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29,889 results for “Gene expression”
Exploring the utility of regulatory network-based machine learning for gene expression prediction in maize
<p>Relevant Data and Code for <em>Exploring the utility of regulatory network-based machine learning for gene expression prediction in maize </em>by Taylor Ferebee and Edward Buckler.</p> <p><strong>Input Data</strong></p> <p>The inputs of the models are enclosed in <em>Input_data-2022-001.zip</em></p> <p><strong>Output Data</strong></p> <p>The outputs of the models are enclosed in <em>Output_Results-2022-001.zip</em></p> <p><strong>Relevant Code </strong></p> <p>The code for all analyses is enclosed in <em>Code_Archive.zip </em></p>
Spatio-temporal, optogenetic control of gene expression in organoids
<p>Organoids derived from stem cells become increasingly important to study human development and to model disease. However, methods are needed to control and study spatio-temporal patterns of gene expression in organoids. To this aim, we combined optogenetics and gene perturbation technologies to activate or knock-down RNA of target genes, at single-cell resolution and in programmable spatio-temporal patterns. To illustrate the usefulness of our approach, we locally activated Sonic Hedgehog (<em>SHH</em>) signaling in an organoid model for human neurodevelopment. High-resolution spatial transcriptomic and single-cell analyses showed that this local induction was sufficient to generate stereotypically patterned organoids in three dimensions and revealed new insights into <em>SHH</em>’s contribution to gene regulation in neurodevelopment.</p> <p>With this study, we propose optogenetic perturbations in combination with spatial transcriptomics as a powerful technology to reprogram and study cell fates and tissue patterning in organoids.</p>
Gene expression dataset of the Spatially Resolved Single-cell Translatomics at Molecular Resolution
<p>Here are the gene expression datasets of RIBOmap included in "<strong>Spatially Resolved Single-cell Translatomics at Molecular Resolution</strong>" from Zeng et al. Please refer to the README file for more detailed information. </p> <p> </p> <p><strong>Abstract</strong></p> <p>The precise control of mRNA translation is a crucial step in post-transcriptional gene regulation of cellular physiology. However, it remains a major challenge to systematically study mRNA translation at the transcriptomic scale with spatial and single-cell resolution. Here, we report the development of RIBOmap, a three-dimensional (3D) in situ profiling method to detect mRNA translation of thousands of genes simultaneously in intact cells and tissues. By applying RIBOmap to 981 genes in HeLa cells, we revealed a remarkable dependency of translation on cell-cycle stages and subcellular localization. Furthermore, we profiled single-cell translatomes of 5,413 genes in adult mouse brain tissues yielding a spatial cell atlas of 119,173 cells. The pairwise spatial mapping of single-cell translatome and transcriptome in two adjacent mouse brain slices revealed cell-type and brain-region-dependent translational regulation and suggested a translation remodeling during oligodendrocyte lineage maturation. The spatial translatome profiling detected widespread patterns of localized translation in neuronal and glial cells in intact brain tissue networks. Together, RIBOmap presents the first spatially resolved single-cell translatomics technology, accelerating our understanding of protein synthesis in the context of subcellular architecture, cell types, and tissue anatomy.</p>
Ivy Gap GBM Gene Expression
<p><strong>Abstract:</strong></p> <p>The Ivy Glioblastoma Atlas Project represents a fundamental tool for investigating the cellular and molecular underpinnings of glioblastoma. It offers an accessible online atlas and database containing valuable clinical and genomic information, which will undoubtedly facilitate future studies on glioblastoma pathogenesis, diagnosis, and therapeutic approaches. Glioblastoma is a highly aggressive brain tumor with a bleak prognosis, and its intricate molecular and cellular characteristics have not been fully elucidated in relation to conventional diagnostic histologic features. The dataset provided is comprised of gene expression values for each sample and gene. </p> <p><strong>Inspiration:</strong></p> <p>This dataset was uploaded to UBRITE for GTKB project. </p> <p><strong>Acknowledgments:</strong></p> <p>Puchalski RB, Shah N, Miller J, et al. An anatomic transcriptional atlas of human glioblastoma. Science. 2018;360(6389):660-663. doi:10.1126/science.aaf2666</p> <p><strong>U-BRITE last update: </strong>07/28/2023</p> <p> </p>
Alliance of Genome Resources Gene Expression Data
<p>Tab separated formatted spreadsheets of gene expression annotations from the Alliance of Genome Resources. Gene expression data include temporal and/or spatial localization of transcripts and proteins in a wild-type background.</p> <p>File includes annotations for the following organisms:</p> <ul> <li>Caenorhabditis elegans (nematode; NCBI:txid 6239)</li> <li>Danio rerio (zebrafish;NCBI:txid 7955)</li> <li>Drosophila melanogaster (fruit fly; NCBI:txid 7227)</li> <li>Mus musculus (mouse; NCBI:txid10090)</li> <li>Rattus norvegicus (rat; NCBI:txid 10116)</li> <li>Saccharomyces cerevisiae (yeast; NCBI:txid 559292)</li> <li>Xenopus laevis (African clawed frog; NCBI:txid 8355)</li> <li>Xenopus tropicalis (Western clawed frog; NCBI:txid 8364)</li> </ul>
