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129 results for “structural variants”
Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the Chocolate Tree
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Data from: Population genomics reveals structure at the individual, host-tree scale and persistence of genotypic variants of the undomesticated yeast Saccharomyces paradoxus in a natural woodland
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SVXplorer: three-tier approach to identification of structural variants via sequential recombination of discordant cluster signatures
<p>This repository contains the bgzipped variants calls in VCF format for CHM1, NA12878 and AJ trio dataset that are used in the SVXplorer manuscript. The names of the files contain the name of the sample (CHM1/NA12878/HG002/HG003/HG004), the name of the method (SVXplorer/DELLY/LUMPY/TIDDIT/TARDIS/MANTA) used to call the variants. There are three separate files for the DELLY calls which have the deletions, duplications and the inversion calls made by DELLY for each of the samples. For NA12878, there are two sets of calls, one for each of the libraries (ERR194147/SRR505885)</p> <p> </p>
Supplementary material 3 from: Padilla-Sanchez V (2021) SARS-CoV-2 Structural Analysis of Receptor Binding Domain New Variants from United Kingdom and South Africa. Research Ideas and Outcomes 7: e62936. https://doi.org/10.3897/rio.7.e62936
United Kingdom variant interactions
Supplementary material 1 from: Padilla-Sanchez V (2021) SARS-CoV-2 Structural Analysis of Receptor Binding Domain New Variants from United Kingdom and South Africa. Research Ideas and Outcomes 7: e62936. https://doi.org/10.3897/rio.7.e62936
RBD-ACE2 complexes
Supplementary material 2 from: Padilla-Sanchez V (2021) SARS-CoV-2 Structural Analysis of Receptor Binding Domain New Variants from United Kingdom and South Africa. Research Ideas and Outcomes 7: e62936. https://doi.org/10.3897/rio.7.e62936
RBD-ACE2 interface detail
Figure 1 from: Padilla-Sanchez V (2021) SARS-CoV-2 Structural Analysis of Receptor Binding Domain New Variants from United Kingdom and South Africa. Research Ideas and Outcomes 7: e62936. https://doi.org/10.3897/rio.7.e62936
Figure 1 SARS-CoV-2 viral infection at atomic resolution. Counting eight viruses, each of which has spikes (big protrusions) and E membrane proteins (small protrusions) rainbow colored and a core in sienna color, this picture shows how the viruses approach the cell membrane (green). The ACE2 receptors are colored magenta. The field of view is 1 micrometer.
Figure 3 from: Padilla-Sanchez V (2021) SARS-CoV-2 Structural Analysis of Receptor Binding Domain New Variants from United Kingdom and South Africa. Research Ideas and Outcomes 7: e62936. https://doi.org/10.3897/rio.7.e62936
Figure 3 Detail of interface between ACE2 and SARS-CoV-2 RBD. Amino acids are labeled as well as distances. For more details please see the movies in supplementary files. Wild type is beige, UK variant is light blue and SA variant is pink (Suppl. material 2, Suppl. material 3).
Figure 2 from: Padilla-Sanchez V (2021) SARS-CoV-2 Structural Analysis of Receptor Binding Domain New Variants from United Kingdom and South Africa. Research Ideas and Outcomes 7: e62936. https://doi.org/10.3897/rio.7.e62936
Figure 2 Spike glycoprotein bound to ACE2 receptor. PDB 7DF4 (Xu et al. 2020) where ACE2 is cyan and the spike has been colored red, yellow and blue for each subunit of the trimer. This structure has been recently determined at atomic resolution. In spheres, we can see the mutations in the spike glycoprotein from the United Kingdom variant but the only mutation in the receptor binding domain (magenta) is N501Y which is labeled.
Exploring Conformational Landscapes and Binding Mechanisms of Convergent Evolition for the SARS-CoV-2 Spike Omicron Variant Complexes with the ACE2 Receptor Using AlphaFold2-Based Structural Ensembles and Molecular Dynamics Simulations
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Haplotype-phasing of long-read HiFi data to enhance structural variant detection through a Skip-Gram model
<p>Example dataset for DipPAV</p>
A joint embedding of protein sequence and structure enables robust variant effect predictions
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Emerging variants of SARS-CoV-2 NSP10 highlight strong and functional conservation of its binding to two non-structural protein, NSP14 and NSP16
<p>The data set contains: (1) topology (prmtop), (2) coordinate files to the run the simulation (3) A plumed.dat file (4) COLVAR and (5) HILLS files; (6) Trajectory (xtc) file and (7) corresponding pdb file. </p> <p>The simulations were run as replicates.</p>
VCF of structural variant calls of Nanopore data aligned to dm6 reference genome
<p>Heterozygous chromosome inversions suppress meiotic crossover (CO) formation within an inversion, potentially because they lead to gross chromosome rearrangements that produce inviable gametes. Interestingly, COs are also severely reduced in regions nearby but outside of inversion breakpoints even though COs in these regions do not result in rearrangements. Our mechanistic understanding of why COs are suppressed outside of inversion breakpoints is limited by a lack of data on the frequency of noncrossover gene conversions (NCOGCs) in these regions. To address this critical gap, we mapped the location and frequency of rare CO and NCOGC events that occurred outside of the <em>dl</em>-<em>49</em> <em>chrX</em> inversion in <em>D</em>. <em>melanogaster</em>. We created full-sibling wildtype and inversion stocks and recovered COs and NCOGCs in the syntenic regions of both stocks, allowing us to directly compare rates and distributions of recombination events. We show that COs are completely suppressed within 500 kb of inversion breakpoints, are severely reduced within 2 Mb of an inversion breakpoint, and increase above wildtype levels 2–4 Mb from the breakpoint. We find that NCOGCs occur evenly throughout the chromosome and, importantly, occur at wild-type levels near inversion breakpoints. We propose a model in which COs are suppressed by inversion breakpoints in a distance-dependent manner through mechanisms that influence DNA double-strand break repair outcome but not double-strand break location or frequency. We suggest that subtle changes in the synaptonemal complex and chromosome pairing might lead to unstable interhomolog interactions during recombination that permits NCOGC formation but not CO formation.</p>
VCF of structural variant calls of Nanopore data aligned to dm6 reference genome
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Multiplex generation and single cell analysis of structural variants in mammalian genomes [scRNA-seq]
GEO Series GSE282634. Homo sapiens; Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing; Other.
Post-zygotic structural variants in histologically normal breast tissue may predispose to sporadic breast cancer [SET 6]
GEO Series GSE64724. Homo sapiens. 100 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
Post-zygotic structural variants in histologically normal breast tissue may predispose to sporadic breast cancer [SET 10]
GEO Series GSE64728. Homo sapiens. 100 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
Post-zygotic structural variants in histologically normal breast tissue may predispose to sporadic breast cancer [SET 11]
GEO Series GSE64729. Homo sapiens. 100 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
Polymer Physics Predicts the Effects of Structural Variants on Chromatin Architecture (mouse)
GEO Series GSE92291. Mus musculus. 4 samples. Type: Other.
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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.