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.
522
datasets available to search
ShareScore release 0.9.0
Dataset results
522 results for “gene regulatory network”
Extending the gene regulatory network model for B cell differentiation
<p>Scripts used for modelling the gene regulatory network of B cell differentiation</p>
Data from: Comparative developmental transcriptomics reveals rewiring of a highly conserved gene regulatory network during a major life history switch in the sea urchin genus Heliocidaris
The ecologically significant shift in developmental strategy from planktotrophic (feeding) to lecithotrophic (nonfeeding) development in the sea urchin genus Heliocidaris is one of the most comprehensively studied life history transitions in any animal. Although the evolution of lecithotrophy involved substantial changes to larval development and morphology, it is not known to what extent changes in gene expression underlie the developmental differences between species, nor do we understand how these changes evolved within the context of the well-defined gene regulatory network (GRN) underlying sea urchin development. To address these questions, we used RNA-seq to measure expression dynamics across development in three species: the lecithotroph Heliocidaris erythrogramma, the closely related planktotroph H. tuberculata, and an outgroup planktotroph Lytechinus variegatus. Using well-established statistical methods, we developed a novel framework for identifying, quantifying, and polarizing evolutionary changes in gene expression profiles across the transcriptome and within the GRN. We found that major changes in gene expression profiles were more numerous during the evolution of lecithotrophy than during the persistence of planktotrophy, and that genes with derived expression profiles in the lecithotroph displayed specific characteristics as a group that are consistent with the dramatically altered developmental program in this species. Compared to the transcriptome, changes in gene expression profiles within the GRN were even more pronounced in the lecithotroph. We found evidence for conservation and likely divergence of particular GRN regulatory interactions in the lecithotroph, as well as significant changes in the expression of genes with known roles in larval skeletogenesis. We further use coexpression analysis to identify genes of unknown function that may contribute to both conserved and derived developmental traits between species. Collectively, our results indicate that distinct evolutionary processes operate on gene expression during periods of life history conservation and periods of life history divergence, and that this contrast is even more pronounced within the GRN than across the transcriptome as a whole.
Regulatory Network and Diagnostic Value of Key Autophagy-related Genes in Sepsis
ClinicalTrials.gov study NCT05524376. IPD Sharing: UNDECIDED. Countries: 0. Publications: 4.
Data from: Odd-paired controls frequency doubling in Drosophila segmentation by altering the pair-rule gene regulatory network
Open the record for dataset details and reuse information.
Data from: Comparative developmental transcriptomics reveals rewiring of a highly conserved gene regulatory network during a major life history switch in the sea urchin genus Heliocidaris
Open the record for dataset details and reuse information.
Data from:A method for estimating Hill function-based dynamic models of gene regulatory networks
Open the record for dataset details and reuse information.
Data from: Identification of ZEB1 as a central component of the adipogenic gene regulatory network
Open the record for dataset details and reuse information.
Single cell evaluation of endocardial HAND2 gene regulatory networks reveals critical HAND2 dependent pathways impacting cardiac morphogenesis.
GEO Series GSE210221. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets
GEO Series GSE208620. Mus musculus. 6 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Pancreatic and intestinal endocrine cells share common transcriptomic signatures and gene regulatory networks
GEO Series GSE149081. Danio rerio. 13 samples. Type: Expression profiling by high throughput sequencing.
Deep tissue profiling of Populus stem at single nucleus level reveals uncharacterized cell types and cell-specific gene regulatory networks
GEO Series GSE290732. Populus trichocarpa. 2 samples. Type: Expression profiling by high throughput sequencing.
TRIM28 controls a gene regulatory network based on endogenous retroviruses in human neural progenitor cells
GEO Series GSE84259. Homo sapiens. 34 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Molecular insights into induced pluripotency mediated by the OCT4, SOX2, KLF and c-MYC gene regulatory network
GEO Series GSE28688. Homo sapiens. 14 samples. Type: Expression profiling by array.
An atlas of gene regulatory networks for T memory cells in youth and old age [scATAC-seq]
GEO Series GSE228660. Mus musculus. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Evolution of gene regulatory networks during human cardiogenesis
GEO Series GSE192365. Homo sapiens. 53 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Identification of microRNA-dependent gene regulatory networks driving human pancreatic endocrine cell differentiation [Islet RNA-Seq]
GEO Series GSE140403. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing.
Decoding the gene regulatory network of endosperm differentiation in maize [scRNA-seq]
GEO Series GSE201640. Zea mays. 4 samples. Type: Expression profiling by high throughput sequencing.
A genome-wide assessment of the ancestral neural crest gene regulatory network
GEO Series GSE112072. Lampetra planeri; Petromyzon marinus. 28 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy 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.
Identification of gene regulatory networks affected across drug-resistant epilepsies
GEO Series GSE256068. Homo sapiens. 162 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.