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54,099 results for “Expression”
Biogeographic parallels in thermal tolerance and gene expression variation under temperature stress in a widespread bumble bee
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Data for: Weaker selection on genes with treatment-specific expression consistent with a limit on plasticity evolution in Arabidopsis thaliana
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Medial amygdala ERα expression influences monogamous behavior of male prairie voles in the field
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Differentially-expressed genes in blood in response to lipopolysaccharide in three rodent species
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On the cross-population generalizability of gene expression prediction models
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Co-exposure of uranyl acetate and sodium arsenite differentially alters gene expression in CD3/CD28 activated CD4+ T-cells.
Communities in the western region of the United States experience environmental exposure to metal mixtures from living in proximity to numerous unremediated abandoned uranium mines. Metals including arsenic and uranium co-occur in and around these sites at levels higher than the United States Environmental Protection Agency maximum contaminant levels. To address the potential effect of these metals on the activation of CD4+ T-cells, we used RNA sequencing methods to determine the effect of exposure to uranyl acetate, sodium arsenite or a mixture of uranyl acetate and sodium arsenite. Oxidative stress is a mechanism proposed for metal toxicity, but findings for uranium differ across cell models. No significant changes in oxidative stress genes were detected for uranyl acetate, in contrast to sodium arsenite. Sodium arsenite induced a dose dependent effect on activation associated gene expression, targeting immune response genes at the lower dose. While uranyl acetate alone did not significantly alter activation associated gene expression, the mixture demonstrated a combined effect relative to sodium arsenite alone. The results demonstrate the need to investigate uranium alone and in metalloid mixtures at environmentally relevant concentrations to better understand the toxicological impact of these mixtures on T-cell activation, function and immune dysregulation.
Raw microarray gene expression datasets included in the eQTL Catalogue
<p>Raw microarray intensity values for five datasets:</p> <ul> <li>CEDAR</li> <li>Fairfax_2012</li> <li>Fairfax_2014</li> <li>Naranbhai_2015</li> <li>Kasela_2017</li> </ul>
Rare and common genetic variations in the Keap1/Nrf2 antioxidant response pathway impact thyroglobulin gene expression and circulating levels, respectively
<p>This is about publication PMID: 31421134, DOI: 10.1016/j.bcp.2019.08.007</p> <p>Each book in the excel file indicates the figure number it refers to.</p> <p>The file is about the relative luciferase units used in Figure 2 of main paper. </p> <p>Values are relative to WT1_C relative luciferase units <br> </p>
Expression and solubility test of SETDB1 catalytic domain constructs
<p>Here, we designed four constructs for SETDB1 catalytic domain for insect cell expression systems. This section includes expression test results of different fragments of SETDB1.</p>
Generating an expression matrix for droplet single-cell RNA-seq (dscRNA-seq) data
<p>This tutorial is adapted from the 'Generating an expression matrix' training session at the EBI (https://www.ebi.ac.uk/training/events/2019/single-cell-rna-seq-analysis-questions-clusters).</p>
Stochastic pulsing of gene expression enables the generation of spatial patterns in Bacillus subtilis biofilms
<p>Data extracted from confocal microscopy associated with the paper "Stochastic pulsing of gene expression enables the generation of spatial patterns in Bacillus subtilis biofilms"</p> <p>Stochastic pulsing of gene expression can generate phenotypic diversity in a genetically identical population of cells, but it is unclear whether it has a role in the development of multicellular systems. Here, we show how stochastic pulsing of gene expression enables spatial patterns to form in a model multicellular system, Bacillus subtilis bacterial biofilms. We use quantitative microscopy and time-lapse imaging to observe pulses in the activity of the general stress response sigma factor σ<sup>B</sup> in individual cells during biofilm development. Both σ<sup>B</sup> and sporulation activity increase in a gradient, peaking at the top of the biofilm, even though σ<sup>B</sup> represses sporulation. As predicted by a simple mathematical model, increasing σ<sup>B</sup> expression shifts the peak of sporulation to the middle of the biofilm. Our results demonstrate how stochastic pulsing of gene expression can play a key role in pattern formation during biofilm development.</p>
