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.
612
datasets available to search
ShareScore release 0.9.0
Dataset results
612 results for “Regulatory elements”
G-quadruplexes as pivotal components of cis-regulatory elements in the human genome
<p>This repository stores the scripts for analyzing the relationship between G-quadruplexes (G4s) and <em>cis</em>-regulatory elements (CREs), as well as the data generated directly from the manuscript.</p> <p>Manuscript: <a href="https://doi.org/10.1186/s12915-024-01971-5" target="_blank" rel="noopener">G-quadruplexes as pivotal components of <em>cis</em>-regulatory elements in the human genome</a></p> <p>G4Hunter_w25_s1.5_hg38.txt: All potential G-quadruplexes in the human genome predicted by the G4Hunter software. </p> <ul> <li>Genome assembly: hg38.</li> <li>G4Hunter software parameters were set as follows: score threshold 1.5, window size 25.</li> </ul> <p>G4_cCRE_annotation.txt: Annotation file indicating the presence of G4s in cCREs (candidate CREs; from <a title="SCREEN database" href="https://screen.encodeproject.org/" target="_blank" rel="noopener">SCREEN database</a>).</p> <p>scripts.zip: Source code used for data analysis in this project, based on the R language.</p>
Partitioned linkage disequilibrium scores for active regulatory elements in ROADMAP datasets
<p>Partitioned linkage disequilibrium scores for active regulatory elements in ROADMAP epigenomics datasets, to accompany paper Lynall et al 2021</p> <p>Accompanying code available at https://github.com/maryellenlynall/psychimmgen2021</p> <p>Active regulatory elements annotations are a union of the following IDEAS annotations, representing enhancers and active promoters (see http://bx.psu.edu/~yuzhang/Roadmap_ideas/trackDb_test.txt for IDEAS track hubs): </p> <p>4_Enh<br> 6_EnhG<br> 8_TssAFlnk<br> 10_TssA<br> 14_TssWk<br> 17_EnhGA</p> <p>tissues.txt provides the list of ROADMAP tissues </p> <p>The partitioned_LD_scores folder contains partitioned LD scores in a format suitable for stratified LDSC analysis for European participants</p>
Data from: DCDC2 READ1 regulatory element: how temporal processing differences may shape language
<p>Classic linguistic theory ascribes language change and diversity to population migrations, conquests, and geographic isolation, with the assumption that human populations have equivalent language processing abilities. We hypothesize that spectral and temporal characteristics make some consonant manners vulnerable to differences in temporal precision associated with specific population allele frequencies. To test this hypothesis, we modeled association between RU1-1 alleles of <i>DCDC2</i> and manner of articulation in 51 populations spanning five continents, and adjusting for geographic proximity, genetic and linguistic relatedness. RU1-1 alleles, acting through increased expression of <i>DCDC2</i>, appear to increase auditory processing precision that enhances stop-consonant discrimination, favoring retention in some populations and loss by others. These findings enhance classical linguistic theories by adding a genetic dimension, which until recently, has not been considered to be a significant catalyst for language change.</p>
Regulatory spine RS3 residue of protein kinases: a lipophilic bystander or a decisive element in the small-molecule kinase inhibitor binding?
