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54,099 results for “Expression”
Example measurements of electron energy and pitch angle distributions from Venus Express
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Pollen diet mediates how pesticide exposure impacts brain gene expression in nest-founding bumble bee queens
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Inflammatory gene expression during acute high‐altitude exposure
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Supplemental figures: Calcium response behaviors and biomarker expression in human parathyroid tumors
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Retinofugal projections from melanopsin-expressing retinal ganglion cells revealed by intraocular injections of Cre-dependent virus
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A study of gene expression, structure, and contractility of iPSC-Derived Cardiac Myocytes from a family with heart disease due to LMNA mutation
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Housekeeping genes expression in human striated muscle in resting and effort conditions
<p>The figures report the results of PCR analyses of mRNA expression of 14 housekeeping genes from Vastus Lateralis tissue of 3 athletic subjects (1 female) in both resting and post- maximum effort BRUCE protocol for the treadmill: <br> [light-PINK] - Female, rest</p> <p>[dark-PINK] - Female, effort</p> <p>[light-BLUE] - Male, rest</p> <p>[dark-BLUE] - Male, effort</p> <p>Genes:</p> <p>ACTB, B2M, G6PD, GAPDH, GUSB, HMBS, HPRT1, PGK1, RPL13A, RPLPO, RPS18, TBP, TFRC, YWHAZ.</p>
Over-expression of Ki-67 as a predictor of lymph node metastasis in penile cancer patients
<p>In this study, we will look at the association of Ki-67 with lymph node metastasis in patients with penile cancer.</p>
Supplemental Figure for Circulating MiRNA 887 is Differentially Expressed in ARDS and Modulates Endothelial Function
<p>Supplemental Figure 1. A) Among subjects who developed ARDS, there was no difference in plasma miR-887-3p levels between subjects who were (n = 9) or were not (n = 10) receiving mechanical ventilation when the sample was collected. B) Similarly, among subjects who did not develop ARDS, there was no difference in plasma-887-3p levels between subjects who were (n = 13) or were not (n = 9) receiving mechanical ventilation when the sample was collected. Standard deviation shown.</p>
PÂTÉ: A Corpus of Temporal Expressions for the In-car Voice Assistant Domain
<p><strong>PÂTÉ: A Corpus of Temporal Expressions for the In-car Voice Assistant Domain</strong></p> <p>We present <strong>PÂTÉ: A Corpus of Temporal Expressions for the In-car Voice Assistant Domain</strong>. PÂTÉ is a dataset of natural-language commands containing temporal expressions for an AI voice assistant.</p> <p>The dataset is presented in:</p> <p>Zarcone, Alessandra and Alam, Touhidul and Kolagar, Zahra (2020). "PÂTÉ: A Corpus of Temporal Expressions for the In-car Voice Assistant Domain". <em>Proceedings of the 12th Conference on Language Resources and Evaluation (LREC)</em>. Marseille, France, May 11-16, 2020.</p> <p>The dataset is annotated according to the TimeML/TIMEX3 annotation guidelines (Saurı et al., 2006; TimeML Working Group, 2009). In our paper we also describe how we annotated cases which were not covered by the guidelines. We also provide an annotation of the Snips dataset (Coucke et al., 2018) following the same guidelines. </p> <p>Please refer to the README.md file inside PATE.zip for details about the files. </p>
Raw data related to: Molecular Mechanisms Controlling Foxp3 Expression in Health and Autoimmunity: From Epigenetic to Post-translational Regulation.