TagSeq for gene expression in non-model plants: a pilot study at the Santa Rita Experimental Range NEON core site
<p>TagSeq analysis scripts and assembled transcriptomes for four vascular plant species from the Santa Rita Experimental Range, AZ. Transcriptomes for each species were sequenced and assembled as described below. Additional details available in the associated manuscript: MS LINK. Raw reads for each available at NCBI BioProject #PRJNA599443.</p> <p> </p> <p><strong>Taxon selection and sampling </strong></p> <p>This study focused on four commonly-occurring species at the Santa Rita Experimental Range Long Term Research and Core NEON site (SRER). These include the native species <em>Tidestromia</em> <em>lanuginosa</em> (Nutt.) Standl. (Amaranthaceae; ‘woolly tidestromia’), <em>Parkinsonia</em> <em>florida</em> (Benth. ex A. Gray) S. Watson. (Fabaceae; ‘blue palo verde’), and <em>Bouteloua</em> <em>aristidoides</em> (Kunth) Griseb. (Poaceae; ‘needle grama’), as well as the introduced species <em>Eragrostis</em> <em>lehmanniana</em> Nees (Poaceae; ‘Lehmann lovegrass’; native to southern Africa). All species were identified using a combination of the historical flora of the Santa Rita Experimental Range (Medina, 2003), the Arizona Flora (Kearney et al., 1960), and the Flora of North America (Flora of North America Editorial Committee, eds. 1993). Vouchers were deposited in the University of Arizona herbarium (ARIZ). Tissue from mature plants was collected from an apparently healthy individual representing each target species during the 2017 growing season. An entire stem was sampled for <em>B. aristidoides</em> (with flowers and fruits) and <em>E. lehmanniana</em> (without flowers or fruits). Leaves and leaflets only were sampled for <em>P. florida</em> and <em>T. lanuginosa</em>.</p> <p> </p> <p><strong>RNA extraction and RNA-seq</strong></p> <p>Total RNA was extracted from tissue using the Spectrum Plant Total RNA Kit (Sigma-Aldrich Co., St. Louis, MO, USA) following Protocol A. RNA was used to prepare cDNA using Nugen’s Ovation RNA-Seq System via single primer isothermal amplification (Catalogue # 7102-A01) and automated on the Apollo 324 liquid handler (Wafergen). cDNA was quantified on the Nanodrop (Thermo Fisher Scientific) and was sheared to approximately 300 bp fragments using the Covaris M220 ultrasonicator. Libraries were generated using Kapa Biosystem’s library preparation kit (KK8201). Fragments were end repaired and A-tailed, and individual indexes and adapters (Bioo, catalogue #520999) were ligated on each separate sample. The adapter ligated molecules were cleaned using AMPure beads (Agencourt Bioscience/Beckman Coulter, A63883), and amplified with Kapa’s HIFI enzyme (KK2502). Each library was then analyzed for fragment size on an Agilent’s Tapestation, and quantified by qPCR (KAPA Library Quantification Kit, KK4835) on Thermo Fisher Scientific’s Quantstudio 5 before multiplex pooling (13-16 samples per lane) and paired-end sequencing at 2x150 bp on the Illumina NextSeq500 platform at Arizona State University’s CLAS Genomics Core facility. Raw read quality was assessed using fastQC (Andrews, 2010).</p> <p> </p> <p><strong><em>De novo</em> transcriptome assembly</strong></p> <p>Raw sequence reads were processed using the SnoWhite pipeline (Barker et al., 2010a; Dlugosch et al., 2013), which included trimming adapter sequences and bases with a quality score below 20 from the 3' ends of all reads, removing reads that are entirely primer and/or adapter fragments using TagDust (Lassmann et al., 2009), and removing polyA/T tails with SeqClean (https://sourceforge.net/projects/seqclean/). All transcriptomes were assembled with SOAPdenovo-Trans v1.03 (Xie et al., 2014) using a k-mer of 57. Assembled sequences for each species are in the files ending ".scafSeq".</p> <p> </p> <p><strong>Protein Translations</strong></p> <p>We used TransPipe (Barker et al., 2010) to identify plant proteins within the assembled transcripts for each reference transcriptome and provide protein and in-frame nucleic acid sequences for each species. The reading frame and protein translation for each sequence was identified by comparison to protein sequences from 25 sequenced and annotated plant genomes from Phytozome (Goodstein et al., 2012). Using BLASTX (Wheeler et al., 2008), best hit proteins were paired with each gene at a minimum cutoff of 30% sequence similarity over at least 150 sites. Genes that did not have a best hit protein at this level were removed. To determine the reading frame and generate estimated amino acid sequences, each gene was aligned against its best hit protein by Genewise 2.2.2 (Birney et al., 2004). Based on the highest scoring Genewise DNA-protein alignments, stop and 'N' containing codons were removed to produce estimated amino acid sequences for each gene. Output included paired DNA and protein sequences with the DNA sequence reading frame corresponding to each protein sequence. Nucleic acid sequence files end in “.fna”, whereas amino acid sequence files end in “.faa”. Numbers of sequences in each of these files correspond to the position of the sequence in the associated assembly file.