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293 results for “nanostring”
NanoString dataset for study: Impairment of cancer-associated fibroblasts promotes CD8+ T cell infiltration and enhances sensitivity to immune checkpoint blockade
<p>Pre-processed NanoString mRNA abundance data and associated sample sheet for study:</p> <p>Impairment of cancer-associated fibroblasts promotes CD8+ T cell infiltration and enhances sensitivity to immune checkpoint blockade</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>
Increased spatial coupling of integrin and collagen IV in the immunoresistant clear-cell renal-cell carcinoma tumor microenvironment - Nanostring CosMx SMI Data
<p>Data export from Nanostring CosMx SMI, directly from Nanostring, in Seurat Object format for use in R. Clear cell renal cell carcinoma and papillary renal cell carcinoma were profiled before and after exposure to immunotherapy, with and without sarcomatoid features in clear cell tumors. Each tumor had a field of view in the stromal compartment and field of view in the tumor compartment.</p> <p>For appropriate clinical information associated with this study, please contact Dr. Brandon Manley.</p>
NanoString GeoMx DSP dataset from 50 ROIs under maternal obesity and chow diet treatments.
<p>NanoString GeoMx Digital Spatial Profiler data from 49 ROIs under maternal obesity conditions. Details of each ROIs are included in Annotation files.</p>
Normalized linear counts from NanoString autoimmune profiling panel and summary of statistical analyses
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NanoString nCounter copy number variation assay
<p>The sex chromosomes often follow unusual evolutionary trajectories. In particular, the sex-limited Y and W chromosomes frequently exhibit a small but unusual gene content in numerous species, where many genes have undergone massive gene amplification. The reasons for this remain elusive with a number of recent studies implicating meiotic drive, sperm competition, genetic drift and gene conversion in the expansion of gene families. However, our understanding is primarily based on Y chromosome studies, and the W chromosome has been largely overlooked. Here, we conduct a comprehensive investigation into the abundance, variability, and evolution of ampliconic genes on the W both across and within avian species. We find a striking deficit of gene families on the duck W chromosome, as well as conservation in W-linked gene copy number across duck breeds, indicating that gene amplification may not be such a general feature of sex chromosome evolution as Y studies would initially suggest. Furthermore, we show that gene families have expanded independently in the duck and chicken. In particular, using contrasts between modern chicken and duck breeds selected for different female-specific selection regimes and their wild ancestors, we investigate the factors driving the expansion of HINTW, a prominent ampliconic gene family hypothesized to play a role in female reproduction and oogenesis. While we find that HINTW is ampliconic in both species, our results support a role of female-specific selection in driving gene amplification in the chicken but not the duck, challenging the assumption that HINTW is key for female fecundity across the avian phylogeny.</p>
Nanostring mRNA expression profiling of P7 Arx(GCG)10+7 neonatal cortex using nCounter® mouse Neuropathology Plus Panel
<p>X-linked infantile spasms syndrome (ISSX) is a clinically devastating developmental epileptic encephalopathy with life-long impact. <em>Arx<sup>(GCG)10+7</sup></em>, a mouse model of the most common triplet-repeat expansion mutation of ARX, exhibits neonatal spasms, electrographic phenotypes and abnormal migration of GABAergic interneuron subtypes. Neonatal presymptomatic treatment with 17β-estradiol (E2) in <em>Arx<sup>(GCG)10+7</sup></em> reduces spasms and modifies progression of epilepsy. Cortical pathology during this period, a crucial point for clinical intervention in ISSX, has largely been unexplored, and the pathogenic cellular defects that are targeted by early interventions are unknown. In the first postnatal week, we identified a transient wave of elevated apoptosis in <em>Arx<sup>(GCG)10+7</sup></em> mouse cortex that is non-Arx cell autonomous, since mutant Arx-immunoreactive (Arx+) cells are not preferentially impacted by cell death. NeuN+ (also known as Rbfox3) survival was also not impacted, suggesting a vulnerable subpopulation in the immature <em>Arx<sup>(GCG)10+7</sup></em> cortex. Inflammatory processes during this period might explain this transient elevation in apoptosis; however, transcriptomic and immunohistochemical profiling of several markers of inflammation revealed no innate immune activation in <em>Arx<sup>(GCG)10+7</sup></em> cortex. Neither neonatal E2 hormone therapy, nor ACTH(1-24), the frontline clinical therapy for ISSX, diminished the augmented apoptosis in <em>Arx<sup>(GCG)10+7</sup></em>, but both rescued neocortical Arx+ cell density. Since early E2 treatment effectively prevents seizures in this model, enhanced apoptosis does not solely account for the seizure phenotype, but may contribute to other aberrant brain function in ISSX. However, since both hormone therapies, E2 and ACTH(1-24), elevate the density of cortical Arx+-interneurons, their early therapeutic role in other neurological disorders hallmarked by interneuronopathy should be explored.</p>
NanoString dataset for study: Dynamic changes in the NK-, Neutrophil-, and B-cell immunophenotypes relevant in high metastatic risk post neoadjuvant chemotherapy–resistant early breast cancers
<p>Pre-processed DSP and mRNA abundance datasets used in this study.</p>
ROIs NanoString Digital Spatial Profiler protein assay van Hijfte et al. 2024
<p><span>Images that show ROIs of the NanoString Digital Spatial Profiler protein assay from Van Hijfte et al. 2024. See associated publication for more information.</span></p>
Nanostring PanCancer IO360 Data of Gastroenteropancreatic High-Grade Neuroendocrine Carcinoma
<p>Zip file includes raw RCC files used by Nanostring for data visualization of genomic information along with links to the Nanostring website where this data can be viewed in graphical format. </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 nCounter copy number variation assay
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NanoString autoimmune profiling panel normalized linear counts and summary of statistical analyses
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Nanostring mRNA expression profiling of P7 Arx(GCG)10+7 neonatal cortex using nCounter® mouse Neuropathology Plus Panel
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NanoString DSP Human Cortex Tansey Lab
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NanoString dataset for study: Real-time ex vivo perfusion of human lymph nodes invaded by cancer (REPLICANT): a feasibility study
<p>Raw NanoString data for study DOI:10.1002/path.5367</p>
Raw data files for Nanostring analysis of experimental TBI study
<p>Raw Nanostring Data Files </p>
NanoString nCounter Cancer CN panel assay CNV detection of high-grade serous carcinoma samples
GEO Series GSE244329. Homo sapiens. 26 samples. Type: Genome variation profiling by genome tiling array.
Transcriptomic analysis of orthotopic pancreatic tumors treated by Axl inhibitor TP-0903 or combination with chemo/immunotherapy using the nCounter PanCancer Immune Profiling panel (Nanostring Technol
GEO Series GSE185110. Mus musculus. 36 samples. Type: Expression profiling by array.
Nanostring gene expression of tissues from MC4R WT and KO mice
GEO Series GSE291838. Mus musculus. 45 samples. Type: Other.
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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.