<p>Datasets related to publication: </p> <p>Shevchenko E, Pantsar T: Regulatory spine RS3 residue of protein kinases: a lipophilic bystander or a decisive element in the small-molecule kinase inhibitor binding?. <em><em>Biochem Soc Trans</em></em> 28 February 2022; 50 (1): 633–648</p> <p>https://doi.org/10.1042/bst20210837</p> <p> </p> <p> </p>
[Demo Input Data] for SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells
<p>This archive (input.tar.gz) contains the demo data for SCAFE v1.0.0 (on <a href="https://doi.org/10.5281/zenodo.7023163">Zenodo</a> or <a href="https://github.com/chung-lab/SCAFE/releases/tag/v1.0.0">Github</a>)</p> <p><em>SCAFE</em> (Single Cell Analysis of Five-prime Ends) provides an end-to-end solution for processing of single cell 5’end RNA-seq data. It takes a read alignment file (*.bam) from single-cell RNA-5’end-sequencing (e.g. 10xGenomics Chromimum®), precisely maps the cDNA 5'ends (i.e. transcription start sites, TSS), filters for the artefacts and identifies genuine TSS clusters using logistic regression. Based on the TSS clusters, it defines transcribed cis-regulatory elements (tCRE) and annotated them to gene models. It then counts the UMI in tCRE in single cells and returns a tCRE UMI/cellbarcode matrix ready for downstream analyses, e.g. cell-type clustering, linking promoters to enhancers by co-activity <em>etc</em>.</p> <p>For details on installation, usage and test run on demo data, visit <a href="https://github.com/chung-lab/SCAFE">https://github.com/chung-lab/SCAFE</a></p>
Machine learning models, and training, validation and test datasets for: "Sequence determinants of human gene regulatory elements"
<p>This record contains the training, test and validation datasets used to train and evaluate the machine learning models in manuscript:</p> <p><strong>Sahu, Biswajyoti, et al. "Sequence determinants of human gene regulatory elements." (2021).</strong></p> <p><br> This record contains also the final hyperparameter-optimized models for each training dataset/task combination described in the manuscript. The README-files provided with the record describe the datasets and models in more detail. The datasets deposited here are derived from the original raw data (GEO accession: GSE180158) as described in the Methods of the manuscript.</p>
Mammalian Evolution of Human cis-regulatory Elements and Transcription Factor Binding Sites
<p>Code and data associated with the manuscript entitled "Mammalian Evolution of Human cis-regulatory Elements and Transcription Factor Binding Sites "</p>
Data from: DCDC2 READ1 regulatory element: how temporal processing differences may shape language
Open the record for dataset details and reuse information.
GREEN-DB: Genomic Regulatory Elements ENcyclopedia
<p>GREEN-DB is a comprehensive collection of 2.4 million regulatory elements in the human genome collected from previously published databases, high-throughput screenings and functional studies. Regulatory regions are classified as enhancers, promoters, silencers, bivalent and information on the controlled gene(s), tissue(s) and associated phenotype(s) are provided for each element when possible. We also calculated a variation constraint metric (range 0-1) for these regulatory regions and showed that genes controlled by constrained regions are enriched for disease-associated genes and essential genes from mouse knock-out screenings.</p> <p>The database also includes information from ENCODE TFBS and DNase peaks; ultra-conserved non-coding elements (UCNE), super-enhancers (dbSuper) and TAD domains (TAD-KB).</p> <p>This release includes 5 files:</p> <ul> <li>GREEN-DB_v2.5.db.gz: The full database in SQLite format</li> <li>GRCh37_GREEN-DB.bed.gz[.csi]: A indexed BED file using GRCh37 genome coordinates describing the regulatory regions and associated information useful for variant annotations (controlled genes, closest gene/TSS, constraint metric).</li> <li>GRCh38_GREEN-DB.bed.gz[.csi]: A indexed BED file using GRCh38 genome coordinates describing the regulatory regions and associated information useful for variant annotations (controlled genes, closest gene/TSS, constraint metric).</li> </ul> <p>To annotate a VCF file with information from GREEN-DB you can use the bed files and our tool GREEN-VARAN (<a href="https://github.com/edg1983/GREEN-VARAN">https://github.com/edg1983/GREEN-VARAN</a>).</p> <p>For more information on the GREEN-DB please refer to our publication (<a href="https://doi.org/10.1101/2020.09.17.301960">https://doi.org/10.1101/2020.09.17.301960</a>) and to online documentation (<a href="https://green-varan.readthedocs.io/en/latest/">https://green-varan.readthedocs.io/en/latest/</a>)</p> <p>GREEN-DB is free to use for academic users, please refer to the attached LICENSE file.</p> <p> </p> <p><strong>Changes from the previous version:</strong></p> <p>- We fixed an issue with alias symbols conversion that caused a small fraction of region-gene links to point to the wrong gene</p> <p>- Due to the problem above, we removed any region-gene link where the region and the controlled gene were located on different chromosomes</p> <p>- GREEN-DB now includes also TAD domain information from TAD-KB (http://dna.cs.miami.edu/TADKB/) and region-gene interactions are now annotated for occurrence within the same TAD</p> <p>- Better constraint metric model that now takes into account overlap with exonic regions</p> <p>- In addition to the closest gene, an annotation for the closest TSS and its distance is now provided </p>
