cattle breeds of Korea. The outcomes of this study will help in prioritization and designing of the conservation plans.
Genomic Structural Variation in Cancer Susceptibility
ClinicalTrials.gov study NCT00996710. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Genomics of Fibrin Clot Structure in Patients With Constitutional Dysfibrinogenemia
ClinicalTrials.gov study NCT05233384. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Genomic Sequencing for Evaluation of Fetal Structural Anomalies
ClinicalTrials.gov study NCT06054230. IPD Sharing: NO. Countries: 1. Publications: 0.
High copy number variation burdens in cranial meningiomas from patients with diverse clinical phenotypes characterized by hot genomic structure changes
GEO Series GSE147673. Homo sapiens. 383 samples. Type: SNP genotyping by SNP array; Genome variation profiling by SNP array.
An analysis fo genomic structural alterations in iPS cells derived from xeroderma pigmentosum patients
GEO Series GSE55520. Homo sapiens. 6 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
The three-dimensional structure of the EBV genome plays a crucial role in regulating viral gene expression in EBVaGC [HiChIP]
GEO Series GSE239992. Homo sapiens; human gammaherpesvirus 4. 4 samples. Type: Other.
Linking genome structures to functions during lineage specification by simultaneous single-cell Hi-C and RNA-seq simultaneous single-cell Hi-C and RNA-seq
GEO Series GSE223917. Mus musculus. 7895 samples. Type: Other; Expression profiling by high throughput sequencing.
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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.