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4,580 results for “Gene Regulation”
Light-regulated gene expression and alternative splicing data from rice seedlings.
<p>This data contains analyzed data from the experiment conducted on rice seedlings under dark and light conditions. Seeds of rice (Oryza sativa spp. japonica cv. Nipponbare) were sown in the dark and germinated on day 2 and continued to grow in the dark for another 6 days. 3 biological replicates of the dark-grown etiolated shoots were harvested on day 8 after sowing. The remaining dark-grown seedlings were exposed to continuous white light at 120 mol/m2/sec for 48 hours or another 2 days (Days 9 and 10 after sowing). Three replicates of the light-treated green-colored seedling samples were harvested at the end of day 10. Harvested samples were frozen in liquid nitrogen and stored at -80C until further processing.</p>
Relief from nitrogen starvation entails quick unexpected down-regulation of glycolytic/lipid metabolism genes in enological Saccharomyces cerevisiae
<p>Data and code supporting the manuscript "Relief from nitrogen starvation entails quick unexpected down-regulation of glycolytic/lipid metabolism genes in enological Saccharomyces cerevisiae" by Tesnière et al. (2019) PLoS ONE 14(4): e0215870. https://doi.org/10.1371/journal.pone.0215870</p> <p>README.pdf or README.md files contain information about the files in this archive.</p>
Supplementary Data to "Disparate regulation of Smad3 phosphorylation and collagen gene transcription by full-length IL-33"
<p>These are Supplementary Figures for the article "Disparate regulation of Smad3 phosphorylation and collagen transcription by full-length IL-33"</p>
Regulation of Dye-decolorizing Peroxidases Gene Expression in Pleurotus ostreatus Grown on Glycerol as the Carbon Source
<p>This dataset contains the raw data and code necessary to reproduce the results of: Regulation of dye peroxidas gene expression in Pleurotus ostreatus grown on glycerol as the carbon source.</p> <p> </p> <p>These data are also available at github: <a href="https://github.com/JLuisCuamatzi/Pleurotus_ostreatus_CarbonSources">JLuisCuamatzi/Pleurotus_ostreatus_CarbonSources: Data and scripts to reproduce the analysis performed at Regulation of dye peroxidas gene expression in Pleurotus ostreatus grown on glycerol as the carbon source (github.com)</a></p>
Stimulating Wnt signaling reveals context-dependent genetic effects on gene regulation in primary human neural progenitors
<p>Summary statistics for chromatin accessibility and gene expression quantitative trait loci (ca/eQTLs) from Matoba, N., Le, B.D., Valone, J.M. <em>et al.</em> Stimulating Wnt signaling reveals context-dependent genetic effects on gene regulation in primary human neural progenitors. <em>Nat Neurosci</em> (2024). https://doi.org/10.1038/s41593-024-01773-6</p>
Identification of Genes Regulating Dexamethasone Resistance and Prognostic Model Development in Acute Lymphoblastic Leukemia
<p>This study investigates the mechanisms of dexamethasone resistance in acute lymphoblastic leukemia (ALL) and presents a prognostic model to predict patient outcomes and immunotherapy responses. By analyzing gene expression data, we identified autophagy-related genes associated with dexamethasone resistance, particularly focusing on STK38L’s role in modulating autophagy via ULK1. Our results reveal that high STK38L expression enhances dexamethasone resistance by promoting autophagy markers LC3II/LC3I and beclin-1. This study provides valuable insights into the molecular basis of dexamethasone resistance and highlights STK38L as a potential biomarker and therapeutic target for improving ALL treatment strategies.</p>
Direct molecular evidence for an ancient, conserved developmental toolkit controlling post-transcriptional gene regulation in land plants
