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98 results for “chromatin network”
Chromatin Network Retards Nucleoli Coalescence
<p>This repository contains the simulated trajectories in our investigation of the role of the chromatin network in retarding nucleoli coalescence. </p>
Evolutionary changes in the chromatin landscape contribute to reorganization of a developmental gene network during rapid life history evolution in sea urchins
<p>Chromatin configuration is highly dynamic during embryonic development in animals, exerting an important point of control in transcriptional regulation. Yet there exists remarkably little information about the role of evolutionary changes in chromatin configuration to the evolution of gene expression and organismal traits. Genome-wide assays of chromatin configuration, coupled with whole-genome alignments, can help address this gap in knowledge in several ways. In this study, we present a comparative analysis of regulatory element sequences and accessibility throughout embryogenesis in three sea urchin species with divergent life histories: a lecithotroph <em>Heliocidaris erythrogramma</em>, a closely related planktotroph <em>H. tuberculata</em>, and a distantly related planktotroph <em>Lytechinus variegatus</em>. We identified distinct epigenetic and mutational signatures of evolutionary modifications to the function of putative <em>cis</em>-regulatory elements in <em>H. erythrogramma</em> that have accumulated non-uniformly throughout the genome, suggesting selection, rather than drift, underlies many modifications associated with the derived life history. Specifically, regulatory elements composing the sea urchin developmental gene regulatory network are enriched for signatures of positive selection and accessibility changes which may function to alter binding affinity and access of developmental transcription factors to these sites. Furthermore, regulatory element changes often correlate with divergent expression patterns of genes involved in cell type specification, morphogenesis, and development of other derived traits, suggesting these evolutionary modifications have been consequential for phenotypic evolution in <em>H. erythrogramma</em>. Collectively, our results demonstrate that selective pressures imposed by changes in developmental life history rapidly reshape the <em>cis</em>-regulatory landscape of core developmental genes to generate novel traits and embryonic programs.</p>
Evolutionary changes in the chromatin landscape contribute to reorganization of a developmental gene network during rapid life history evolution in sea urchins
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Expression proteomics and histone analysis reveals extensive chromatin network changes and a role for histone tail trimming during cellular differentiation
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The network of targeting interactions in chromatin
GEO Series GSE15807. Drosophila melanogaster. 16 samples. Type: Genome binding/occupancy profiling by array; Genome binding/occupancy profiling by genome tiling array.
Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development [RNA-seq]
GEO Series GSE214738. Triticum aestivum. 8 samples. Type: Expression profiling by high throughput sequencing.
Chromatin Accessibility-Based Characterization of the Gene Regulatory Networks Underpinning Phenotypic Plasticity in the Honey Bee
GEO Series GSE206995. Apis mellifera. 39 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Chromatin Capture Identifies SCARB1-LAG3 Proinflammatory Cardiovascular Disease Gene Networks [4C-Seq]
GEO Series GSE110752. Homo sapiens. 8 samples. Type: Other.
Genome-wide interference of chromatin architecture and Mediator in transcriptional bursting and gene network regulation
GEO Series GSE241338. Homo sapiens; Mus musculus. 250 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
DeepC: Predicting chromatin interactions using megabase scaled deep neural networks and transfer learning (NG Capture-C)
GEO Series GSE137435. Homo sapiens. 4 samples. Type: Other.
Molecular insights into the role of desmin intermediate filament network in chromatin landscape, cardiomyocyte differentiation, and maturation
GEO Series GSE274613. Mus musculus. 38 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
An AR-ERG co-mediated chromatin interactome defines the transcriptional network in prostate cancer cells
GEO Series GSE54946. Homo sapiens. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
Chromatin Interaction Neural Network (ChINN): A machine learning-based method for predicting chromatin interactions from DNA sequences
GEO Series GSE163896. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells [RNA-seq]
GEO Series GSE113720. Mus musculus. 99 samples. Type: Expression profiling by high throughput sequencing.
Activating mutations remodeled the chromatin accessibility landscape to drive distinct regulatory networks in KMT2A-rearranged acute leukemia
GEO Series GSE248468. Mus musculus. 16 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
ZBTB16/PLZF regulates self-renewal and differentiation of spermatogonial stem cells through an extensive transcription factor-chromatin poising network
GEO Series GSE202818. Mus musculus. 20 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks.
GEO Series GSE116193. Homo sapiens. 112 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
DeepC: Predicting chromatin interactions using megabase scaled deep neural networks and transfer learning (Tiled-C)
GEO Series GSE137436. Homo sapiens. 2 samples. Type: Other.
Chromatin binding protein PHF6 regulates activity-dependent transcription networks to promote hunger response [RNA-Seq]
GEO Series GSE139543. Mus musculus. 20 samples. Type: Expression profiling by high throughput sequencing.
Mapping the global chromatin connectivity network in colorectal cancer cell HCT116 and Oxaliplatin-resistant cell HCT116OxR [Hi-C]
GEO Series GSE138652. Homo sapiens. 2 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.