<p><strong>Abstract</strong></p> <p>The discovery of the transcription factor Forkhead box-p3 (Foxp3) has shed fundamental insights into the understanding of the molecular determinants leading to generation and maintenance of T regulatory (Treg) cells, a cell population with a key immunoregulatory role. Work over the past few years has shown that fine-tuned transcriptional and epigenetic events are required to ensure stable expression of Foxp3 in Treg cells. The equilibrium between phenotypic plasticity and stability of Treg cells is controlled at the molecular level by networks of transcription factors that bind regulatory sequences, such as enhancers and promoters, to regulate Foxp3 expression. Recent reports have suggested that specific modifications of DNA and histones are required for the establishment of the chromatin structure in conventional CD4+ T (Tconv) cells for their future differentiation into the Treg cell lineage. In this review, we discuss the molecular events that control Foxp3 gene expression and address the associated alterations observed in human diseases. Also, we explore how Foxp3 influences the gene expression programs in Treg cells and how unique properties of Treg cell subsets are defined by other transcription factors.</p> <p> </p> <p><strong>Progetto giovani ricercatori</strong>[GR-2016-02363725] dal titolo: "Immune Tolerance, Metabolism and Multiple Sclerosis: Novel Molecular Tools to Monitor Disease Pathogenesis and Progression"</p> <p> </p> <p> </p> <p> </p>
Raw data relative to: "Distinct Expression of Inflammatory Features in T Helper 17 Cells from Multiple Sclerosis Patients"
<p><strong>Introduction</strong></p> <p> Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS). T helper (Th) 17 lymphocytes play a role in the pathogenesis of MS. Indeed, Th17 cells are abundant in the cerebrospinal fluid and peripheral blood of MS patients and promote pathogenesis in the mouse model of MS. To gain insight into the function of Th17 cells in MS, we tested whether Th17 cells polarized from naïve CD4 T cells of healthy donors and MS patients display different features</p> <p><strong>Methods</strong></p> <p>We analysed several parameters that typify the Th17 profile during the differentiation process of naïve CD4 T cells obtained from relapsing-remitting (RR)-MS patients and healthy donors (HD), such as expression of surface receptors by flow cytometry.</p> <p><strong>Results</strong></p> <p>The analysis revealed that expression of IL-1R1 is significantly increased in Th17 cells derived from MS patients compared to healthy donor-derived cells. Interestingly, IL-1R1 expression is also increased in Th17 cells circulating in the blood of MS patients compared to healthy donors. Since IL-1R1 play a crucial role in the activation of immune cells, our data indicate that high expression of these molecules in Th17 cells from MS patients could be related to their high inflammatory status.</p>
Enhancement of Bacillus thuringiensis toxicity by feeding Spodoptera littoralis larvae with bacteria expressing immune suppressive dsRNA
<p><strong>Figure 1C</strong></p> <p>Calibration curves used for qRT-PCR absolute quantification of <em>Sl 102</em> and <em>GFP</em> dsRNA present in <em>E. coli</em> suspensions used in the bioassays</p> <p> </p> <p><strong>Figure 2</strong></p> <p>Transcript levels of <em>Sl 102</em> gene in <em>S. littoralis</em> 4th instar larvae orally treated for 3 days with dsRNA. The <em>Sl</em> <em>102</em> gene was down-regulated upon ingestion of <em>Sl</em> <em>102</em> dsRNA administered by oral gavage, both in the case of dsRNA synthesized in vitro (<em>Sl</em> <em>102</em> dsRNA-synt) and suspensions of sonicated bacteria expressing <em>Sl</em> <em>102</em> dsRNA (<em>Sl</em> <em>102</em> dsRNA-bac). Delivery with artificial diet showed a silencing response that was dose-dependent and more pronounced when bacteria were used as delivery vectors. <em>GFP</em> dsRNA synthesized in vitro and bacteria expressing <em>GFP</em> dsRNA were used in control experiments. The values reported are the mean ± standard errors (*<em>P </em>< 0.0001, Student’s <em>t</em> test)</p> <p><strong>Figure 3</strong></p> <p>Encapsulation assay in <em>S. littoralis</em> 4th larvae treated for 3 days with <em>Sl 102</em> dsRNA synthesized in vitro (<em>Sl</em> <em>102</em> dsRNA-synt) or transformed HT115 <em>E. coli</em> expressing <em>Sl</em> <em>102</em> dsRNA (<em>Sl</em> <em>102</em> dsRNA-bac). Chromatography beads injected into the body cavity of control larvae were encapsulated and melanized (<strong>a</strong>). On the contrary, the