OPT data from: A novel cis-regulatory element drives early expression of Nkx3.2 in the gnathostome primary jaw joint
<p><span>The acquisition of movable jaws was a major event during vertebrate evolution. The role of NK3 homeobox 2 (Nkx3.2) transcription factor in patterning the primary jaw joint of gnathostomes (jawed vertebrates) is well known, however, knowledge about its regulatory mechanism is lacking. In this study, we report a proximal enhancer element of <em>Nkx3.2</em> that is deeply conserved in most gnathostomes but undetectable in the jawless hagfish and lamprey. This enhancer is active in the developing jaw joint region of the zebrafish <em>Danio rerio</em>, and was thus designated as <em>jaw joint regulatory sequence 1</em> (JRS1). We further show that JRS1 enhancer sequences from a range of gnathostome species, including a chondrichthyan and mammals, have the same activity in the jaw joint as the native zebrafish enhancer, indicating a high degree of functional conservation despite the divergence of cartilaginous and bony fish lineages or the transition of the primary jaw joint into the middle ear of mammals. Finally, we show that deletion of JRS1 from the zebrafish genome using CRISPR/Cas9 results in a significant reduction of early gene expression of <em>Nkx3.2</em> and leads to transient jaw joint deformation and partial fusion. The emergence of this <em>Nkx3.2 </em>enhancer in early gnathostomes may have contributed to the origin and shaping of the articulating surfaces of vertebrate jaws.</span></p>
CREdb: A comprehensive database of Cis-Regulatory Elements and their activity in human cells and tissues
<p>Cis-regulatory elements (CREs) play a pivotal role in gene expression regulation, allowing cells to serve diverse functions and respond to external stimuli. To address this gap, we have created CREdb, a comprehensive database of over 10 million human regulatory elements across 1,058 cell types and 315 tissues. Data from 11 sources were curated and mapped to standard ontological terms. 11,223,434 combined elements are present in the final database, and these were merged into 5,666,240 consensus elements representing the combined ranges of the individual elements informed by their overlap. Each consensus element contains metadata including the number of elements supporting it and a hash linking to the source databases. The inferred activity of each consensus element in various cell-type and tissue context is also provided.</p>
Integrated maize cis-regulatory elements (iCREs)
<p>Files containing the genomic coordinates of the conserved non-coding sequences (BLSSpeller, msa_pipeline, funTFBS, and Song-2021), the accessible chromatin regions (ACRs) and the unmethylated regions (UMRs) in the maize genome version 5 employed to generate the integrated cis-regulatory-elements (iCREs), both the all and maxF1 sets.</p> <p>Version 1.1 includes the "all" iCREs and the "maxF1" iCREs annotated to their closest gene.</p> <p>Version 1.2 includes an extra version of the same files as the previous one but with the genome coordinates in the maize genome version 4 (AGPv4)</p> <p>Version 1.3 includes the "all" iCREs and the "maxF1" iCREs annotated to their closest gene in the coordinates of the maize genome version 4 (AGPv4).</p> <p>Version 1.4 includes Supplementary Table 3 and 4 (which in the reserach chapter version of the article, included in the doctoral dissertation of Nicolás Manosalva, they correspond to Supporting Datasets 5 and 6):</p> <ul> <li>Table S3/Dataset S5: Gene ontology (GO) enrichment of the genes associated with different repetitive element types and transposable element (TE) superfamilies that are found within iCREs. </li> <li>Table S4/Dataset S6: Number of, median value of the transcripts per million, and p-value of the genes associated with TEs within, outside, and within and outside iCREs. The computations were binned per distance to the closest gene.</li> </ul>
Structure of phospholipase Cε reveals an integrated RA1 domain and previously unidentified regulatory elements
<p><span><span><span><span><span><span><span><span><span><span><span>Phospholipase Cepsilon (PLCepsilon) generates lipid-derived second messengers in the cardiovascular system at the plasma and perinuclear membranes. It is activated in response to a wide variety of signals, such as those conveyed by Rap1A and Ras, through a mechanism that involves its C-terminal Ras association (RA) domains (RA1 and RA2). However, the complexity and size of PLCepsilon has hindered its structural and functional analysis. In this manuscript, we report the 2.7 Å crystal structure of fragment of PLCepsilon that retains catalytic activity. The strutcure includes the RA1 domain, which forms an integral part of the conserved core. In addition, a highly conserved amphipathic helix in the autoinhibitory X–Y linker is shown to modulate activity <em>in vitro</em> and in cells. </span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>The studies provide a structural framework for the core of this critical cardiovascular enzyme that will allow for a better understanding of its regulation and roles in disease.</span></span></span></span></span></span></span></span></span></span></span></p>
Massively Parallel Reporter Assays for High-Throughput In Vivo Analysis of Cis-Regulatory Elements