</p> <p> </p> <p><strong>Custom scripts</strong></p> <p>“removePCRdups57.pl” is a Perl script that takes an input FASTQ file and removes exact duplicates identified over a supplied length at the beginning (3’ end) of the read. </p> <p>Run: perl removePCRdups57.pl <inputFASTQ> <length></p> <p> </p> <p>“create_GTF.pl” is a Perl script that takes an input FASTA file and creates a GTF file suitable for input into HtSeq-count v.0.5.4 (Anders et al., 2015).</p> <p>Run: perl create_GTF.pl <inputFASTA></p> <p> </p> <p>“combine_HtSeq.pl” is a Perl script that takes a set of htseq output files and makes a tab delim table of counts with header of sample names and first col of row names. The input file list file should be a text file with lists of Htseq files to combine on each line, where lines are tab delimited of the following form:</p> <p> <NameForOutputFile> <firstHtseqFile> <NextHtseqFile> <...etc...></p> <p>Run: perl combine_HtSeq.pl <inputFileList></p> <p> </p>
Data from: Single cell RNA-seq analysis reveals that prenatal arsenic exposure results in long-term, adverse effects on immune gene expression in response to Influenza A infection
<p>Arsenic exposure via drinking water is a serious environmental health concern. Epidemiological studies suggest a strong association between prenatal<i> </i>arsenic exposure and subsequent childhood respiratory infections, as well as morbidity from respiratory diseases in adulthood, long after systemic clearance of arsenic.<i> </i>We investigated the impact of exclusive prenatal arsenic exposure on the inflammatory immune response and respiratory health after an adult influenza A (IAV) lung infection. C57BL/6J mice were exposed to 100 ppb sodium arsenite<i> in utero,</i> and subsequently infected with IAV (H1N1) after maturation to adulthood. Assessment of lung tissue and bronchoalveolar lavage fluid (BALF) at various time points post IAV infection reveals greater lung damage and inflammation in arsenic exposed mice versus control mice. Single-cell RNA sequencing analysis of immune cells harvested from IAV infected lungs suggests that the enhanced inflammatory response is mediated by dysregulation of innate immune function of monocyte derived macrophages, neutrophils, NK cells, and alveolar macrophages. Our results suggest that prenatal arsenic exposure results in lasting effects on the adult host innate immune response to IAV infection, long after exposure to arsenic, leading to greater immunopathology. This study provides the first direct evidence that exclusive prenatal exposure to arsenic in drinking water causes predisposition to a hyperinflammatory response to IAV infection in adult mice, which is associated with significant lung damage.</p>
Accompanied data files used in the paper "Analysis of chromatin organization and gene expression in T cells identifies functional genes for rheumatoid arthritis"
<p>lists of source file used in the paper "Analysis of chromatin organization and gene expression in T cells identifies functional genes for rheumatoid arthritis" by Jing Yang, Amanda McGovern, Paul Martin, Kate Duffus, Xiangyu Ge, Peyman Zarrineh, Andrew P Morris, Antony Adamson, Peter Fraser, Magnus Rattray & Stephen Eyre. The paper has been accepted by Nature Communications.</p>
Data from: Expressed mutational load increases towards the edge of a species' geographic range
There is no general explanation for why species have restricted geographic distributions. One hypothesis posits that range expansion or increasing scarcity of suitable habitat result in accumulation of mutational load due to enhanced genetic drift, which constrains population performance towards range limits and further expansion. We tested this hypothesis in the North American plant, Arabidopsis lyrata. We experimentally assessed mutational load by crossing plants of 20 populations from across the entire species range and by raising the offspring of within- and between-population crosses at five common garden sites within and beyond the range. Offspring performance was tracked over three growing seasons. The heterosis effect, depicting expressed mutational load, was increased in populations with heightened genomic estimates of load, longer expansion distance or long-term isolation, and a selfing mating system. The decline in performance of within-population crosses amounted to 80%. Mutation accumulation due to past range expansion and long-term isolation of populations in the area of range margins is therefore a strong determinant of population-mean performance, and the magnitude of effect may be sufficient to cause range limits.