efficiency of encapsulation was lower in silenced larvae, independently from the dsRNA administration method (gavage or with artificial diet) (<strong>b</strong>). The encapsulation index was affected by oral delivery method and, in the case of oral administration on artificial diet, by dsRNA quantity. <em>GFP</em> dsRNA synthesized in vitro and bacteria expressing <em>GFP</em> dsRNA were used in control experiments. The values reported are the mean ± standard errors (*<em>P </em>< 0.0001, Student’s <em>t</em> test)</p> <p><strong>Figure 4</strong></p> <p>Bioassay with <em>S. littoralis</em> 4th instar larvae exposed to dsRNA before <em>Bt</em> treatment. Newly molted larvae were treated for 3 days with artificial diet layered with transformed HT115 <em>E. coli</em> expressing <em>Sl</em> <em>102</em> dsRNA (<em>Sl</em> <em>102</em> dsRNA-Bac, corresponding to 200 ng of dsRNA) and then with 12 µg/cm<sup>2</sup> of Xentari™ for 3 more days (see “<a href="https://link.springer.com/article/10.1007/s10340-019-01140-6#Sec3">Materials and methods</a>” section for experimental details). Survival was monitored until day 8 (<strong>a</strong>), when the weight was assessed on the surviving experimental larvae (<strong>b</strong>). Bacteria expressing <em>GFP</em> dsRNA were used in control experiments. The timing of the treatments is indicated with arrows. The values reported are the mean ± standard errors (in <strong>a</strong> *<em>P </em>< 0.0001 based on log-rank test; in <strong>b</strong> different letters denote statistical difference based on Kruskal–Wallis test, followed by Dunn’s multiple-comparison post hoc test)</p> <p> </p> <p><strong>Fig. 5</strong></p> <p>Bioassay with <em>S. littoralis</em> 4th instar larvae simultaneously exposed to dsRNA and <em>Bt</em>. Newly molted larvae were treated for 3 days with artificial diet layered with transformed HT115 <em>E. coli</em> expressing <em>Sl</em> <em>102</em> dsRNA (<em>Sl</em> <em>102</em> dsRNA-Bac, corresponding to 200 ng of dsRNA) and with 9 µg/cm<sup>2</sup> of Xentari (see “<a href="https://link.springer.com/article/10.1007/s10340-019-01140-6#Sec3">Materials and methods</a>” section for experimental details). Survival was monitored until day 8 (<strong>a</strong>) when the weight was assessed on the surviving experimental larvae (<strong>b</strong>). Bacteria expressing <em>GFP</em> dsRNA were used in control experiments. The timing of the treatments is indicated by arrows The values reported are the mean ± standard errors (in <strong>a</strong> **<em>P </em>< 0.0001 and *<em>P </em>< 0.0046 based on log-rank test; in <strong>b</strong> different letters denote statistical difference based on Kruskal–Wallis, followed by Dunn’s multiple comparisons post hoc test)</p> <p><strong>Fig. 6</strong></p> <p>Bioassays with <em>S. littoralis</em> 5th instar larvae simultaneously exposed to dsRNA and <em>Bt</em>. Newly molted larvae were treated for 3 days with artificial diet layered with transformed HT115 <em>E. coli</em> expressing <em>Sl</em> <em>102</em> dsRNA (<em>Sl</em> <em>102</em> dsRNA-Bac, corresponding to 200 ng of dsRNA) and with 12 µg/cm<sup>2</sup> of Xentari (see “<a href="https://link.springer.com/article/10.1007/s10340-019-01140-6#Sec3">Materials and methods</a>” section for experimental details). Survival was monitored until day 8 (<strong>a</strong>), when the weight was assessed on the surviving experimental larvae (<strong>b</strong>). Bacteria expressing <em>GFP</em> dsRNA were used in control experiments. The timing of the treatments is indicated by arrows. The values reported are the mean ± standard errors (in <strong>a</strong> *<em>P </em>< 0.0001 based on log-rank test; in <strong>b</strong> different letters denote statistical difference based on Kruskal–Wallis test followed by Dunn’s multiple-comparison post hoc test)</p> <p> </p>
According to this the mutual affinities of the species of the simpleX group might be expressed as follows t (the Ethiopian species are marked with an asterisk):— each other at base; in 4 p2 is half in row. To this latter I find no parallel in any specimen of ferrum-equinum (all races) I have seen, and in 4 skulls only, out of 33, there is a more or less distinct remnant of the interspace between the canine and p4. Of _R7z. deckeni I have seen one skull only; the dentition is as in many specimens of Ph. augur: c and p4 separated, p2 external. f I give the diagram the form of a genealogical tree, only because it is convenient to in On some Bats of the Genus Rhinolophus, with Remarks on their Mutual Affinities, and Descriptions of Twenty-six new Forms.
