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88 results for “genome rearrangements”
Figure 1 in Molecular phylogeny of Acanthochitonina (Mollusca: Polyplacophora: Chitonida): three new mitochondrial genomes, rearranged gene orders and systematics
Figure 1. Phylogenetic relationships and gene arrangements of available chiton mitochondrial genomes. Majority-rule consensus tree from the Bayesian analysis of the mitochondrial genome nucleotide data set (outgroup taxa is omitted for simplicity). Identical topologies were recovered from all other analyses of mitochondrial genome data sets (see main text). Numbers at nodes are posterior probabilities and maximum likelihood bootstrap proportions, respectively. Scale bar is in substitutions per site. Mitochondrial gene orders of Haliotis rubra (Gastropoda), Octopus vulgaris (Cephalopoda) and Solemya velum (Bivalvia) are shown for comparison. Genes encoded by the minus strand are underlined; rearranged genes are highlighted in red (translocations) and green (changes of coding strands).
Data from: Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes
The number of de novo genome sequence assemblies is increasing exponentially; however, relatively few contain one scaffold/contig per chromosome. Such assemblies are essential for studies of genotype-to-phenotype association, gross genomic evolution, and speciation. Inter-species differences can arise from chromosomal changes fixed during evolution, and we previously hypothesized that a higher fraction of elements under negative selection contributed to avian-specific phenotypes and avian genome organization stability. The objective of this study is to generate chromosome-level assemblies of three avian species (saker falcon, budgerigar, and ostrich) previously reported as karyotypically rearranged compared to most birds. We also test the hypothesis that the density of conserved non-coding elements is associated with the positions of evolutionary breakpoint regions.
Data from: Intrachromosomal rearrangements in avian genome evolution: evidence for regions prone to breakpoints
It is generally believed that the organization of avian genomes remains highly conserved in evolution as chromosome number is constant and comparative chromosome painting demonstrated there to be very few interchromosomal rearrangements. The recent sequencing of the zebra finch (Taeniopygia guttata) genome allowed an assessment of the number of intra-chromosomal rearrangements between it and the chicken (Gallus gallus) genome, revealing a surprisingly high number of intra-chromosomal rearrangements. With the publication of the turkey (Meleagris gallopavo) genome it has become possible to describe intrachromosomal rearrangements between these three important avian species, gain insight into the direction of evolutionary change and assess whether breakpoint regions are reused in birds. To this end, we aligned entire chromosomes between chicken, turkey and zebra finch, identifying syntenic blocks of at least 250kb. Potential optimal pathways of rearrangements between each of the three genomes were determined, as was a potential Galliform ancestral organization. From this, our data suggest that around one third of chromosomal breakpoint regions may recur during avian evolution, with 10% of breakpoints apparently recurring in different lineages. This agrees with our previous hypothesis that mechanisms of genome evolution are driven by hotspots of non-allelic homologous recombination.
Data from: Intrachromosomal rearrangements in avian genome evolution: evidence for regions prone to breakpoints
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Data from: Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes
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Data from: Forward genetic screen of human transposase genomic rearrangements
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The mole genome reveals regulatory rearrangements associated with adaptive intersexuality (RNA-Seq)
GEO Series GSE120582. Mus musculus; Talpa occidentalis. 35 samples. Type: Expression profiling by high throughput sequencing.
The mole genome reveals regulatory rearrangements associated with adaptive intersexuality (ATAC-Seq)
GEO Series GSE120586. Talpa occidentalis. 6 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Nuclear compensation to a lineage-specific mitochondrial genomic rearrangement in plants
GEO Series GSE166459. Arabidopsis thaliana. 14 samples. Type: Expression profiling by high throughput sequencing.
Genomic rearrangements in C3 glomerulopathies
GEO Series GSE45585. Homo sapiens. 1 samples. Type: Genome variation profiling by array.
Recurring urothelial carcinomas show genomic rearrangements incompatible with a direct relationship, implications for tumor development.
GEO Series GSE146870. Homo sapiens. 47 samples. Type: Expression profiling by array.
Genomic Balancing Act: Deciphering DNA rearrangements in the Complex Chromosomal Aberration involving 5p15.2, 2q31.1 and 18q21.32
GEO Series GSE265815. Homo sapiens. 3 samples. Type: Methylation profiling by array.
Genomic and Clinical Findings in Myeloid Neoplasms with PDGFRB Rearrangement [seq]
GEO Series GSE182817. Homo sapiens. 22 samples. Type: Genome variation profiling by high throughput sequencing.
Genome-wide analysis of H3K79 methylation in CD34+ CD19+ cells from normal marrow, MLL-rearranged or MLL-germline ALL
GEO Series GSE12360. Homo sapiens. 3 samples. Type: Genome binding/occupancy profiling by genome tiling array.
Verification of predicted hotspots of Alu/Alu-mediated rearrangements in the human genome
GEO Series GSE100590. Homo sapiens. 89 samples. Type: Genome variation profiling by array.
Complex Genomic Rearrangements at the PLP1 Locus Include Triplication and Quadruplication
GEO Series GSE63594. Homo sapiens. 12 samples. Type: Genome variation profiling by array.
Genome-wide rearrangement of protein translation levels for cell and organelle proliferation in a simple unicellular alga
GEO Series GSE273424. Cyanidioschyzon merolae. 4 samples. Type: Other.
Genome Rearrangements and Pervasive Meiotic Drive Cause Hybrid Infertility in Fission Yeast
GEO Series GSE57039. Schizosaccharomyces pombe; Schizosaccharomyces kambucha (nom. inval.). 1 samples. Type: Expression profiling by array.
CTCF mutation at R567 causes developmental disorders by 3D genome rearrangement, premature exhaustion of stem cells and abnormal neurodevelopment [scRNA-seq]
GEO Series GSE231847. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide survey of adjacent gene rearrangements in breast cancer identifies triple-negative specific BCL2L14-ETV6 fusions
GEO Series GSE120919. Homo sapiens. 15 samples. Type: 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.