Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
27
datasets available to search
ShareScore release 0.9.0
Dataset results
27 results for “nuclear compartments”
Cohesin depleted cells rebuild functional nuclear compartments after endomitosis
<p class="Standa49"><span>Cohesin plays an essential role in chromatin loop extrusion, but its impact on a compartmentalized nuclear architecture is debatable. Using live-cell and super-resolved 3D microscopy, we demonstrate that cohesin-depleted cells pass through an endomitosis and rebuild a single multilobulated nucleus (MLN) with chromosome territories (CTs) pervaded by interchromatin channels. CTs contain chromatin domain clusters with a zonal organization of repressed chromatin domains in the interior and transcriptionally competent domains located at the periphery. Splicing speckles are located nearby within the lining channel system. These clusters form microscopically defined, active and inactive compartments, which correspond to A and B compartments, respectively, in ensemble Hi-C. Functionality of MLN despite continuous absence of cohesin was demonstrated by their ability to pass through S-phase with typical spatio-temporal patterns of replication domains. Evidence for structural changes of these domains compared to controls suggests that cohesin is required for their full integrity.</span></p>
Data from: New quantitative approaches reveal the spatial preference of nuclear compartments in mammalian fibroblasts
The nuclei of higher eukaryotic cells display compartmentalization and certain nuclear compartments have been shown to follow a degree of spatial organization. To date, the study of nuclear organization has often involved simple quantitative procedures that struggle with both the irregularity of the nuclear boundary and the problem of handling replicate images. Such studies typically focus on inter-object distance, rather than spatial location within the nucleus. The concern of this paper is the spatial preference of nuclear compartments, for which we have developed statistical tools to quantitatively study and explore nuclear organization. These tools combine replicate images to generate 'aggregate maps' which represent the spatial preferences of nuclear compartments. We present two examples of different compartments in mammalian fibroblasts (WI-38 and MRC-5) that demonstrate new knowledge of spatial preference within the cell nucleus. Specifically, the spatial preference of RNA polymerase II is preserved across normal and immortalized cells, whereas PML nuclear bodies exhibit a change in spatial preference from avoiding the centre in normal cells to exhibiting a preference for the centre in immortalized cells. In addition, we show that SC35 splicing speckles are excluded from the nuclear boundary and localize throughout the nucleoplasm and in the interchromatin space in non-transformed WI-38 cells. This new methodology is thus able to reveal the effect of large-scale perturbation on spatial architecture and preferences that would not be obvious from single cell imaging.
Data from: New quantitative approaches reveal the spatial preference of nuclear compartments in mammalian fibroblasts
Open the record for dataset details and reuse information.
Cohesin depleted cells rebuild functional nuclear compartments after endomitosis
Open the record for dataset details and reuse information.
Bacterial artificial chromosomes establish replication timing and sub-nuclear compartment de novo as extra-chromosomal vectors [4C]
GEO Series GSE102521. Homo sapiens. 1 samples. Type: Other.
Distinct nuclear compartment-associated genome architecture in the developing mammalian brain
GEO Series GSE175679. Macaca mulatta; Mus musculus; Homo sapiens. 62 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Highly parallel quantification and compartment localization of transcription factors and nuclear proteins
GEO Series GSE140325. Homo sapiens. 9 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Nuclear Receptor NR2F6 as an Alternative Cancer Immune Checkpoint in the T Cell Compartment
GEO Series GSE111796. Mus musculus. 18 samples. Type: Expression profiling by high throughput sequencing.
Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription
GEO Series GSE211287. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Bacterial artificial chromosomes establish replication timing and sub-nuclear compartment de novo as extra-chromosomal vectors [repli-seq]
GEO Series GSE102522. Homo sapiens. 8 samples. Type: Other.
The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation
GEO Series GSE98123. human papillomavirus 31; Homo sapiens; Human papillomavirus 16; human gammaherpesvirus 4; Human gammaherpesvirus 8. 46 samples. Type: Other; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function.
GEO Series GSE296389. Homo sapiens. 28 samples. Type: Other.
The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation [HiC-seq]
GEO Series GSE98120. Homo sapiens; human gammaherpesvirus 4; human papillomavirus 31; Human papillomavirus 16; Human gammaherpesvirus 8. 32 samples. Type: Other.
Bacterial artificial chromosomes establish replication timing and sub-nuclear compartment de novo as extra-chromosomal vectors
GEO Series GSE102704. Homo sapiens. 9 samples. Type: Other.
Loops, TADs, Compartments, and Territories are Elastic and Robust to Dramatic Nuclear Volume Swelling
GEO Series GSE182665. Homo sapiens. 9 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Profiling transcriptome composition and dynamics within nuclear compartments using SLAM-RT&Tag
GEO Series GSE272219. Homo sapiens. 140 samples. Type: Other; Expression profiling by high throughput sequencing.
Cohesin depleted cells rebuild active and inactive nuclear compartments after mitosis
GEO Series GSE145099. Homo sapiens. 13 samples. Type: Other.
Guanine- and cytosine-rich genes are actively transcribed at the nuclear Lmnb1 compartment
GEO Series GSE246040. Mus musculus. 6 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Cause and consequence of tethering a sub-TAD to different nuclear compartments
GEO Series GSE76174. Mus musculus. 45 samples. Type: Other.
The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation [ChIP-seq]
GEO Series GSE98121. Homo sapiens; human gammaherpesvirus 4. 2 samples. Type: Genome binding/occupancy 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.