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191 results for “cis-regulatory element”
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>
[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>
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>
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>
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>
OPT data from: A novel cis-regulatory element drives early expression of Nkx3.2 in the gnathostome primary jaw joint
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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.
Investigating the cis-regulatory functions of transposable elements
<p>This repository contains the data and code associated with the article ‘<strong><span>Multi</span></strong><strong>-</strong><strong><span>omics analysis reveals critical cis-regulatory roles of transposable elements in livestock genomes</span></strong>'</p>
Data from: The evolution of heat shock protein sequences, cis-regulatory elements, and expression profiles in the eusocial Hymenoptera
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Comprehensive dissection of cis-regulatory elements in a 2.8 Mb topologically associated domain in six human cancers
GEO Series GSE278245. Homo sapiens. 21 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other.
High-throughput discovery of post-transcriptional cis-regulatory elements
GEO Series GSE75161. Homo sapiens. 4 samples. Type: Other; Non-coding RNA profiling by high throughput sequencing.
FOXP3 Expression Depends on Cell-Type Specific Cis-Regulatory Element and Transcription Factor Circuitry [human_Tconv_ChIP-seq]
GEO Series GSE305063. Homo sapiens. 38 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Dissection of nucleosome remodeling at cis-regulatory elements in stimulated macrophages
GEO Series GSE119693. Mus musculus. 60 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other.
Cis-regulatory elements driving motor neuron-selective viral payload expression within the mammalian spinal cord
GEO Series GSE278180. Mus musculus. 10 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
FOXP3 Expression Depends on Cell-Type Specific Cis-Regulatory Element and Transcription Factor Circuitry [human_Treg_ChIP-seq]
GEO Series GSE286472. Homo sapiens. 18 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Drug-induced cis-regulatory elements in human hepatocytes affect molecular phenotypes associated with drug efficacy and adverse reactions
GEO Series GSE272109. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Effect of CRY2 stabilizer and proteasome inhibitor on the activity of cis-regulatory elements in MDA-MB-231 cells [STARR-seq]
GEO Series GSE266012. Homo sapiens. 4 samples. Type: Other.
FOXP3 Expression Depends on Cell-Type Specific Cis-Regulatory Element and Transcription Factor Circuitry
GEO Series GSE286473. Mus musculus; Homo sapiens. 95 samples. Type: Other; Genome binding/occupancy profiling by high throughput sequencing.
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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)
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DANDI Archive for NWB datasets
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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.