Data from: Gene expression correlates of social evolution in coral reef butterflyfishes
<p>Animals display remarkable variation in social behavior. However, outside of rodents, little is known about the neural mechanisms of social variation, and whether they are shared across species and sexes, limiting our understanding of how sociality evolves. Using coral reef butterflyfishes, we examined gene expression correlates of social variation (i.e., pair bonding vs. solitary living) within and between species and sexes. In several brain regions, we quantified gene expression of receptors important for social variation in mammals: oxytocin (<i>OTR</i>), arginine vasopressin (<i>V1aR</i>), dopamine (<i>D1R, D2R</i>), and mu-opioid (<i>MOR</i>). We found that social variation across individuals of the oval butterflyfish, <i>Chaetodon lunulatus,</i> is linked to differences in <i>OTR</i>,<i>V1aR, D1R, D2R, </i>and <i>MOR</i> gene expression within several forebrain regions in a sexually dimorphic manner. However, this contrasted with social variation among six species representing a single evolutionary transition from pair bonded to solitary living. Here, <i>OTR </i>expression within the supracommissural part of the ventral telencephalon was higher in pair bonded than solitary species, specifically in males. These results contribute to the emerging idea that nonapeptide, dopamine, and opioid signaling is a central theme to the evolution of sociality across individuals, although the precise mechanism may be flexible across sexes and species.</p>
Data from: Divergence of seminal fluid gene expression and function among natural snail populations
Seminal fluid proteins (SFPs) can trigger drastic changes in mating partners, mediating post-mating sexual selection and associated sexual conflict. Also, cross-species comparisons have demonstrated that SFPs evolve rapidly and hint that post-mating sexual selection drives their rapid evolution. In principle, this pattern should be detectable within species as rapid among-population divergence in SFP expression and function. However, given the multiple other factors that could vary among populations, isolating divergence in SFP-mediated effects is not straightforward. Here we attempted to address this gap by combining the power of a common garden design with functional assays involving artificial injection of SFPs in the simultaneously hermaphroditic freshwater snail, Lymnaea stagnalis. We detected among-population divergence in SFP gene expression, suggesting that seminal fluid composition differs among four populations collected in western Europe. Furthermore, by artificially injecting seminal fluid extracted from these field-derived snails into standardized mating partners, we also detected among-population divergence in the strength of post-mating effects induced by seminal fluid. Both egg production and subsequent sperm transfer of partners differed depending on the population origin of seminal fluid, with the response in egg production seemingly closely corresponding to among-population divergence in SFP gene expression. Our results thus lend strong intraspecific support to the notion that SFP expression and function evolve rapidly, and confirm L. stagnalis as an amenable system for studying processes driving SFP evolution.