Visual opsin gene expression evolution in the adaptive radiation of cichlid fishes of Lake Tanganyika
<p>Tuning the visual sensory system to the ambient light is essential for survival in many animal species. This is often achieved through duplication, functional diversification, and/or differential expression of visual opsin genes. Here, we examined 753 new retinal transcriptomes from 112 species of cichlid fishes from Lake Tanganyika to unravel adaptive changes in gene expression at the macro-evolutionary and ecosystem level of one of the largest vertebrate adaptive radiations. We found that, across the radiation, all seven cone opsins – but not the rhodopsin – rank among the most differentially expressed genes in the retina, together with other vision-, circadian-rhythm-, and haemoglobin-related genes. We propose two new visual palettes characteristic of very shallow- and deep-water living species, respectively, and show that visual system adaptations along two major ecological axes, macro-habitat and diet, occur primarily via gene expression variation in a subset of cone opsin genes.</p>
Results of the differential gene expression analysis in SIV infection in Chlorocebus sabaeus and Macaca mulatta
<p>Results of differential gene expression analysis in SIV infection in Chlorocebus sabaeus and Macaca mulatta.</p> <p>From the transcriptome data repository MACE (http://mace.ihes.fr)</p>
Transcriptome analysis of anuran breeding glands reveals a surprisingly high expression and diversity of NNMT-like genes
<p><strong>Abstract</strong></p> <p>In many amphibians, males have sexually dimorphic breeding glands, which can produce proteinaceous or volatile pheromones, used for intraspecific communication. In this study we analyse two types of glands in the Mexican treefrog species <em>Ptychohyla macrotympanum </em>(Hylidae) – large ventrolateral glands and small nuptial pads on their fingers – using histology, whole-transcriptome sequencing and phylogenetic analyses. We found strong differences in glandular tissue composition and gene expression patterns between the two breeding gland types. In both glands we only found low expression of protein pheromone candidates. Instead, in the ventrolateral glands, gene expression was strikingly dominated by nicotinamide N-methyltransferase (NNMT)-like genes. Diversity of these genes was remarkably high, with at least 68 distinct NNMT-like genes. Our phylogenetic comparative analysis of the diversity of NNMT-like genes across vertebrates indicates that the extreme diversity of this gene is largely a frog-specific phenomenon and can be traced to large numbers of relatively recent gene duplications occurring independently in many lineages. The strong dominance and astonishing diversity of NNMT-like genes found in anurans in general, and in their sexually dimorphic breeding glands specifically, suggests an important function of NNMT-like proteins for anuran reproduction, possibly being related to volatile pheromone production.In many amphibians, males have sexually dimorphic breeding glands, which can produce proteinaceous or volatile pheromones, used for intraspecific communication. In this study we analyse two types of glands in the Mexican treefrog species <em>Ptychohyla macrotympanum </em>(Hylidae) – large ventrolateral glands and small nuptial pads on their fingers – using histology, whole-transcriptome sequencing and phylogenetic analyses. We found strong differences in glandular tissue composition and gene expression patterns between the two breeding gland types. In both glands we only found low expression of protein pheromone candidates. Instead, in the ventrolateral glands, gene expression was strikingly dominated by nicotinamide N-methyltransferase (NNMT)-like genes. Diversity of these genes was remarkably high, with at least 68 distinct NNMT-like genes. Our phylogenetic comparative analysis of the diversity of NNMT-like genes across vertebrates indicates that the extreme diversity of this gene is largely a frog-specific phenomenon and can be traced to large numbers of relatively recent gene duplications occurring independently in many lineages. The strong dominance and astonishing diversity of NNMT-like genes found in anurans in general, and in their sexually dimorphic breeding glands specifically, suggests an important function of NNMT-like proteins for anuran reproduction, possibly being related to volatile pheromone production.</p> <p> </p> <p><strong>Supplementary datasets accompanying the paper:</strong></p> <p>- final RNAseq assemblies of the ventrolateral glands and the nuptial pads of <em>Ptychohyla macrotympanum</em><br> - fasta-file of all <em>Ptychohyla</em>-NNMT-like genes found in this study</p>
Synthetic gene expression data with underlying gene network