<p>In plants, miRNA production is orchestrated by a suite of proteins that control transcription of the pri-miRNA gene, post-transcriptional processing and nuclear export of the mature miRNA. Post-transcriptional processing of miRNAs is controlled by a pair of physically-interacting proteins, HYL1 and DCL1. However, the evolutionary history and structural basis of the HYL1-DCL1 interaction is unknown. Here we use ancestral sequence reconstruction and functional characterization of ancestral HYL1 <em>in vitro</em> and in <em>Arabidopsis thaliana </em>to better understand the origin and evolution of the HYL1-DCL1 interaction and its impact on miRNA production and plant development. We found the ancestral plant HYL1 evolved high affinity for both double-stranded RNA (dsRNA) and its DCL1 partner before the divergence of mosses from seed plants (~500 Ma), and these high-affinity interactions remained largely conserved throughout plant evolutionary history. Structural modeling and molecular binding experiments suggest that the second of two double-stranded RNA-binding motifs (DSRMs) in HYL1 may interact tightly with the first of two C-terminal DCL1 DSRMs to mediate the HYL1-DCL1 physical interaction necessary for efficient miRNA production. Transgenic expression of the nearly 200 Ma-old ancestral flowering-plant HYL1 in <em>A. thaliana</em> was sufficient to rescue many key aspects of plant development disrupted by HYL1<sup>-</sup> knockout and restored near-native miRNA production, suggesting that the functional partnership of HYL1-DCL1 originated very early in and was strongly conserved throughout the evolutionary history of terrestrial plants. Overall, our results are consistent with a model in which miRNA-based gene regulation evolved as part of a conserved plant ‘developmental toolkit’.</p>
Riboswitch-inspired toehold riboregulators for gene regulation in Escherichia coli
<p>This dataset comprises flow cytometry data accompanying a publication on the development of synthetic riboregulators.</p> <p>These riboregulators were inspired by the architecture of naturally occurring riboswitches and toehold-mediated strand displacement. Specifically, we adopt the toehold switch hairpin and inserted regulatory sequences within the loop region of which accessibility can be controlled by toehold-mediated strand displacement. We utilized this design principle to develop toehold translation repressor and toehold transcriptional repressor, which regulate mCherry expression in <em>E. coli </em>in translational and transcriptional levels with certain ON/OFF ratios. Furthermore, we combined these two riboregulators and developed them into a NOR gate switch that can regulate downstream GFP expression in <em>E. coli </em>with different input conditions of trigger RNA. We used flow cytometry to quantify the expression level of the NOR gate switch under different inputs.</p>
Chromatin activity identifies differential gene regulation across human ancestries
<p>This repository contains data related to:</p> <p>Chromatin activity identifies differential gene regulation across human ancestries</p> <p>Kade P. Pettie, Maxwell Mumbach, Amanda J. Lea, Julien Ayroles, Howard Y. Chang, Maya Kasowski, Hunter B. Fraser</p> <p> </p>
Dataset related to article "TNF-Stimulated Gene-6 Is a Key Regulator in Switching Stemness and Biological Properties of Mesenchymal Stem Cells."
<p>Mesenchymal stem cells (MSCs) are well established to have promising therapeutic properties. TNF-stimulated gene-6 (TSG-6), a potent tissue-protective and anti-inflammatory factor, has been demonstrated to be responsible for a significant part of the tissue-protecting properties mediated by MSCs. Nevertheless, current knowledge about the biological function of TSG-6 in MSCs is limited. Here, we demonstrated that TSG-6 is a crucial factor that influences many functional properties of MSCs. The transcriptomic sequencing analysis of wild-type (WT) and TSG-6<sup>-/-</sup> -MSCs shows that the loss of TSG-6 expression leads to the perturbation of several transcription factors, cytokines, and other key biological pathways. TSG-6<sup>-/-</sup> -MSCs appeared morphologically different with dissimilar cytoskeleton organization, significantly reduced size of extracellular vesicles, decreased cell proliferative rate, and loss of differentiation abilities compared with the WT cells. These cellular effects may be due to TSG-6-mediated changes in the extracellular matrix (ECM) environment. The supplementation of ECM with exogenous TSG-6, in fact, rescued cell proliferation and changes in morphology. Importantly, TSG-6-deficient MSCs displayed an increased capacity to release interleukin-6 conferring pro-inflammatory and pro-tumorigenic properties to the MSCs. Overall, our data provide strong evidence that TSG-6 is crucial for the maintenance of stemness and other biological properties of murine MSCs.</p> <p> </p> <p>Some dataset of this research are in prism format, to ensure open access we attach a pdf instruction about this format and a link where downoladed it</p>
# Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer's disease
