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6,225 results for “expression analysis”
Identification and selection of optimal reference genes for qPCR-based gene expression analysis in Fucus distichus under various abiotic stresses
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Large Scale Computational Analysis of Coding and Non-coding Element Expression in Mycobacterium tuberculosis Unannotated CDS
<p>Large Scale Computational Analysis of Coding and Non-coding Element Expression in Mycobacterium tuberculosis Unannotated CDS data for the Applied Medical Science MSci Research Project. </p>
Data from: Transcriptome analysis reveals nutrition‐ and age‐related patterns of gene expression in the fat body of pre‐overwintering bumble bee queens
<p>Many diapausing insects undergo a nutrient storage period prior to their entry into diapause. Bumble bee queens diapause as adults in the winter preceding their spring nest initiation period. Before diapause, they sequester glycogen and lipids, which they metabolize during the overwintering period. We used RNA sequencing to examine how age and nectar diet (specifically, the concentration of sucrose in nectar) impact gene expression in the pre-overwintering bumble bee queen fat body, the "liver-like" organ in insects with broad functions related to nutrient storage and metabolism. We found that diet on its own, and in combination with age, impacts the expression of genes involved in detoxification. Age was also a strong driver of gene expression, especially at earlier ages (up to 3 days). In addition to these molecular correlates of diet and age, we also found a putative molecular signature of diapause entry or preparation in adult queens in the oldest age group (12 days) fed the most sucrose-rich diet, based on comparisons between our data set and another transcriptome data set from bumble bee queens. This transcriptomic pattern suggests that preparation for (or entry into) diapause might be in part mediated by nutritional state in bumble bee queens. Collectively, these findings show that there are molecular processes in the fat body that are responsive to sucrose levels in the diet and/or associated with age-related maturational changes. A better understanding of these processes may shed light on important aspects of bumble bee biology, such as queen responses to nutritional and other forms of stress, and the factors that regulate their entrance into diapause.</p>
Transcriptome analysis of WT versus H2A.J-KO MEFs for the paper entitled: The H2A.J histone variant contributes to Interferon-Stimulated Gene expression in senescence by its weak interaction with H1 and the derepression of repeated DNA sequences
<p>Abstract for overall study:</p> <p>The histone variant H2A.J was previously shown to accumulate in senescent human fibroblasts with persistent DNA damage to promote inflammatory gene expression, but its mechanism of action was unknown. We show that H2A.J accumulation contributes to weakening the association of histone H1 to chromatin and increasing its turnover. Decreased H1 in senescence is correlated with increased expression of some repeated DNA sequences, increased expression of STAT/IRF transcription factors, and transcriptional activation of Interferon-Stimulated Genes (ISGs). The H2A.J-specific Val-11 moderates the transcriptional activity of H2A.J, and H2A.J-specific Ser-123 can be phosphorylated in response to DNA damage with potentiation of its transcriptional activity by the phospho-mimetic S123E mutation. Our work demonstrates the functional importance of H2A.J-specific residues and potential mechanisms for its function in promoting inflammatory gene expression in senescence.</p> <p>Specific description for this dataset:</p> <p>We further tested a role for H2A.J in Interferon-Stimulated Gene expression by analyzing the transcriptome of WT and H2A.J MEFs induced into senescence by etoposide. TruSeq stranded DNA libraries were prepared from polyA-selected RNA and sequenced as 43 bp paired-end reads. The fastq sequences were mapped to Gencode.vM24.transcripts.fa.gz (GRCm38 transcriptome) with salmon. Read counts were then aggregated to the gene level with tximeta, and differential gene expression was analysed with DESeq2, edgeR, and limma-voom. Gene set enrichment analysis was performed with camera.</p> <p>The transciptomes of senescent WT and H2AFJ-KO showed strong separation from proliferating MEFs, and a weaker separation distinguished WT and H2A.J-KO MEFs. Strikingly, gene set enrichment analysis indicated highly significant defects in Interferon Response Gene Expression in the H2A.J-KO MEFs in senescence with significant down-regulation in senescent H2A.J-KO cells of a series of oligoadenylate synthase genes (Oas1g, Oas1a, Oasl1, Oas2, Oasl2) and several ISGs. Thus, H2A.J also contributes to ISG expression in the heterologous context of senescent MEFs.</p>
Comparative gene expression analysis reveals mechanism of Pinus contorta response to the fungal pathogen Dothistroma septosporum
