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13,349 results for “mice”
Mice infected with Low shedder S. mansoni parasites from cross A - cage 2 - Liver histopathology data.
<p>The present dataset contains all the histopathology images used to quantify fibrotic areas, parasite egg counts and to quantify granuloma areas in liver of mice infected with <em>S. mansoni</em> Low shedder line. These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 5/11).<br> Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area and egg counts (_TRICH.czi), to quantify granuloma area (_HE.czi), and the annotation file (.annotations) containing all the annotated granuloma areas.</p>
Mice infected with Low shedder S. mansoni parasites from cross A - cage 1 - Liver histopathology data.
<p>The present dataset contains all the histopathology images used to quantify fibrotic areas, parasite egg counts and to quantify granuloma areas in liver of mice infected with <em>S. mansoni</em> Low shedder line. These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 4/11).<br> Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area and egg counts (_TRICH.czi), to quantify granuloma area (_HE.czi), and the annotation file (.annotations) containing all the annotated granuloma areas.</p>
Control mice (non-infected with S. mansoni parasites) - cage 2 - Liver histopathology data (mouse ID 2C.1 / 2C.2 / 2C.3).
<p>The present dataset contains all the histopathology images used to quantify fibrotic areas in liver of mice (non-infected with S. mansoni parasite). These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 11.1/11).<br> Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area (_TRICH.czi) and (_HE.czi) files.</p>
Control mice (non-infected with S. mansoni parasites) - cage 2 - Liver histopathology data (mouse ID 2C.4 / 2C.5).
<p>The present dataset contains all the histopathology images used to quantify fibrotic areas in liver of mice (non-infected with S. mansoni parasite). These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 11.2/11).<br> Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area (_TRICH.czi) and (_HE.czi) files.</p>
Mice infected with High shedder S. mansoni parasites from cross B - cage 2 - Liver histopathology data.
<p>The present dataset contains all the histopathology images used to quantify fibrotic areas, parasite egg counts and to quantify granuloma areas in liver of mice infected with <em>S. mansoni</em> High shedder line. These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 7/11).<br> Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area and egg counts (_TRICH.czi), to quantify granuloma area (_HE.czi), and the annotation file (.annotations) containing all the annotated granuloma areas.</p>
Mice infected with Low shedder S. mansoni parasites from cross B - cage 2 - Liver histopathology data.
<p>The present dataset contains all the histopathology images used to quantify fibrotic areas, parasite egg counts and to quantify granuloma areas in liver of mice infected with <em>S. mansoni</em> Low shedder line. These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 9/11).<br> Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area and egg counts (_TRICH.czi), to quantify granuloma area (_HE.czi), and the annotation file (.annotations) containing all the annotated granuloma areas.</p>
Mice infected with Low shedder S. mansoni parasites from cross B - cage 1 - Liver histopathology data.