<p>This is the synthetic gene expression data along with the underlying gene network used in the simulation studies of Hu and Szymczak (2023) for evaluating network-guided random forest.</p> <p>In this dataset we consider the situation of 1000 genes and 1000 samples each for training and testing sets. Each file contains a list of 100 replications of the considered scenario which can be identified via the file name. In particular, we consider 6 different scenarios depending on the number of disease modules and how are the effects of disease genes distributed within the disease module. When there are disease genes, we also consider 3 different levels of effect sizes. The binary responses are then generated via a logistic regression model. More details on these scenarios and the data generation mechanism can be found in Hu and Szymczak (2023).</p> <p>The data is generated by the function <em>gen_data</em> in R package <em>networkRF</em> which can be accessed at https://github.com/imbs-hl/networkRF. To obtain the datasets with 3000 genes, which is the other part of the data used in the simulation studies of Hu and Szymczak (2023), simply modify the <em>num.var</em> argument of the function <em>gen_data.</em> More descriptions on the implementation and the format of the output can be found in the help page of the R package.</p>
Differentially-expressed genes in blood in response to lipopolysaccharide in three rodent species
<p>Infection tolerance in rodents was examined by injecting single-dose lipopolysaccharide (LPS) to induce inflammation in <span><em>Peromyscus</em> <em>leucopus</em></span><span> (LL stock), the white-footed deermouse also reservoir for Lyme disease and </span><span><em>Mus</em> <em>musculus</em></span><span> (outbred CD-1 breed), the house mouse, and </span><span><em>Rattus</em> <em>norvegicus</em></span><span>, the brown rat (Fischer strain). Reaction to LPS was analyzed in the blood of challenged rodents and compared to control animals. As natural reservoirs of zoonoses deermice show significant anti-inflammatory response as described in "An Infection-Tolerant Mammalian Reservoir for Several Zoonotic Agents Broadly Counters the Inflammatory Effects of Endotoxin" (</span><a href="https://doi.org/10.1128/mBio.00588-21)" rel="noopener"><span>https://doi.org/10.1128/mBio.00588-21)</span></a><span>. The project and the description of the samples are described under the following NCBI BioProjects: PRJNA975149 (</span><a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA975149" rel="noopener"><span>https://www.ncbi.nlm.nih.gov/bioproject/PRJNA975149)</span></a><span> for mouse and deermouse and PRJNA973677 (</span><a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA973677)" rel="noopener"><span>https://www.ncbi.nlm.nih.gov/bioproject/PRJNA973677)</span></a><span>. This project is a follow-up project focusing on the transcriptomic analysis of the whole blood bulk RNA-seq and further analysis of differentially expressed genes (DEG) between the treatment arm and controls. Complete fold change and false discovery rate for all three rodent species used for the current Dryad set are previously published (<a href="https://doi.org/10.7280/D1470Z">https://doi.org/10.7280/D1470Z</a>). Here we report that deermice tolerance to infection is partly due to lower expression of interferon-gamma in comparison to mice and rats. <br></span></p>
Inter-generational nuclear crosstalk links the control of gene expression to programmed genome rearrangements during the Paramecium sexual cycle
<p>Multinucleate cells are found in many eukaryotes, but how multiple nuclei coordinate their functions is still poorly understood. In the cytoplasm of the ciliate <em>Paramecium tetraurelia</em>, two micronuclei (MIC) serving sexual reproduction coexist with a somatic macronucleus (MAC) dedicated to gene expression. During sexual processes, the MAC is progressively destroyed while still ensuring transcription and new MACs develop from copies of the zygotic MIC. Several gene clusters are successively induced and switched off before vegetative growth resumes. Concomitantly, programmed genome rearrangements (PGR) remove transposons and their relics from the new MACs. Development of the new MACs is controlled by the old MAC, since the latter expresses genes involved in PGR, including the <em>PGM</em> gene encoding the essential PiggyMac endonuclease that cleaves the ends of eliminated sequences. Using RNA deep sequencing and transcriptome analysis, we show that impairing PGR up-deregulates key PGR genes, together with ~600 other genes possibly also involved in PGR. Among these genes, 42% are no longer induced when no new MACs are formed, including 180 genes that are co-expressed with <em>PGM </em>under all tested conditions. We propose that bi-directional crosstalk between the two coexisting generations of MACs links gene expression to the progression of MAC development.</p>
Spectral decomposition coefficients for spatiotemporal gene expression pattern identification in Bacillus subtilis swarm development