<p>Many conifers have distributions that span wide ranges in both biotic and abiotic conditions, but the basis of response to biotic stress has received much less attention than response to abiotic stress. In this study,<span> w</span>e investigated the gene expression response of lodgepole pine (<i>Pinus contorta</i>) to attack by the fungal pathogen <i>Dothistroma septosporum</i>, which causes <i>Dothistroma </i>needle blight (DNB), a disease that has caused severe climate-related outbreaks in northwestern British Columbia. We inoculated tolerant and susceptible pines with two <i>D. septosporum</i> isolates and analyzed the differentially expressed genes, differential exon usage, and co-expressed gene modules using RNA-seq data. We found a rapid and strong transcriptomic response in tolerant lodgepole pine samples inoculated with one <i>D. septosporum</i> isolate, and a late and weak response in susceptible samples inoculated with another isolate. We mapped 43 of the DEG- or gene-module-identified genes to the reference plant-pathogen interaction pathway deposited in KEGG database. These genes are present in PAMP-triggered and effector-triggered immunity pathways, including genes encoding mitogen-activated protein kinase and disease resistance protein. Genes comprising pathways and gene modules had signatures of strong selective constraint, while the highly expressed genes in tolerant samples appear to have been favored by selection to counterattack the pathogen. We identified candidate resistance genes that may respond to <i>D. septosporum</i> effectors. Taken together, our results show that gene expression response to <i>D. septosporum</i> infection in lodgepole pine varies both among tree genotypes and pathogen strains, and involves both known candidate genes and a number of genes with previously unknown functions.</p>
Data from: Quantifying the effects of ecological constraints on trait expression using novel trait-gradient analysis parameters
1. Complex processes related to biotic and abiotic forces can impose limitations to assembly and composition of plant communities. Quantifying the effects of these constraints on plant functional traits across environmental gradients, and among communities, remains challenging. We define ecological constraint (Ci) as the combined, limiting effect of biotic interactions and environmental filtering on trait expression (i.e., the mean value and range of functional traits). 2. Here we propose a set of novel parameters to quantify this constraint by extending the trait-gradient analysis (TGA) methodology. The key parameter is ecological constraint, which is dimensionless and can be measured at various scales, e.g., on population and community levels. It facilitates comparing the effects of ecological constraints on trait expressions across environmental gradients, as well as within and among communities. 3. We illustrate the implementation of the proposed parameters using the bark thickness of 14 woody species along an aridity gradient on granite outcrops in southwestern Australia. We found a positive correlation between increasing environmental stress and strength of ecological constraint on bark thickness expression. Also, plants from more stressful habitats (shrublands on shallow soils and in sun-exposed locations) displayed higher ecological constraint for bark thickness than plants in more benign habitats (woodlands on deep soils and in sheltered locations). 4. The relative ease of calculation and dimensionless nature of Ci allow it to be readily implemented at various scales and make it widely applicable. It therefore has the potential to advance the mechanistic understanding of the ecological processes shaping trait expression. Some future applications of the new parameters could be investigating the patterns of ecological constraints i) among communities from different regions, ii) on different traits across similar environmental gradients, and iii) for the same trait across different gradient-types.
Data from: Differential gene expression analysis of symbiotic and aposymbiotic Exaiptasia anemones under immune challenge with Vibrio coralliilyticus
Anthozoans are a class of Cnidarians that includes scleractinian corals, anemones and their relatives. Despite a global rise in disease epizootics impacting scleractinian corals, little is known about the immune response of this key group of invertebrates. To better characterize the anthozoan immune response, we used the model anemone Exaiptasia pallida to explore the genetic links between the anthozoan-algal symbioses and immunity in a two-factor RNA-Seq experiment using both symbiotic and aposymbiotic(menthol-bleached) Exaiptasia pallida exposed to the bacterial pathogen Vibrio coralliilyticus. Multivariate and univariate analyses of Exaiptasia gene expression demonstrated that exposure to live Vibrio coralliilyticus had strong and significant impacts on transcriptome-wide gene expression for both symbiotic and aposymbiotic anemones, but we did not observe strong interactions between symbiotic state and Vibrio exposure. There were 4,164 significantly differentially expressed (DE) genes for Vibrio exposure, 1,114 DE genes for aposymbiosis, and 472 DE genes for the additive combinations of Vibrio and aposymbiosis. KEGG enrichment analyses identified 11 pathways - involved in immunity (5), transport and catabolism (4) and cell growth and death (2) - that were enriched due to both Vibrio and/or aposymbiosis. Immune pathways showing strongest differential expression included complement, coagulation, nucleotide-binding and oligomerization domain (NOD), and Toll for Vibrio exposure and coagulation and apoptosis for aposymbiosis.
