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ShareScore release 0.9.0
Dataset results
409 results for “genome organization”
Data from: Comparative analysis of 2D and 3D distance measurements to study spatial genome organization
The spatial organization of genomes is non-random, cell-type specific, and has been linked to cellular function. The investigation of spatial organization has traditionally relied extensively on fluorescence microscopy. The validity of the imaging methods used to probe spatial genome organization often depends on the accuracy and precision of distance measurements. Imaging-based measurements may either use 2 dimensional datasets or 3D datasets which include the z-axis information in image stacks. Here we compare the suitability of 2D vs 3D distance measurements in the analysis of various features of spatial genome organization. We find in general good agreement between 2D and 3D analysis with higher convergence of measurements as the interrogated distance increases, especially in flat cells. Overall, 3D distance measurements are more accurate than 2D distances, but are also more susceptible to noise. In particular, z-stacks are prone to error due to imaging properties such as limited resolution along the z-axis and optical aberrations, and we also find significant deviations from unimodal distance distributions caused by low sampling frequency in z. These deviations are ameliorated by significantly higher sampling frequency in the z-direction. We conclude that 2D distances are preferred for comparative analyses between cells, but 3D distances are preferred when comparing to theoretical models in large samples of cells. In general and for practical purposes, 2D distance measurements are preferable for many applications of analysis of spatial genome organization.
Data from: Comparative analysis of 2D and 3D distance measurements to study spatial genome organization
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Genome size drives morphological evolution in organ-specific ways
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Data from: Genus-wide screening reveals four distinct types of structural plastid genome organization in Pelargonium (Geraniaceae)
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Genome wide identification, genomic organization, and expression profiling of the CONSTANS-like (COL) gene family in petunia under multiple stresses
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Data from: Developing reduced SNP assays from whole-genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis)
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Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes
GEO Series GSE126952. Drosophila melanogaster. 19 samples. Type: Expression profiling by high throughput sequencing; Other.
SATB2 organizes the 3D genome architecture of cognition in cortical neurons [ATAC-seq]
GEO Series GSE222607. Mus musculus. 6 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Global analyses of cell cycle dependent changes in fission yeast genome organization reveal correlations with alterations in transcript levels
GEO Series GSE52287. Schizosaccharomyces pombe. 12 samples. Type: Expression profiling by high throughput sequencing; Other.
Histone deacetylation and cytosine methylation are required for the normal compartmentalization of heterochromatin in the genome organization of Neurospora crassa
GEO Series GSE232935. Neurospora crassa. 31 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other.
Organization, genomic targeting and assembly of three distinct SWI/SNF chromatin remodeling complexes in Arabidopsis [ChIP-seq]
GEO Series GSE218841. Arabidopsis. 26 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Genome-wide identification of FHY3 binding sites in Arabidopsis floral organ (RNA-Seq)
GEO Series GSE69424. Arabidopsis thaliana. 8 samples. Type: Expression profiling by high throughput sequencing.
Antagonism between H3K27me3 and genome-lamina association drives atypical spatial genome organization in the totipotent embryo [scDamID]
GEO Series GSE217462. Mus musculus. 9 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other.
3D genome organization coordinates key regulators of lineage specification in mammary epithelial cells [T8_Omni-C]
GEO Series GSE228954. Mus musculus. 6 samples. Type: Other.
TSA-Seq Mapping of Nuclear Genome Organization [seq]
GEO Series GSE81553. Homo sapiens. 43 samples. Type: Other.
Genome organization regulates nuclear pore complex formation and promotes differentiation during Drosophila oogenesis [CUT&RUN]
GEO Series GSE250350. Drosophila melanogaster. 24 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
NFIB Is a Pioneer Factor for DNA Replication by Acting as a Genome Organizer [WGS]
GEO Series GSE201866. Homo sapiens. 18 samples. Type: Other.
The effects of Arabidopsis genome duplication on the chromatin organization and transcriptional regulation
GEO Series GSE114950. Arabidopsis thaliana. 28 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories (Wheat_RNAseq)
GEO Series GSE133884. Triticum aestivum. 3 samples. Type: Expression profiling by high throughput sequencing.
Elementary 3D organization of active and silenced E. coli genome
GEO Series GSE272160. Escherichia coli. 4 samples. Type: Other.
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.