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13 results for “Normalized Counts”
Cacao gene atlas: Additional file 13 (CPM normalized read counts) and Additional file 14 (fractional counts)
<p class="MsoNormal">A large dataset of replicated transcriptomes was developed to accelerate<span class="MsoCommentReference"> <em>T</em></span><em>heobroma cocoa</em> genomics research with the long-term goal of progressing breeding towards developing high-yielding elite varieties of cacao. RNAs were extracted and transcriptomes were sequenced from 123 different tissues and stages of development representing major organs and developmental stages of the cacao lifecycle. In addition, several experimental treatments and time courses were performed to measure gene expression in tissues responding to biotic and abiotic stressors. Samples were collected in replicates (3-5) to enable statistical analysis of gene expression levels for a total of 390 transcriptomes. We describe the creation of the atlas,and its global characterization and define sets of genes co-regulated in highly organ- and temporally-specific manners. To promote wider use of these data, all raw sequencing data, expression read mapping matrices, scripts, and other information used to create the resource are freely available online. A gene expression browser with a graphical user interface was developed to display gene expression patterns and to provide easy access of raw data and statistical analyses.</p>
Normalized linear counts from NanoString autoimmune profiling panel and summary of statistical analyses
<p>Though dependent on genetic anomalies, clinical manifestations of the human autoimmune disease systemic lupus erythematosus (lupus) can be triggered by environmental exposures including inhalation toxicants such as crystalline silica dust (cSiO<sub>2</sub>), tobacco smoke, and ambient air particles. Prednisone, a glucocorticoid (GC), is a keystone therapy for managing lupus flaring and progression, however, long-term use is associated with many adverse side effects. Here, we characterized the dose-dependent immunomodulation and toxicity of prednisone in a preclinical model that emulates onset and progression of cSiO<sub>2</sub>-triggered lupus. Two cohorts of 6-wk-old female NZBWF1 mice were fed either control AIN-93G diet or one of three AIN-93G diets containing prednisone at 5, 15, or 50 mg/kg diet which span human equivalent oral doses (HED) currently considered to be low (PL; 5 mg/d HED), moderate (PM; 14 mg/d HED), or high (PH; 46 mg/d HED), respectively. At 8 wk of age, mice were intranasally instilled with either saline vehicle or 1 mg cSiO<sub>2</sub> once weekly for 4 wk. The experimental plan was to 1) terminate one cohort of mice (n=8/group) 14 wk after the last cSiO<sub>2</sub> instillation for pathology and autoimmunity assessment and 2) to maintain a second cohort (n=9/group) to monitor glomerulonephritis development and survival. Mean blood concentrations of prednisone's chief active metabolite, prednisolone, in mice fed PL, PM, and PH diets were 27, 105, 151 ng/ml, respectively, which are consistent with levels observed in human blood ≤ 12 h after single bolus treatments with equivalent prednisone doses. Results from the first cohort revealed that consumption of PM but not PL diet significantly reduced cSiO<sub>2</sub>-induced pulmonary ectopic lymphoid structure formation, nuclear-specific AAb production, and inflammation/autoimmune gene expression in the lung, splenomegaly, and glomerulonephritis in the kidney. Relative to GC-associated toxicity, PM but not PL diet elicited muscle wasting, but these diets did not affect bone density or cause glucosuria. Importantly, neither PM nor PL diet influenced latency of cSiO<sub>2</sub>-accelerated death. PH-fed mice in both cohorts displayed robust GC-associated toxicity including body weight loss, reduced muscle mass, and hyperglycemia 7 wk after the final cSiO<sub>2</sub> instillation requiring their early removal from the study. Taken together, our results demonstrate that while moderate doses of prednisone can reduce certain pathological endpoints of cSiO<sub>2</sub>-induced autoimmunity in lupus-prone mice, these ameliorative effects come with unwanted GC toxicity and, crucially, none of these three doses extended survival time.</p>
HTP normalized counts via Deseq2
<p>This data was gathered from the Human Trisome project orginally and was processed in a way to try to normalize it. </p>
Normalized linear counts from NanoString autoimmune profiling panel and summary of statistical analyses