According to this the mutual affinities of the species of the simpleX group might be expressed as follows t (the Ethiopian species are marked with an asterisk):— each other at base; in 4 p2 is half in row. To this latter I find no parallel in any specimen of ferrum-equinum (all races) I have seen, and in 4 skulls only, out of 33, there is a more or less distinct remnant of the interspace between the canine and p4. Of _R7z. deckeni I have seen one skull only; the dentition is as in many specimens of Ph. augur: c and p4 separated, p2 external. f I give the diagram the form of a genealogical tree, only because it is convenient to
Can we assume the gene expression profile as a proxy for signaling network activity? (Supplementary Materials)
<p>These are just supplementary files.</p>
Data from: Gene editing to induce FOXP3 expression in human CD4+ T cells leads to a stable regulatory phenotype and function.
<p>Thymic regulatory T cells (tTreg) are potent inhibitors of autoreactive immune responses and loss of tTreg function results in fatal autoimmune disease. Defects in Treg number or function are also implicated in multiple autoimmune diseases, leading to growing interest in use of Treg as cell therapies to establish immune tolerance. Because tTreg are present at low numbers in circulating blood and may be challenging to purify and expand, and also inherently defective in some subjects, we designed an alternative strategy to creating autologous Treg-like cells from bulk CD4+ T cells. We utilized homology-directed-repair (HDR)-based gene-editing to enforce FOXP3 expression. Targeted insertion of a robust enhancer/promoter proximal to the first coding exon bypassed epigenetic silencing, permitting stable, high level endogenous FOXP3 expression. HDR-edited T cells, edTreg, manifested a transcriptional program leading to sustained expression of canonical markers and suppressive activity of tTreg. Both human and murine edTreg mediated immunosuppression in vivo in models of inflammatory disease. Further, this engineering strategy permitted generation of antigen-specific edTreg with robust in vitro and in vivo functional activity. Finally, edTreg could be enriched and expanded at scale using clinically-relevant methods. Together, these finding suggest edTreg production may permit broad future clinical application.</p>
Data from R. C. Schofield et al., "Polymer-encapsulated organic nanocrystals for single photon emission" Opt. Mater. Express 10, 1586-1596 (2020).
<p>Raw data files to accompany R. C. Schofield et al., "Polymer-encapsulated organic nanocrystals for single photon emission" Opt. Mater. Express <strong>10</strong>, 1586-1596 (2020), and a Mathematica notebook which can be used to import the data files.</p> <p> </p>
Differentially expressed alternatively spliced genes associated with carcass and meat traits in Nelore cattle
<p>Quality control report from Qualimap 2.2.1. Basic statistics of the alignment (number of reads, coverage, GC-content, junction detection, etc.) were summarized. Quality control was performed with RNA-seq data from muscle tissue of Nelore Cattle. Transcript data were used to identify genes for which alternatively spliced transcripts were differentially expressed in ribeye muscle tissue between Nelore cattle that differed in their ribeye muscle area (REA) or intramuscular fat content (IF).</p>
Generation of stable mammalian cell lines for the expression of proteins related to COVID-19 through random integration
<p>Scientists centred around University of Oxford came together in the current COVID-19 pandemic to contribute to relevant studies collaboratively. Researchers with no prior experience in virology studies, myself included, had volunteered our time to contribute whichever way we can based on our field of expertise. The Biotech team of SGC Oxford, headed by Nicola Burgess-Brown had taken up the role of producing proteins used in serological assays, basic research to understand COVID-19 pathophysiology and hunt for treatment compounds. The initial production of these proteins was based on transient transfection of expression construct DNA into mammalian cells. This approach was laborious and consumed large amounts of plasmid DNA. Therefore, I volunteered to generate stable expression cell lines that will negate the constant need for transfection.