<p>The present dataset contains all the histopathology images used to quantify fibrotic areas, parasite egg counts and to quantify granuloma areas in liver of mice infected with <em>S. mansoni</em> Low shedder line. These data are presented in the manuscript entitled "No evidence for schistosome parasite fitness trade-offs in the intermediate and definitive host" (dataset # 8/11).<br> Each folder corresponds to one mouse sample and contain, along with a readme file, all the files used to quantify fibrotic area and egg counts (_TRICH.czi), to quantify granuloma area (_HE.czi), and the annotation file (.annotations) containing all the annotated granuloma areas.</p>
raw data of Gut microbiota remodeling and intestinal adaptation to lipid malabsorption after enteroendocrine cell loss in adult mice
<p>Microbiome dataset for "Gut microbiota remodeling and intestinal adaptation to lipid malabsorption after enteroendocrine cell loss in adult mice" publication</p> <p>https://doi.org/10.1016/j.jcmgh.2023.02.013</p> <p> </p>
Antibody landscape of C57BL/6 mice cured of B78 melanoma via immunotherapy
<p>Antibodies can play an important role in innate and adaptive immune responses against cancer, and in preventing infectious disease. Using a Nimble Therapeutics high-density peptide array, we assessed potential protein-targets for antibodies found in sera of immune mice, that were previously cured of their melanoma through a combined immunotherapy regimen with long-term memory. Using flow cytometry, immune sera showed strong antibody-binding against melanoma tumor cell lines. Sera from 6 of these cured mice were analyzed with this high-density, whole-proteome peptide-array to determine specific antibody-binding sites and their linear peptide sequence. We identified thousands of peptides that were targeted by 2 or more of these 6 mice and exhibited strong antibody binding only by immune, not naive sera. Confirmatory studies were done to validate these results using 2 separate ELISA-based systems. This technology may be helpful in studying the “immunome”. of protein-based epitopes that are recognized by immune sera from mice, or possibly patients, cured of cancer via immunotherapy.</p>
The First Transcriptomic Atlas of the Adult Lacrimal Gland Reveals Epithelial Complexity and Identifies Novel Progenitor Cells in Mice
<p>This project contains the R objects and code to reproduce the analyses and figures presented in the research article:</p> <p>'The First Transcriptomic Atlas of the Adult Lacrimal Gland Reveals Epithelial Complexity and Identifies Novel Progenitor Cells in Mice.' <em>Cells</em> <strong>2023</strong>, <em>12</em>, 1435. https://doi.org/10.3390/cells12101435</p> <p>Raw data (FASTQ files and CellRanger output files used for the preprocessing of individual datasets) can be found on Gene Expression Omnibus database (www.ncbi.nlm.nih.gov/geo/) under accession # GSE232146.</p>
Mu-opioid receptor-dependent changes in social reward across adolescence in mice
<p>Datasets used in publication "Mu-opioid receptor-dependent changes in social reward across adolescence in mice" (in preparation). The social conditioned place preference data were pre-processed before statistical analysis. Three diffrent datatables with the same dataset reflect the steps of the pre-processing:</p> <p>1. Animals that spent more than 70% of the pretest time in one of the contexts were excluded (datable "30_70%")</p> <p>2. Outliers were identified using Grubbs test, and removed (datatable "no_outlier")</p> <p>3. In cases where the final number of animals conditioned in each context was not equal (due to an unequal number of animals passing the 70% criterion or unequal number of animals in the litter), we pseudorandomly trimmed the larger group using a Python script (file number 10). The exception from completely random selection was introduced to preserve a mean 50% initial context preference during the pretest</p>
Data on the fleas of house mice and ship rats in the Orongorongo Valley, New Zealand