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Sequencing data and normalized counts for tripartite RNAseq of Drosophila, Wolbachia, and SINV virus
<p><span><i>Wolbachia</i> is a maternally transmitted bacterium that manipulates arthropod and nematode biology in myriad ways. The <i>Wolbachia</i> strain colonizing <i>Drosophila melanogaster</i> creates sperm-egg incompatibilities and protects its host against RNA viruses, making it a promising tool for vector control. Despite successful trials using <i>Wolbachia</i>-transfected mosquitoes for Dengue control, knowledge of how <i>Wolbachia</i> and viruses jointly affect insect biology remains limited. Using the <i>Drosophila melanogaster </i>model, transcriptomics and gene expression network analyses revealed pathways with altered expression and splicing due to <i>Wolbachia</i> colonization and virus infection. Included are metabolic pathways previously unknown to be important for <i>Wolbachia</i>-host interactions. Additionally, <i>Wolbachia</i>-colonized flies exhibit a dampened transcriptomic response to virus infection, consistent with early blocking of virus replication. Finally, using <i>Drosophila</i> genetics, we show <i>Wolbachia</i> and expression of nucleotide metabolism genes have interactive effects on virus replication. Understanding the mechanisms of pathogen blocking will contribute to the effective development of <i>Wolbachia</i>-mediated vector control programs.</span></p>
Dataset for "Feature-Count Table Normalization" workflow
<p>This dataset is associated with the Galaxy workflow "Feature-Count Table Normalization".</p>
NanoString autoimmune profiling panel normalized linear counts and summary of statistical analyses
<p>Occupational exposure to respirable crystalline silica (cSiO<sub>2</sub>) is linked to the development of lupus. Preclinical studies have revealed weekly repeated intranasal exposure to 1 mg cSiO<sub>2</sub> in young (8-11 wk-old) female NZBWF1 lupus-prone mice, a life-stage equivalent to 12–20-yr-old humans, triggers autoimmunity in the lungs and kidneys that is prevented by dietary supplementation with the omega-3 fatty acid docosahexaenoic acid (DHA).</p> <p><strong>Methods</strong>: Here, we characterized cSiO<sub>2</sub>'s and DHA's effects in mature adult (16–19-wk-old) female NZBWF1 mice, an age period that coincides with the onset of immunological tolerance breach and that is more representative of the age (>20-yr-old) of cSiO<sub>2</sub>-exposed workers. We fed mice either a control diet (CON) or diet amended with DHA calorically equivalent to a human daily dose of 5 g. After 2 wk, we intranasally instilled them with either saline vehicle (VEH) or 1 mg of cSiO<sub>2</sub> weekly for 4 wk. Cohorts were terminated 1 and 5 wk after the final installation. Lungs were then analyzed for inflammatory cell counts, chemokines, histopathology, B-and T-cell infiltration, autoantibody profile, and inflammatory/autoimmune gene signatures and results further related to autoimmune glomerulonephritis onset.</p> <p><strong>Results</strong>: VEH/CON mice displayed no lung or kidney pathology at either time point. In contrast, cSiO<sub>2</sub>/CON mice exhibited mild ectopic lymphoid tissue (ELT) formation in the lungs at 1 wk, which increased significantly by 5 wk. Lungs from cSiO<sub>2</sub>/CON mice also showed elevations in BALF cellularity, chemokine production, CD3 + T-cells, CD45R + B-cells, IgG + plasma cells, inflammatory/autoimmune gene expression, IgG autoantibodies. cSiO<sub>2</sub>/CON mice had visible glomerular hypertrophy and IgG deposition. Dietary DHA supplementation suppressed all these endpoints.</p> <p><strong>Discussion</strong>: Consistent with young mice, intranasal cSiO<sub>2</sub> exposure in mature adult NZBWF1 lupusprone mice elicited early pulmonary inflammation that served as a nexus for autoimmunity, suggesting these life-stage differences are not critical for cSiO2-triggered autoimmune response in this preclinical model. DHA supplementation at a translationally relevant human dosage effectively mitigated cSiO<sub>2</sub>-induced inflammation/autoimmunity in mature adult mice, resembling the protective effects observed in young mice. Together these findings further highlight the therapeutic potential of omega-3 fatty acids in mitigating toxicant-triggered autoimmune responses.</p>
NanoString autoimmune profiling panel normalized linear counts and summary of statistical analyses
Open the record for dataset details and reuse information.