<p>Spectral decomposition coefficients, spatiotemporal gene expression pattern identification and multidimensional scaling coordinates of spatiotemporal transcriptomics data and image analysis results used to create Figure 2 in the scientific article "Simultaneous spatiotemporal transcriptomics and microscopy of <em>Bacillus subtilis</em> swarm development reveal cooperation across generations" by the following authors: Hannah Jeckel*, Kazuki Nosho*, Konstantin Neuhaus, Alasdair D. Hastewell, Dominic J. Skinner, Dibya Saha, Niklas Netter, Nicole Paczia, Jörn Dunkel, Knut Drescher. The symbol "*" indicates an equal contribution.</p> <p>This data consists of two excel sheets, one for the transcriptomics data and one for image analysis results (physical properties).</p> <p>Genes were ranked according to a spatiotemporal information score defined in the publication described above. For each gene, its name and ID (derived from locus tag) are given as identifiers. For information of reference genome used for mapping and convention on how gene names are chosen, see <a href="https://drescherlab.org/data/swarm-transcriptome/">https://drescherlab.org/data/swarm-transcriptome/</a>. Other columns in the sheet represent the spatiotemporal information score, assigned spatiotemporal pattern number, decomposition coefficient, multidimensional scaling coordinates and gene function.</p> <p>Physical properties are measured from short microscopy videos and defined in the publication mentioned above. This excel sheet contains property name, spatiotemporal information score, spectral decomposition coefficients and multidimensional scaling coordinates.</p>
Codeletion of 1p and 19q determines distinct gene methylation and expression profiles in IDH-mutated oligodendroglial tumors _ Dataset
<p>Overall design: Genome-wide DNA methylation profiling of oligodendroglial tumors (OTs) and five non tumoral brain tissue (NTBT) samples. The Illumina Infinium Human DNA methylation 450k Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in tumoral samples. Samples included 46 OTs and 5 NTBT.</p> <p>Bisulphite converted DNA from the 51 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip</p> <p>Extracted molecule: genomic DNA</p> <p>Platform: Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)</p> <p>Label protocol: Standard Illumina Protocol</p> <p>Hybridization protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol</p> <p>Scan protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting </p> <p>Data processing: BeadStudio software v3.2</p> <p>Data format: IDAT files</p>
RNA-seq based analysis of gene expression in thyroids of wild-type and Keap1 knockdown mice after exposure to excess iodide.
<p>C57BL/6J Keap1flox/flox mice were developed by Prof. Masayuki Yamamoto (DOI: 10.1016/j.bbrc.2005.10.185). These mice express lower levels of Keap1 because of the loxP site insertions (DOI: 10.1128/MCB.01591-09) and are designated as Keap1KD. 3-4 months old WT and Keap1KD mice fed a standard diet (KLIBA NAFAG 3242, Switzerland) containing 1.5 mg/kg sodium iodine were given normal tap water with or without 0.05% sodium iodide (Sigma, St Louis, MO, USA) for 7 days. Hence, the following groups of mice were included:</p> <p>WT mice on control water (n=8)-designated as wt in the file</p> <p>WT mice exposed to excess iodide (WT-IOD, n=6)- designated as wti in the file</p> <p>Keap1KD mice on control water (n=8)- designated as kp in the file</p> <p> and Keap1KD mice exposed to excess iodide (Keap1KD-IOD, n=6)- designated as kpI in the file. </p> <p> Mice were maintained in the animal facility of the Department of Physiology at the University of Lausanne in temperature-, light-, and humidity-controlled rooms with a 12-hour light/dark cycle. All animal procedures were in accordance with Swiss legislature and the study was approved by the Canton of Vaud SCAV.</p> <p>RNA from individual mouse thyroids was prepared as previously described (DOI: 10.1007/978-1-4939-3756-1_25) and was submitted to Alithea Genomics (Switzerland). The bulk RNA barcoding and sequencing (BRB-seq) libraries were generated and sequenced as described previously (DOI: 10.1186/s13059-019-1671-x) to a depth of approximately 1.2 million raw reads per sample.</p> <p>This research was funded by the Swiss National Science Foundation Research Grants 310030_212558, IZCOZ0_205415 and IZCOZ0_177070</p> <p></p> <p></p>
Lineage-resolved analysis of embryonic gene expression evolution in C. elegans and C. briggsae
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Data from: Gene network topology drives the mutational landscape of gene expression
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R code for differential gene expression and enrichment analyses
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Data from: Fungal symbionts generate water-saver and water-spender plant drought strategies via diverse effects on host gene expression
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RNAseq analysis of gene counts and expression levels in diabetic foot ulcers
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Data from: Cell type-specific dysregulation of gene expression due to Chd8 haploinsufficiency during mouse cortical development
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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.