<p>A library of 50 enhancers, each tested in three different lengths and with two different promoters (300 combinations), was packaged into AAV9 and delivered to newborn mice. Enhancers were selected from the VISTA Enhancer Browser of transgenic reporter data, and included 25 candidates active in the embryonic myocardium and 25 negative control candidates active in embryonic endothelium but not in myocardium. In the heart, AAV9 selectively transduces cardiomyocytes. After collecting ventricles at P28, the reporter transcripts were sequenced, and the frequency of each barcode was compared to its frequency in the viral pool DNA.</p> <p>Here we provide fastq files for each sample, an Excel spreadsheet (MPRA-Metadata.xls) containing annotation, and an Excel spreadsheet (MPRA-counts.xlsx) containing extracted barcode counts for each enhancer, as well as additional annotation and calculated enhancer activity.</p>
Raw data for: Crosstalk between regulatory elements in the disordered TRPV4 N-terminus modulates lipid-dependent channel activity
<p>This repository contains raw data and code related to "Crosstalk between regulatory elements in the disordered TRPV4 N-terminus modulates lipid-dependent channel activity" by Goretzki et al.</p> <p>Included are molecular dynamics parameter files, initial structures after system equilibration, production trajectories, and final structures of simulations of:<br> 1. coarse-grained IDRs on membrane, and force and position data for restrained c-termini. Trajectories are subsampled with one frame every 50 ns.<br> 2. The tetrameric TRPV4 core in a POPC in atomistic resolution. Trajectories are sampled with one frame every 1 ns. <br> 3. The isolated ARD in solution in atomistic resolution. Trajectories are subsampled with one frame every 1 ns.</p> <p>Contact information:<br> Name: Stefan L. Schaefer<br> Institution: Department of Theoretical Biophysics, Max Planck Institute of Biophysics<br> Address: Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany<br> Email: stefan.schaefer@biophys.mpg.de</p> <p>Name: Ainara Claveras Cabezudo<br> Institution: Department of Theoretical Biophysics, Max Planck Institute of Biophysics<br> Address: Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany<br> Email: ainara.claveras@biophys.mpg.de</p>
Structure of phospholipase Cε reveals an integrated RA1 domain and previously unidentified regulatory elements
Open the record for dataset details and reuse information.
OPT data from: A novel cis-regulatory element drives early expression of Nkx3.2 in the gnathostome primary jaw joint
Open the record for dataset details and reuse information.
Data from: The evolution of heat shock protein sequences, cis-regulatory elements, and expression profiles in the eusocial Hymenoptera
Background: The eusocial Hymenoptera have radiated across a wide range of thermal environments, exposing them to significant physiological stressors. We reconstructed the evolutionary history of three families of Heat Shock Proteins (Hsp90, Hsp70, Hsp40), the primary molecular chaperones protecting against thermal damage, across 12 Hymenopteran species and four other insect orders. We also predicted and tested for thermal inducibility of eight Hsps from the presence of cis-regulatory heat shock elements (HSEs). We tested whether Hsp induction patterns in ants were associated with different thermal environments. Results: We found evidence for duplications, losses, and cis-regulatory changes in two of the three gene families. One member of the Hsp90 gene family, hsp83, duplicated basally in the Hymenoptera, with shifts in HSE motifs in the novel copy. Both copies were retained in bees, but ants retained only the novel HSE copy. For Hsp70, Hymenoptera lack the primary heat-inducible orthologue from Drosophila melanogaster and instead induce the cognate form, hsc70-4, which also underwent an early duplication. Episodic diversifying selection was detected along the branch predating the duplication of hsc70-4 and continued along one of the paralogue branches after duplication. Four out of eight Hsp genes were heat-inducible and matched the predictions based on presence of conserved HSEs. For the inducible homologues, the more thermally tolerant species, Pogonomyrmex barbatus, had greater Hsp basal expression and induction in response to heat stress than did the less thermally tolerant species, Aphaenogaster picea. Furthermore, there was no trade-off between basal expression and induction. Conclusions: Our results highlight the unique evolutionary history of Hsps in eusocial Hymenoptera, which has been shaped by gains, losses, and changes in cis-regulation. Ants, and most likely other Hymenoptera, utilize lineage-specific heat inducible Hsps, whose expression patterns are associated with adaptive variation in thermal tolerance between two ant species. Collectively, our analyses suggest that Hsp sequence and expression patterns may reflect the forces of selection acting on thermal tolerance in ants and other social Hymenoptera.
Processed data from "Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits"
<p>This is the processed data from our manscript "Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits"</p>
Processed data from "Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits"
<p>This is the processed data from our manscript "Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits"</p>
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.