Sequencing data and normalized counts for tripartite RNAseq of Drosophila, Wolbachia, and SINV virus
Open the record for dataset details and reuse information.
Raw and normalized count data for "Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling"
<p>SingleCellExperiment objects containing raw and normalized counts, as well as reduced dimension representations and cell type annotations for both the follicular lymphoma samples (sce_follicular_annotated_final.rds) and high grade serous ovarian cancer samples (sce_hgsc_annotated_final.rds) as detailed in the paper, as well as reactive lymph node data (sce_RLN_normalized.rds).</p>
Results of comparison among count, normalized count and pearson residual
<p>Results of comparison among count, normalized count and pearson residual</p>
Clinical Diagnosis of Acute Appendicitis with Normal WBCS Count with Role of Inflammatory Markers and Radiology
ClinicalTrials.gov study NCT06834958. IPD Sharing: YES. Countries: 1. Publications: 0.
STEREO-A PLasma and Supra-Thermal Ion Composition (PLASTIC) He⁺ Counts and Relative Energy Flux in four Velocity Ranges normalized by the Solar Wind Speed, Level 3 (L3), Daily Data
STEREO-A Plasma and Suprathermal Ion Composition, Singly-charged Helium, He⁺, counts and relative differential energy fluxes binned by the ion speed relative to the solar wind bulk speed, four speed ratio bins. STEREO PLASTIC daily suprathermal He⁺ pickup ion signatures include He⁺ energy spectra, directional information, and contenxt information, such as the H⁺ plasma velocity. The four speed ratio, V/Vsw, bin ranges of are: 1.44 to 1.85, 1.85 to 2.50, 2.50 to 3.50, and 3.50 to 8.00. The identification of He⁺ is based on the measurement of energy per charge, E/q, time-of-flight, TOF, and total energy deposited in the solid state detector, SSD. These data include double coincidence measurements by using E/Qi and TOF and triple coincidence measurements by using E/Q, TOF, and SSD, see for example Galvin et al., Space Sci. Rev. 136, p 437-468, 2008. The proton bulk parameters including speed, Vsw, thermal velocity, Vth, and Density, Np, in this file are derived from a one-deminsional, 1-D, Maxwellian fit to a single detector rate with no coincidence required. These proton bulk parameters are corrected for background and dead time. The software version number used to derive the proton bulk parameters is shown in the file header and is described in the section on file formats. The most recent update of the proton bulk parameters can be found on the following STEREO website: http://stereo-ssc.nascom.nasa.gov/data/ins_data/plastic/level2/Protons/ For a full explanation, see the description at: https://stereo-ssc.nascom.nasa.gov/data/ins_data/plastic/level3/HePlus/HePlus_flux/READ_ME_PLASTIC_HePlus_Fluxes.pdf The singly-charged Helium, He⁺, flux data are also available from the STEREO Science Center in ASCII format via: https://stereo-ssc.nascom.nasa.gov/data/ins_data/plastic/level3/HePlus/ Note that this SPASE Numerical Description only describes the MESSENGER Magnetometer data stored in Common Data Files.
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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.