Data from: Antennal transcriptome analysis and expression profiles of odorant binding proteins in Eogystia hippophaecolus (Lepidoptera: Cossidae)
Background: Eogystia hippophaecolus (Hua et al.) (Lepidoptera: Cossidae) is the major threat to seabuckthorn plantations in China. Specific and highly efficient artificial sex pheromone traps was developed and used to control it. However, the molecular basis for the pheromone recognition is not known. So we established the antennal transcriptome of E. hippophaecolus and characterized the expression profiles of odorant binding proteins. These results establish and improve the basis knowledge of the olfactory receptive system, furthermore provide a theoretical basis for the development of new pest control method. Results: We identified 29 transcripts encoding putative odorant-binding proteins (OBPs), 18 putative chemosensory proteins (CSPs), 63 odorant receptors (ORs), 13 gustatory receptors (GRs), 12 ionotropic receptors (IRs), and two sensory neuron membrane proteins (SNMPs). Based on phylogenetic analysis, we found one Orco and three pheromone receptors of E. hippophaecolus and found that EhipGR13 detects sugar, EhipGR11 and EhipGR3 detect bitter. Nine OBPs expression profile indicated that most were the highest expression in antennae, consistent with functions of OBPs in binding and transporting odors during the antennal recognition process. OBP6 was external expressed in male genital-biased in, and this locus may be responsible for pheromone binding and recognition as well as mating. OBP1 was the highest and biased expressed in the foot and may function as identification of host plant volatiles. Conclusions: One hundred thirty-seven chemosensory proteins were identified and the accurate functions and groups of part proteins were obtained by phylogenetic analysis. The most OBPs were antenna-biased expressed, which are involved in antennal recognition. However, few OBP was detected biased expression in the foot and external genitalia, and these loci may function in pheromone recognition, mating, and the recognition of plant volatiles.
Comparative analysis of statistical methods used for detecting differential expression in label-free mass spectrometry proteomics - Data Supplement
<p>This the is Data Supplement for the article "Comparative analysis of statistical methods used for detecting differential expression in label-free mass spectrometry proteomics" submitted to the Journal of Proteomics 2015.</p>
Follow up analysis from huntingtin test expression experiments (2016/07/19)
<p>Huntingtin structure-function open lab notebook</p>
Fig. 3. Network modules for suberin-associated metabolism genes. Expression profiles for 317 in Transcriptomic analysis of wound-healing in Solanum tuberosum (potato) tubers: Evidence for a stepwise induction of suberin-associated genes
Fig. 3. Network modules for suberin-associated metabolism genes. Expression profiles for 317 wound-induced and suberin-associated genes encompassing primary carbohydrate metabolism and the formation of suberin phenolic and aliphatic monomers were subjected to WGCNA. Genes belonging to carbohydrate (C), tricarboxylic acid cycle (TCA), shikimate pathway (S), phenolic metabolism (P), phenolic assembly (PA), fatty acid biosynthesis (FAB), fatty acid modification (FAM) and aliphatic assembly (AA) are colour-coded (see legend). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Comparative analysis of differential gene expression indicates divergence in ontogenetic strategies of leaves in two conifer genera
<p><em>Juniperus flaccida</em> (drooping juniper) and <em>Pinus cembroides</em> (pinyon pine) are conifers native to North America, spanning Mexico and the Southwestern region of the United States. Although from two different lineages, both species exhibit heteroblastic growth. Morphologically, their leaves undergo a change between the juvenile and adult life stage. <em>J. flaccida</em> leaves appear needle-like at youth and scale-like at maturity, whereas the <em>P. cembroides</em> will transition from needle-like leaves to brown scale-like leaves. The objective was to perform a comparative transcriptomic analysis to quantify and examine differential expression in juvenile and adult individuals from both species. RNA from twelve samples was sequenced on HiSeq 1500 (100bp PE) and analyzed with available software. Because there are no reference genomes for these species, they were assembled<em> de novo </em>from the RNA-Seq reads. Following assembly, the coding regions were identified and redundant transcripts were removed. Quality filtered reads were aligned to the reference transcriptomes (one for each species), counts were generated from the alignment files, and differential expression analysis was performed with DESeq2 via Kallisto. Up and down-regulated genes (padj<0.1) across both age classes (juvenile vs adult) were observed in each species and compared.</p>