Data from: Gene expression differs in codominant prairie grasses under drought
<p>Grasslands of the Central US are expected to experience severe droughts and other climate extremes in the future, yet we know little about how these grasses will respond in terms of gene expression. We compared gene expression in Andropogon gerardii and Sorghastrum nutans, two closely related co-dominant C4 grasses responsible for the majority of ecosystem function, using RNA-seq.</p> <p>We compared Trinity assemblies within each species to determine annotated functions of transcripts responding to drought. Subsequently, we compared homologous annotated gene-groups across the two species using cross-species meta-level analysis and functional clustering based on key terms. The majority of variation was found between species, as opposed to between drought and watered treatments. However, there is evidence for differential responses; Andropogon allocated gene expression differently compared to Sorghastrum, suggesting Andropogon focuses on stress alleviation (such as oxygen radical scavenging) rather than prevention.</p> <p>In contrast, Sorghastrum may employ a drought avoidance strategy by modulating osmotic response, especially with hormonal regulation. We found Sorghastrum tended to be more sensitive within 10 key gene-groups related to stress, abscisic acid, and trichomes, suggesting gene expression may mechanistically parallel sensitivity at the physiological level. Our findings corroborate phenotypic and physiological differences in the field, and may help explain the phenotypic mechanisms of these two species in the tallgrass prairie community under future drought scenarios.</p>
Effects of soil salinity on the expression of direct and indirect defences in wild cotton (Gossypium hirsutum)
<p>Previous studies have reported effects of abiotic factors on herbivore-induced plant defences based on effects on single plant traits. However, plants commonly express multiple defences simultaneously and these traits are often correlated. Thus, a fuller understanding of abiotic-context dependency in plant defence requires measuring multiple traits and addressing their patterns of correlated expression.</p> <p>We evaluated the effects of soil salinity on the induction of direct (phenolic compounds, gossypol gland density) and indirect (volatile organic compounds, extrafloral nectar) defensive traits in wild cotton (Gossypium hirsutum). We asked whether soil salinity affects the induction of these traits, and whether it shapes trait correlations potentially underlying salinity effects on trait induction. We conducted a factorial experiment with 16 cotton genotypes where we manipulated soil salinity and defence induction by applying artificial leaf damage (25% mechanical damage and caterpillar oral secretions) and measured defence levels at different time points post-damage.</p> <p>Leaf damage induced most traits except gossypol gland density, whereas salinity did not have a mean effect (across constitutive and induced levels) on any of the measured traits. Nonetheless, salinity prevented the induction of phenolic compounds (condensed and hydrolysable tannins), and also affected trait correlations. Specifically, phenolic compounds were negatively associated with nectar production only under salinized conditions, an apparent trade-off that presumably affects the induced levels of phenolic compounds. In addition, positive correlations between phenolic compounds and gland density and root biomass observed under control conditions were lost under salinized conditions.</p> <p>By investigating the effects of soil salinity on the expression of multiple direct and indirect defensive traits and their underlying correlations, these findings build toward a better understanding of how abiotic context-dependency shapes plant allocation to and expression of multiple defensive traits.</p>
Data from: Cis-regulatory differences in isoform expression associate with life history strategy variation in Atlantic salmon
<p><span><span><span><span><span><span><span><span><span><span><span><b>A major goal in biology is to understand how evolution shapes variation in individual life histories. Genome-wide association studies have been successful in uncovering genome regions linked with traits underlying life history variation in a range of species. However, lack of functional studies of the discovered genotype-phenotype associations severely restrains our understanding how alternative life history traits evolved and are mediated at the molecular level. Here, we report a <i>cis</i>-regulatory mechanism whereby expression of alternative isoforms of the transcription co-factor <i>vestigial-like 3</i> (<i>vgll3</i>) associate with variation in a key life history trait, age at maturity, in Atlantic salmon (<i>Salmo salar</i>). Using a common-garden experiment, we first show that <i>vgll3 </i>genotype associates with puberty timing in one-year-old salmon males. By way of temporal sampling of <i>vgll3 </i>expression in ten tissues across the first year of salmon development, we identify a pubertal transition in <i>vgll3</i> expression where maturation coincided with a 66% reduction in testicular <i>vgll3</i> expression. The <i>late </i>maturation allele was not only associated with a tendency to delay puberty, but also with expression of a rare transcript isoform of <i>vgll3</i> pre-puberty. By comparing absolute <i>vgll3 </i>mRNA copies in heterozygotes we show that the expression difference between the <i>early</i>and <i>late</i> maturity alleles is largely <i>cis</i>-regulatory. We propose a model whereby expression of a rare isoform from the <i>late </i>allele shifts the liability of its carriers towards delaying puberty. These results exemplify the potential importance of regulatory differences as a mechanism for the evolution of life history traits.</b></span></span></span></span></span></span></span></span></span></span></span></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.