<p>Dysregulation of gene expression in Alzheimer’s disease (AD) remains elusive, especially at the cell type level. Gene regulatory network, a key molecular mechanism linking transcription factors (TFs) and regulatory elements to govern target gene expression, can change across cell types in the human brain and thus serve as a model for studying gene dysregulation in AD. However, it is still challenging to understand how cell type networks work abnormally under AD. To address this, we integrated single-cell multi-omics data and predicted the gene regulatory networks in AD and control for four major cell types, excitatory and inhibitory neurons, microglia and oligodendrocytes. Importantly, we applied network biology approaches to analyze the changes of network characteristics across these cell types, and between AD and control. For instance, many hub TFs target different genes between AD and control (rewiring). Also, these networks show strong hierarchical structures in which top TFs (master regulators) are largely common across cell types, whereas different TFs operate at the middle levels in some cell types (e.g., microglia). The regulatory logics of enriched network motifs (e.g., feed-forward loops) further uncover cell type-specific TF-TF cooperativities in gene regulation. The cell type networks are highly modular and several network modules with cell-type-specific expression changes in AD pathology are enriched with AD-risk genes and putative targets of approved and pending AD drugs, suggesting possible cell-type genomic medicine in AD. Finally, using the cell type gene regulatory networks, we developed machine learning models to classify and prioritize additional AD genes. We found that top prioritized genes predict clinical phenotypes (e.g., cognitive impairment) with reasonable accuracy. Overall, this single-cell network biology analysis provides a comprehensive map linking genes, regulatory networks, cell types and drug targets and reveals dysregulated cell type gene dysregulatory mechanisms in AD.</p>
Summary Statistics from "Genetically regulated gene expression and proteins revealed discordant effects" (LWAS of biomarker)
<p>Summary statistics of 92 blood protein levels. The corresponding publication is currently under revision.</p> <p> The zipped txt file is tab-delimited and contains the following columns:</p> <ul> <li>protein: protein name abbreviation</li> <li>cytoband: genomic region</li> <li>gene: gene name abbreviation</li> <li>setting: either "combined" (adj. for sex & age) or sex-stratified ("males", "females"; adj. for age)</li> <li>variant_id_hg19: SNP ID according to hg19</li> <li>variant_id_hg38: SNP ID according to hg19</li> <li>chr: chromosome</li> <li>pos_hg19: base position according to hg19</li> <li>pos_hg38: base position according to hg19</li> <li>effect_allele: also known as counted allele in additive model</li> <li>other_allele: not-counted allele</li> <li>eaf: effect allele frequency</li> <li>maf: minor allele frequency</li> <li>info: imputation info score</li> <li>n_samples: number of samples</li> <li>beta: effect estimate</li> <li>se: standard error</li> <li>zscore: Z-statistic</li> <li>pvalue: p-value</li> <li>FDR: FDR by gene and setting</li> <li>BBFDR: hierarchical FDR by setting</li> <li>hierFDR: TRUE if SNP is significant after hierarchical FDR</li> </ul>
The yellow gene regulates behavioral plasticity by repressing male courtship in Bicyclus anynana butterflies
<p>Seasonal plasticity in male courtship in Bicyclus anynana butterflies is due to variation in levels of the steroid hormone 20E (20-hydroxyecdysone) during pupation. Wet season (WS) males have high levels of 20E and become active courters. Dry season (DS) males, have lower levels of 20E and reduced courtship rates, although WS courtship rates can be achieved if DS male pupae are injected with 20E at 30% of pupation. Here we investigated the genes involved in male courtship plasticity and examine whether 20E plays an organizational role in the pupal brain that later influences the sexual behaviour of adults. We show that DS pupal brains have a 7-fold upregulation of the yellow gene relative to the WS and that knocking out yellow leads to increased male courtship. We find that injecting 20E into DS pupa reduced yellow expression although not significantly. Our results show that yellow is a repressor of the neural circuity for male courtship behaviour in B. anynana. 20E levels experienced during pupation could play an organizational role during pupal brain development by regulating yellow expression, however, other factors might also be involved. Our findings are in striking contrast to Drosophila where yellow is required for male courtship.</p>