Time-series transcriptome analysis identified differentially expressed genes in broiler chicken infected with mixed Eimeria species
<p>Coccidiosis caused by the <em>Eimeria</em> species is a highly problematic disease in the chicken industry. Here, we used RNA sequencing to observe the time-dependent host responses of <em>Eimeria</em>-infected chickens to examine the genes and biological functions associated with immunity to the parasite. Transcriptome analysis was performed at three time points: 4, 7, and 21 days post-infection (dpi). Based on the changes in gene expression patterns, we defined three groups of genes that showed differential expression. This enabled us to capture evidence of endoplasmic reticulum stress at the initial stage of <em>Eimeria</em> infection. Furthermore, we found that innate immune responses against the parasite were activated at the first exposure; they then showed gradual normalization. Although the cytokine-cytokine receptor interaction pathway was significantly operative at 4 dpi, its downregulation led to an anti-inflammatory effect. Additionally, the construction of gene co-expression networks enabled identification of immunoregulation hub genes and critical pattern recognition receptors after <em>Eimeria</em> infection. Our results provide a detailed understanding of the host-pathogen interaction between chicken and <em>Eimeria</em>. The clusters of genes defined in this study can be utilized to improve chickens for coccidiosis control.</p>
On taming the effect of transcript level intra-condition count variation during differential expression analysis: a story of dogs, foxes and wolves: Bowtie2 counts and kallisto abundances
<p>Intra [1] and inter [2-5] study RNA-seq read datasets representing the varying brain compartments of foxes (n=24), as well as dogs (n=14) and wolves (n=6), as described in Lobo <em>et al.</em>, (2022) (under review), were mapped to the dog reference transcriptome [6], which contained 26,107 annotated transcripts (Ensembl CanFam3.1, release 92) [7], using Bowtie2 v.2.3.4.1 [8] and using kallisto v0.46.1 [9]. Count data obtained following each mapping approach for each dataset had high correlations (Lobo <em>et al.</em>, Figure S2). Bowtie2 counts were subsequently used in multiple differential analysis experiments in order to explore the effects of intra-condition count variation on the detection of differentially expressed transcripts. The individual count and abundance datasets for each corresponding RNA-seq dataset are available here.</p> <p> </p> <p>A preprint of Lobo et al., 2022, currently under review for PLOS ONE, is available [10]. The preprint however does not contain reviewer requested information on simulations as this, along with other additions including an additional author RL, has been subsequently added during the review process. These additions will be made available following review via a link to the final paper. </p> <p> </p> <p>Related software to this project are:<br> 1. <a href="http://sourceforge.net/projects/cstone/">CStone</a> <br> 2. <a href="http://sourceforge.net/projects/csreadgen/">CSReadGen</a><br> 3. <a href="https://sourceforge.net/projects/cview/">CView</a> <br> 4. <a href="https://sourceforge.net/projects/chimsim/">ChimSim</a><br> 5. <a href="https://sourceforge.net/projects/tvscript/">TVScript</a> <</p> <p> </p> <p>General details of the projects involved are available: <a href="https://cibio.up.pt/en/projects/is-hybridization-between-wolves-and-dogs-shaping-the-evolutionary-trajectory-of-wolf-populations-in-human-dominated-landscapes/">dog-wolf</a> and <a href="https://cibio.up.pt/en/projects/de-novo-based-sequence-assembly-of-next-generation-sequence-data-without-chimeras-improved-annotation-gene-expression-profiles-and-haplotype-br-reconstruction/">chimerism</a>.</p> <p> </p> <p><strong>References</strong></p> <p>1. Wang X, Pipes L, Trut L, Herbeck Y, Vladimirova A, Gulevich R, et al. Genomic responses to selection for tame/aggressive behaviors in the silver fox (Vulpes vulpes). Proc Natl Acad Sci. 2018;115: 10398–10403. doi:10.1073/pnas.1800889115</p> <p> </p> <p>2. Roy M, Kim N, Kim K, Chung WH, Achawanantakun R, Sun Y, et al. Analysis of the canine brain transcriptome with an emphasis on the hypothalamus and cerebral cortex. Mamm Genome. 