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1,899 results for “Running”
WRF-Chem Volcano output - Etna Christmas 2018 (run L0)
<p>Output from a model run of a modified version of WRF-Chem, which we refer to as WRF-Chem Volcano (WCV). At the time of submission of this dataset, these data were the basis of the modelling part of a paper submitted to Atmospheric Chemistry and Physics Discussions (ACPD): "WRF-Chem modelling and TROPOMI observations of halogen chemistry within the plume of Etna's Christmas 2018 eruption".</p> <p>The code of WCV is maintained <a href="https://github.com/LukeSurl/WCV">here</a>. Development of this code will continue after the submission of this repository, <a href="https://github.com/LukeSurl/WCV/tree/20200521">This branch</a> is a permanent record of the code as used to create this dataset.<br> This is a simulation without any volcanic emissions, used to determine the difference caused by the volcano</p> <p>"Run L0" refers the internal serial number assigned to this model run.</p> <p><strong>Overview of files</strong></p> <p><strong><em>Output files: wrfout_d0*_YYYY-MM-DD_HH:MM:SS</em></strong></p> <p>Output data is contained in NetCDF files. Each file contains hourly snapshots of the 3D simulation with fields for various parameters. Most of the 4D (three spatial dimensions and time) variables record modelled mixing ratios of various species (in units ppm). Many other variables are standard WRF-Chem output variables; please see <a href="https://ruc.noaa.gov/wrf/wrf-chem/">WRF-Chem's documentation</a>. If the meaning of a variable is unclear, please <a href="mailto:luke.surl@latmos.ipsl.fr?subject=WCV%20run%20L2%20dataset">contact the author</a>.</p> <p>Files are separated by model domain and by time. The "d0x" value specifies the model domain. Domain 1 is the full extent of the modelled area and has grid cells of 30 km × 30 km. Domains 2, 3, 4 each model a successively smaller area subset at a 3x greater resolution than their parent domain. Please see the ACPD paper for further details on this.</p>
Culture KS Superpooled 1st replicate, initial trial run samples for metabolomics analysis, electron shuttle samples
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Dataset Soft tissue and running stiffness
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Companion test_dataset and results for bash: wma_ms_pll.sh running 3DSlicer singularity img. SJN22.sif
<p>Companion test_dataset and results for bash: wma_ms_pll.sh running 3DSlicer singularity img. SJN22.sif</p>
mcmc running scripts (Nautilus)
<p>New set of running scripts for MCMCing using Nautilus as a sampler. </p>
Nautilus WL Runs
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Genome-wide Characterization of Selection Signatures and Runs of Homozygosity in Ugandan Goat Breeds
<p><strong>ABSTRACT</strong></p> <p>Both natural and artificial selection are among the main driving forces shaping genetic variation across the genome of livestock species. Selection typically leaves signatures in the genome, which are often characterized by high genetic differentiation across breeds and/or a strong reduction in genetic diversity in regions associated with traits under intense selection pressure. In this study, we evaluated selection signatures and genomic inbreeding coefficients, based on runs of homozygosity (ROH), in six Ugandan goat breeds: Boer (n = 13), and the indigenous breeds Karamojong (n = 15), Kigezi (n = 29), Mubende (n = 29), Small East African (n = 29) and Sebei (n = 29). After genotyping quality control, 45,294 autosomal single nucleotide polymorphisms (SNPs) remained for further analyses. A total of 394 and 6 breed-specific putative selection signatures were identified across all breeds, based on the fixation index ( -values) and hapFLK statistics respectively. These regions were enriched with genes involved in signalling pathways associated directly or indirectly with environmental adaptation, such as immune response (e.g. <em>IL10RB</em> and <em>IL23A</em>), growth and fatty acid composition (e.g. <em>FGF9</em> and <em>IGF1</em>), and thermo-tolerance (e.g. <em>MTOR</em> and <em>MAPK3</em>). The study revealed little overlap in genomic regions under selection and generally did not display the typical classic selection signatures as expected due to the complex nature of the traits. In the Boer breed, candidate genes associated with production traits, such as body size and growth (e.g. <em>GJB2</em> and <em>GJA3</em>) were also identified. Furthermore, analysis of ROH in indigenous goat breeds showed very low levels of genomic inbreeding (with the mean per breed ranging from 0.8% to 2.4%), as compared to higher inbreeding in Boer (mean = 13.8%). And, short ROH were more frequent than long ROH, except in Karamojong, providing insight in the developmental history of these goat breeds. This study provides important insights into the effects of long-term selection in Boer and indigenous Ugandan goat breeds and its genetic. Our findings are of great relevance to the implementation of breeding programs and conservation of genetic resources, as well as their sustainable use and management.</p> <p> </p> <p> </p> <p> </p>
hnRNPA2B1 promotes osteogenesis differentiation of human adipose-derived stem cells through PHC2/GATA6/BMP axis [CUT&RUN]
GEO Series GSE291175. Homo sapiens. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Run or die in the evolution of de novo microRNAs
GEO Series GSE110086. Drosophila sechellia; Drosophila simulans; Drosophila melanogaster; Drosophila erecta. 10 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
Dissection of the MEF2D-IRF8 transcriptional circuit dependency in acute myeloid leukemia [CUT&RUN]
GEO Series GSE186130. Homo sapiens. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Hnf4 controls gut and liver gene programs in the thymus [CUT&RUN]
GEO Series GSE225657. Mus musculus. 32 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Chromatin Remodeling Drives Immune-Fibroblast Cell Communication in Heart Failure (Cut & Run)
GEO Series GSE221695. Mus musculus. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
LSD1 and CoREST2 Regulate STAT3 Activity to Promote Enteroendocrine Cell Differentiation in Mucinous Colorectal Cancer[CUT&RUN]
GEO Series GSE268956. Homo sapiens. 13 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Impaired bone morphogenetic protein signaling pathways perturb decidualization in patients with endometriosis (Cut&Run-Seq)
GEO Series GSE243156. Homo sapiens. 12 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Paired CRISPR screens to map gene regulation in cis and trans (CUT&RUN)
GEO Series GSE255699. Homo sapiens. 12 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Cut&Run sequencing of WT HSCs with 1-mon M.avium infection
GEO Series GSE206276. Mus musculus. 7 samples. Type: Other.
Heterozygous Kmt2d loss diminishes enhancers to render medulloblastoma cells vulnerable to combinatory inhibition of lysine demethylation and oxidative phosphorylation [CUT&RUN]
GEO Series GSE248456. Mus musculus. 9 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Cellular senescence in skeletal muscle aging: new mechanisms and therapeutic potential for sarcopenia [cut&run_seq_IMR90]
GEO Series GSE268431. Homo sapiens. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Glucose dissociates DDX21 dimers to regulate mRNA processing and promote epidermal differentiation (CUT&RUN)
GEO Series GSE215313. Homo sapiens. 34 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Hit-and-run silencing of endogenous DUX4 by targeting DNA hypomethylation on D4Z4 repeats in facioscapulohumeral muscular dystrophy [EPIC Methylation]
GEO Series GSE199690. Homo sapiens. 7 samples. Type: Methylation profiling by genome tiling array.
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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.