Data from: The roles of growth regulation and appendage patterning genes in the morphogenesis of treehopper pronota
<p>Treehoppers of the insect family Membracidae have evolved enlarged and elaborate pronotal structures, which is hypothesized to involve co-opted expression of genes that are shared with the wings. Here, we investigate the similarity between the pronotum and wings in relation to growth. We show that the ontogenetic allometry of the pronotum is similar to that of wings in Membracidae, but not the outgroup. Using transcriptomics, we find genes related to protein synthesis and translation are mutually upregulated. These genes are implicated in the eIF2, eIF4/p70S6K, and mTOR pathways, and have known roles in regulating cell growth and proliferation. We show that species-specific differential growth patterning of the pronotum begins as early as the third instar. This finding suggests that co-option of appendage patterning genes must occur before the metamorphic molt. We propose that a network related to growth and size determination is the more likely mechanism shared with wings. However, regulators upstream of the shared genes in the pronotum and wings need to be elucidated to substantiate whether co-option has occurred. Finally, we<span> believe it will be helpful to distinguish the mechanisms leading to pronotal size from those regulating pronotal shape as we make sense of this spectacular evolutionary innovation. </span></p>
Genes regulated by CARTp/GPR160 in the dorsal horn of the spinal cord
<p><span>Analysis of the dorsal horn spinal cord (DH-SC) after an intrathecal injection of CARTp or CARTp with a neutralizing GPR160 antibody after 1hr. Results provide insight into genes regulated by CARTp/GPR160-induced behavioral hypersensitivities in the DH-SC.</span></p>
Identification and characterization of ATOH7-regulated target genes and pathways in human neuroretinal development
<p>The files presented here represent the original data collected during the study presented in the Cells (MDPI) publication "Identification and characterization of ATOH7-regulated target genes and pathways in human neuroretinal development" (<a href="https://doi.org/10.3390/cells13131142">https://doi.org/10.3390/cells13131142</a>). The data include:</p> <ul> <li>scRNA sequencing data (matrix, features and barcodes)</li> <li>RNA sequencing data (fastq)</li> <li>CUT&RUN sequencing data (raw data: fastq; coverage: bigWig)</li> <li>RNA sequencing alignments, with custom built reference (RNA_alignments)</li> </ul>
Bidirectional Regulation of Motor Circuits Using Magnetogenetic Gene Therapy
<p><span>Here we report a novel suite of magnetogenetic tools, based on a single anti-ferritin nanobody-TRPV1 receptor fusion protein, which regulated neuronal activity when exposed to magnetic fields. AAV-mediated delivery of a floxed nanobody-TRPV1 into the striatum of adenosine 2a receptor-cre driver mice resulted in motor freezing when placed in an MRI or adjacent to a transcranial magnetic stimulation (TMS) device. Functional imaging and fiber photometry both confirmed activation of the target region in response to the magnetic fields. Expression of the same construct in the striatum of wild-type mice along with a second injection of an AAVretro expressing cre into the globus pallidus led to similar circuit specificity and motor responses. Finally, a mutation was generated to gate chloride and inhibit neuronal activity. Expression of this variant in subthalamic nucleus in PitX2-cre parkinsonian mice resulted in reduced local c-fos expression and motor rotational behavior. These data demonstrate that magnetogenetic constructs can bidirectionally regulate activity of specific neuronal circuits non-invasively <em>in-vivo</em> using clinically available devices.</span></p>
RNA-seq data of "Transcriptome analyses of leaves reveal that hexanoic acid priming differentially regulate gene expression in contrasting Coffea arabica cultivars"