</p> <p>I aimed to stably integrate the expression constructs into the genome of Expi293F human cells commonly used in large scale protein production. The expression constructs carried neomycin marker for selection in mammalian cells. Toxicity to the cells is not a concern in this case because the expressed proteins are secreted into the medium and do not build up in the cells. The expression constructs are randomly integrated into the genome mainly via non-homologous end-joining (NHEJ). An advantage of this approach is that molecular sub-cloning is not necessary.</p> <p>In order to maximise the rate of correct integration of the expression constructs, restriction digestion was performed to cut once between the expression cassette and antibiotic resistance cassette (refer to cartoon in Figure 1). Without this step, the construct DNA will be broken at a random position during the integration step, potentially disrupting the expression cassette. I have also tested the effect of actively creating double strand breaks (DSBs) in the genome of the cells on the integration efficiency. More DSBs in the genome might increase the incidence of NHEJ and integration of our constructs. This was achieved by co-transfection of AAVS1 CRISPR/eSpCas9(1.1) construct (refer to cartoon in Figure 1). The eSpCas9(1.1)_No_FLAG_AAVS1_T2 construct was a gift from Yannick Doyon (Addgene plasmid # 79888 ; http://n2t.net/addgene:79888 ; RRID:Addgene_79888)</p> <p> </p> <p>Please refer to my SGC opennotebook post for my other research work unrelated to the pandemic.</p> <p>https://openlabnotebooks.org/generation-of-stable-mammalian-cell-lines-for-the-expression-of-proteins-related-to-covid-19-through-random-integration/</p>
Gene expression counts from fibroblast, strand-specific, BCM UDN
<p><strong>File description:</strong></p> <ol> <li> <p>Gene-level counts using the gtf file from the release 34 of GENCODE <a href="https://www.gencodegenes.org/human/release_34">https://www.gencodegenes.org/human/release_34</a></p> </li> <li> <p>Split counts spanning from one exon to another using an annotation-free algorithm, therefore capturing new splice sites</p> </li> <li> <p>Non-split counts covering exon-intron boundaries</p> </li> <li> <p>Sample annotation describing each sample from the dataset</p> </li> <li> <p>Description file with global information from the dataset</p> </li> </ol> <p><strong>Use: </strong>The count matrices are intended to help researchers that are interested in using RNA-Seq data with the purpose of diagnostics. Researchers can merge their own dataset with the downloaded ones, provided the tissue, genome build, strand, and paired end specifications match. Afterwards, the DROP pipeline can be used to compute expression and splicing outliers (<a href="https://github.com/gagneurlab/drop">https://github.com/gagneurlab/drop</a>).</p> <p><strong>Maintainer: </strong>Vicente A. Yépez, <a href="mailto:yepez@in.tum.de">yepez@in.tum.de</a></p> <p><strong>URL:</strong> <a href="https://github.com/gagneurlab/drop/">https://github.com/gagneurlab/drop/</a><br> </p> <p><strong>Title</strong>: BCM UDN Fibroblast<br> <strong>Number of samples</strong>: 139<br> <strong>Tissue</strong>: Fibroblast<br> <strong>Organism</strong>: Homo sapiens<br> <strong>Genome assembly:</strong> hg19<br> <strong>Gene annotation</strong>: gencode34<br> <strong>Disease (ICD-10: N)</strong>: : D17: 1, D84: 12, E34: 2, G82: 1, H57: 3, K92: 3, M25: 18, NONE: 35, Q02: 1, Q20: 5, Q33: 2, Q89: 12, R62: 44<br> <strong>Strand specific</strong>: TRUE<br> <strong>Paired end</strong>: TRUE<br> <strong>Protocol</strong>: poly(A) enrichment<br> <strong>Dataset contact</strong>: David Murdock, <a href="mailto:david.murdock@bcm.edu">david.murdock@bcm.edu</a></p> <p><strong>Citation:</strong> Cite both the resource using Zenodo's citation and the publication under References</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.