2013;24: 484–499. doi:10.1007/s00335-013-9480-0</p> <p> </p> <p>3. Fushan AA, Turanov AA, Lee SG, Kim EB, Lobanov A V, Yim SH, et al. Gene expression defines natural changes in mammalian lifespan. Aging Cell. 2015;14: 352–365. doi:10.1111/acel.12283</p> <p> </p> <p>4. Hoeppner MP, Lundquist A, Pirun M, Meadows JRS, Zamani N, Johnson J, et al. An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts. PLoS One. 2014;9(3):91172. doi:10.1371/journal.pone.0091172</p> <p> </p> <p>5. Albert FW, Somel M, Carneiro M, Aximu-Petri A, Halbwax M, Thalmann O, et al. A Comparison of Brain Gene Expression Levels in Domesticated and Wild Animals. Akey JM, editor. PLoS Genet. 2012;8:e1002962. doi:10.1371/journal.pgen.1002962</p> <p> </p> <p>6. Hoeppner MP, Lundquist A, Pirun M, Meadows JRS, Zamani N, Johnson J, et al. An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts. PLoS One. 2014;9(3):91172. doi:10.1371/journal.pone.0091172</p> <p> </p> <p>7. Yates AD, Achuthan P, Akanni W, Allen J, Allen J, Alvarez-Jarreta J, et al. Ensembl 2020. Nucleic Acids Res. 2020;48: D682–D688. doi:10.1093/NAR/GKZ966</p> <p> </p> <p>8. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012. doi:10.1038/nmeth.1923</p> <p> </p> <p>9. Bray NL, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol 2016 345. 2016;34: 525–527. doi:10.1038/nbt.3519</p> <p> </p> <p>10. Lobo D, Godinho R, Archer JP. On taming the effect of transcript level intra-condition count variation during differential expression analysis: a story of dogs, foxes and wolves. bioRxiv. 2022; 2022.01.24.477470. doi:10.1101/2022.01.24.477470</p>
Gene expression data from qPCR analysis of molting relevant genes in Calanus finmarchicus utilizing double delta-Ct method
<p>Gene expression data from qPCR analysis of molting relevant genes in Calanus finmarchicus utilizing double delta-Ct method for calculations of fold change and mean fold change. </p>
Dataset for Improved differential expression analysis of miRNA-seq data by modeling competition to be counted
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Analysis of NSD3 Isoform Expression from TCGA-LUSC Data
<p><strong>SGC Open Notebook Project to Characterize the HMTase NSD3</strong></p> <p><strong>Exp028 Objective: </strong>There are two major NSD3 isoforms expressed, long (aa 1-1437) and short (aa 1-645, differing in sequence from 620-645). Importantly, the short isoform was shown to be required for the maintenance of acute myeloid leukemia (AML) [1]. This isoform lacks a SET domain and thus methyltransferase activity. It is not clear if the two isoforms are co-expressed or independently regulated. As a first attempt to study differential regulation of the two isoforms, I have used the TCGA-LUSC dataset to analyze relative expression levels in the context of squamous cell lung cancer (LUSC) [2]. </p> <p><strong>References:</strong> </p> <p>1. Shen C, Ipsaro JJ, Shi J, et al. NSD3-short is an adaptor protein that couples BRD4 to the CHD8 chromatin remodeler. Molecular cell. 2015;60(6):847-859. doi:10.1016/j.molcel.2015.10.033. <br> 2. Weinstein JN, Collisson EA, Mills GB, et al. The Cancer Genome Atlas Pan-Cancer Analysis Project. Nature genetics. 2013;45(10):1113-1120. doi:10.1038/ng.2764.</p>
Cloud motion vectors used in "Formation of the Y feature at the Venusian cloud top by planetary-scale waves and the mean circulation: analysis of Venus Express VMC images"
<p>This is dataset of cloud motion vectors deduced used in "Formation of the Y feature at the Venusian cloud top by planetary-scale waves and the mean circulation: analysis of Venus Express VMC images".</p>
Datasets for : High-resolution detection and differential expression analysis of transcription start sites using MAPCap
<p>This dataset corresponds to the study: High-resolution detection and differential expression analysis of transcription start sites using MAPCap (Bhardwaj et. al. 2018)</p> <p>It includes:</p> <p> - TSS identified using MAPCap in stage 15 embryos and larvae.</p> <p> - Differentially expressed TSS using MAPCap (FDR < 0.05) in larvae.</p> <p> - Common and stage-specific enhancer TSS identified in this study</p>
Fig. 5 in Transcriptome profiling of Symbion pandora (phylum Cycliophora): insights from a differential gene expression analysis
Fig. 5 Differential transcript expression analysis. Bar charts represent the enriched molecular functions associated with the upregulated genes in a feeding stages with Prometheus larva(e) and b feeding stages alone
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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)
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.