<p>This dataset represent FASTQ gziped files from the study "Transcriptome analyses of leaves reveal that hexanoic acid priming differentially regulate gene expression in contrasting <em>Coffea arabica</em> cultivars" (<a href="https://doi.org/10.3389/fsufs.2021.735893">https://doi.org/10.3389/fsufs.2021.735893</a>). Sequencing was done using an Illumina Novaseq 6000 instrument, paired-sequencing (2 X150 bp). Sample details are also available at https://www.ebi.ac.uk/ena/browser/view/ERA6282544.</p> <p> </p> <p>All filenames have the following naming scheme:</p> <p>LCS7609_DS_AAA_leafBBB_(R1 or R2).fq.gz</p> <p>AAA stands for the abbreviations:</p> <p>- CC (Coffea arabica cv Catuai control)</p> <p>- CHx (Coffea arabica cv Catuai exposed to Hexanoic acid)</p> <p>- OC (Coffea arabica cv Obatã control)</p> <p>- OHx (Coffea arabica cv Obatã exposed to Hexanoic acid)</p> <p>BBB stands for the number of biological replicate (1, 2 or 3).</p> <p> </p> <p> </p> <p> </p>
Chromosome-scale genome assembly and insights into the metabolome and gene regulation of leaf color transition in an important oak species, Quercus dentata
<p><em>Quercus dentata</em> Thunb., a dominant forest tree species in northern China, has significant ecological and ornamental value due to its adaptability and beautiful autumn coloration, with color changes from green to yellow into red resulting from the autumnal shifts in leaf pigmentation. However, the key genes and molecular regulatory mechanisms for leaf color transition remain to be investigated. First, we presented a high-quality chromosome-scale assembly for <em>Q. dentata</em>. This 893.54 Mb sized genome (contig N50=4.21 Mb, scaffold N50=75.55 Mb; 2n=24) harbors 31,584 protein-coding genes. Second, our metabolome analyses uncovered pelargonidin-3-O-glucoside, cyanidin-3-O-arabinoside, and cyanidin-3-O-glucoside as the main pigments involved in leaf color transition. Third, gene co-expression further identified the MYB-bHLH-WD40 (MBW) transcription activation complex as central to anthocyanin biosynthesis regulation. Notably, transcription factor (TF) <em>QdNAC </em>(<em>QD08G038820</em>) was highly co-expressed with this MBW complex and may regulate anthocyanin accumulation and chlorophyll degradation during leaf senescence through direct interaction with another TF, <em>QdMYB </em>(<em>QD01G020890</em>), as revealed by our further protein-protein and DNA-protein interaction assays. Our high-quality genome assembly, metabolome and transcriptome resources further enrich <em>Quercus </em>genomics, and will facilitate upcoming exploration of ornamental values and environmental adaptability in this important genus.</p>
Data from: Extensive, transient, and long-lasting gene regulation in a song-controlling brain area during testosterone-induced song development in adult female canaries
<p>Like other canary reproductive behaviors, song production occurs seasonally and can be triggered by gonadal hormones. Adult female canaries treated with testosterone sing first songs after four days and progressively develop towards typical canary song structure over several weeks, a behavior that females otherwise rarely or never show. We compared gene regulatory networks in the song-controlling brain area HVC after 1 hour (h), 3 h, 8 h, 3 days (d), 7d, and 14d testosterone treatment with placebo-treated control females, paralleling HVC and song development. Rapid onset (1 h or less) of extensive transcriptional changes (2,700 genes) preceded the onset of song production by four days. The highest level of differential gene expression occurred at 14 days when song structure was most elaborate, and song activity was highest. The transcriptomes changed massively several times during the two-week of song production. A total of 9,710 genes were differentially expressed, corresponding to about 60% of the known protein-coding genes of the canary genome. Most (99%) of the differentially expressed genes were regulated only at specific stages. The differentially expressed genes were associated with diverse biological functions, of which cellular level occurring early and nervous system level occurring primarily after prolonged testosterone treatment. Thus, the development of adult songs requires restructuring the entire HVC, including most HVC cell types, rather than altering only neuronal subpopulations or cellular components. Parallel regulation directly by androgen and estrogen receptors and by other hub genes such as the transcription factor SP8, which are under steroidogenic control, lead to massive transcriptomic and neural changes in the specific behavior-controlling brain areas and gradual seasonal occurrence of singing behavior.</p>
ScienceDex guides
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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.