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79 results for “Three-dimensional Genome”
Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen
<p><span>The spatial organization of eukaryotic genomes is linked to their biological functions, although it is not clear how this impacts the overall evolution of a genome. Here, we uncover the three-dimensional (3D) genome organization of the phytopathogen <em>Verticillium dahliae</em>,<em> </em>known to possess distinct genomic regions, designated adaptive genomic regions (AGRs), enriched in transposable elements and genes that mediate host infection. Short-range DNA interactions form clear topologically associating domains (TADs) with gene-rich boundaries that show reduced levels of gene expression and reduced genomic variation. Intriguingly, TADs are less clearly insulated in AGRs than in the core genome. At a global scale, the genome contains bipartite long-range interactions, particularly enriched for AGRs and more generally containing segmental duplications. Notably, the patterns observed for <em>V. dahliae </em>are also present in other <em>Verticillium</em> species. Thus, our analysis links 3D genome organization to evolutionary features conserved throughout the <em>Verticillium</em> genus.</span></p>
Data for: Three-dimensional characterization of osteocyte volumes at multiple scales, and its relationship with bone biology and genome evolution in ray-finned fishes
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Supporting data for: Three-dimensional genome re-wiring in loci with Human Accelerated Regions
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Histone H3K4 methylation regulation and three-dimensional aggregating distribution of a subset of genomic loci mediated by CHD3 homolog PKL in Arabidopsis
GEO Series GSE254858. Arabidopsis thaliana. 58 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
Three-dimensional disorganisation of the cancer genome occurs coincident with long range genetic and epigenetic alterations [RNA-seq]
GEO Series GSE73784. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Histone H3K4 methylation regulation and three-dimensional aggregating distribution of a subset of genomic loci mediated by CHD3 homolog PKL in Arabidopsis [RNA-Seq]
GEO Series GSE305650. Marchantia polymorpha. 12 samples. Type: Expression profiling by high throughput sequencing.
Systematic Study on the Three-Dimensional Genome of Escherichia Coli and Its Thermal Adaptation Mechanism (RNA-Seq)
GEO Series GSE211824. Escherichia coli str. K-12 substr. MG1655. 12 samples. Type: Expression profiling by high throughput sequencing.
Three-dimensional genome architectural CCCTC-binding factor makes choice in duplicated enhancers at Pcdhα locus
GEO Series GSE147286. Homo sapiens. 74 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
Three-dimensional disorganisation of the cancer genome occurs coincident with long range genetic and epigenetic alterations [ChIP-seq]
GEO Series GSE73783. Homo sapiens. 3 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Systematic Study on the Three-Dimensional Genome of Escherichia Coli and Its Thermal Adaptation Mechanism (3C-Seq)
GEO Series GSE211823. Escherichia coli str. K-12 substr. MG1655. 10 samples. Type: Other.
The three-dimensional structure of the EBV genome plays a crucial role in regulating viral gene expression in EBVaGC [HiC]
GEO Series GSE239989. human gammaherpesvirus 4. 10 samples. Type: Other.
The three-dimensional structure of Epstein-Barr virus genome varies by latency type and is regulated by PARP1 enzymatic activity
GEO Series GSE160973. Homo sapiens. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence
GEO Series GSE133292. Homo sapiens. 46 samples. Type: Other; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Simultaneous single-cell three-dimensional genome and gene expression profiling Uncovers Dynamic Enhancer Connectivity Underlying Olfactory Receptor Choice [cell line, single-cell RNA-Seq & Hi-C]
GEO Series GSE240114. Homo sapiens. 778 samples. Type: Expression profiling by high throughput sequencing; Other.
HNF1B induced three-dimensional genome analysis of patient-derived pancreas neoplasm organoids [ChIP-seq]
GEO Series GSE202020. Homo sapiens. 6 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Simultaneous single-cell three-dimensional genome and gene expression profiling Uncovers Dynamic Enhancer Connectivity Underlying Olfactory Receptor Choice [scATAC-Seq, scRNA-seq]
GEO Series GSE239876. Mus musculus. 143 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
The three-dimensional structure of Epstein-Barr virus genome varies by latency type and is regulated by PARP1 enzymatic activity [RNA-Seq]
GEO Series GSE159836. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
TULIPs decorate the three-dimensional genome of PFA ependymoma
GEO Series GSE186599. Homo sapiens. 160 samples. Type: Other; Genome binding/occupancy profiling by high throughput sequencing.
Three-dimensional analysis of genome organization in CTCF-WT and CTCF-KO dendritic cells
GEO Series GSE185884. Mus musculus. 92 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
The three-dimensional structure of the EBV genome plays a crucial role in regulating viral gene expression in EBVaGC [RNA-seq]
GEO Series GSE239994. Homo sapiens; human gammaherpesvirus 4. 3 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.