<p>Data on autopsies and fleas of individual rats and mice snap-trapped in 80 quarterly 3-day trapping sessions over 1971-1991 in the Orongorongo Valley, Wellington, New Zealand. The fleas are preserved as slides in the Pilgrim Collection of Te Papa Tongarewa Museum of New Zealand, Wellington. The data are analysed in a forthcoming paper by Fitzgerald, Efford and Karl.</p> <p>'Autopsy data.csv' is the main spreadsheet.</p> <p>'Data format.csv' defines columns and codes.</p> <p>The autopsy data are a subset of those reported by Fitzgerald, Efford<br> and Karl (2004) and Efford, Fitzgerald, Karl and Berben (2006), both<br> with respect to the sampling period (trapping continued after May 1991,<br> but rats and mice were not searched for fleas) and data columns<br> (some reproductive fields have been omitted).</p> <p>The autopsy data may be read from the csv file into R (R Core Team 2023)<br> with the statement:</p> <p>autopsyF <- read.csv(file = 'Orongorongo fleas 1971-1991 Autopsy data.csv')</p> <p>The resulting dataframe has 31 columns and 3006 rows:</p> <p>names(autopsyF)<br> [1] "Autopsy" "Line" "Date" "Analysis.Year" "Session" <br> [6] "Day" "Season" "Trap" "Traptype" "Alive.dead" <br> [11] "Species" "Sex" "Age" "Weight" "TotLth" <br> [16] "TailLth" "Fleas" "LsegnisM" "LsegnisF" "LsegnisU" <br> [21] "Lsegnis" "NfascM" "NfascF" "NfascU" "Nfasc" <br> [26] "Vagina" "Lact" "Uterus" "EmbryosT" "ScarCond" <br> [31] "Testes" <br> <br> nrow(autopsyF)<br> [1] 3006</p> <p>For completeness, the autopsy data include 64 hosts from these trapping sessions that were<br> not searched for fleas (coded as Fleas = 2).</p> <p>Quarterly indices of host density were tabulated by Fitzgerald et al. (2004; mice) and<br> Efford et al. (2006; rats).</p> <p>References</p> <p>Efford MG, Fitzgerald BM, Karl BJ, Berben PH. 2006. Population dynamics<br> of the ship rat <em>Rattus rattus</em> L. in the Orongorongo Valley, New Zealand.<br> New Zealand Journal of Zoology 33:273-297.</p> <p>Fitzgerald BM, Efford MG, Karl BJ. 2004. Breeding of house mice and the<br> mast seeding of southern beeches in the Orongorongo Valley, New Zealand.<br> New Zealand Journal of Zoology 31:167-184.</p> <p>Fitzgerald BM, Efford MG, Karl BJ. 2023. The fleas of house mice (<em>Mus musculus</em>)<br> and ship rats (<em>Rattus rattus</em>) in forest of the Orongorongo Valley, New Zealand.<br> For submission to New Zealand Journal of Zoology.</p> <p>R Core Team 2023. R: A Language and Environment for Statistical Computing.<br> R Foundation for Statistical Computing, Vienna, Austria.<br> https://www.R-project.org/</p>
Granulosa cell transcriptome data from four different time points before and up to 48 hours after PMSG induction to GTH-depend phase in mice
<p>GTH-dependent follicle development begins with small antrum follicles and ends with preovulatory follicles. GTH-dependent follicle development is mainly controlled by gonadotropins, and the development time is 48h. The purpose of this study is to monitor the changes in gene expression of granulosa cells at four different time points during the GTH-dependent phase to increase our understanding of human GTH-dependent follicle development.Granulosa cell mRNA profiles of GTH-depend phase in mice.There are 12 samples represented four time points 0h (n=3), 12h (n=3), 24h (n=3) and 48h (n=3)</p>
Open data repository, Boehm-Sturm et al., Phenotyping placental oxygenation in Lgals1 deficient mice using 19F MRI
<p>Open data repository of journal article "Phenotyping placental oxygenation in Lgals1 deficient mice using <sup>19</sup>F MRI"</p>
Investigating the Effect of Positional Variation on Mid-Lactation Mammary Gland Transcriptomics in Mice Fed Either a Low-Fat or High-Fat Diet
<p>Investigating the Effect of Positional Variation on Mid-Lactation Mammary Gland Transcriptomics in Mice Fed Either a Low-Fat or High-Fat Diet.</p>
nNOS-expressing interneurons control basal and behaviorally evoked arterial dilation in somatosensory cortex of mice
<p>Cortical neural activity is coupled to local arterial diameter and blood flow. However, which neurons control the dynamics of cerebral arteries is not well understood. We dissected the cellular mechanisms controlling the basal diameter and evoked dilation in cortical arteries in awake, head-fixed mice. Locomotion drove robust arterial dilation, increases in gamma band power in the local field potential (LFP), and increases calcium signals in pyramidal and neuronal nitric oxide synthase (nNOS)-expressing neurons. Chemogenetic or pharmocological modulation of overall neural activity up or down caused corresponding increases or decreases in basal arterial diameter. Modulation of pyramidal neuron activity alone had little effect on basal or evoked arterial dilation, despite pronounced changes in the LFP. Modulation of the activity of nNOS-expressing neurons drove changes in the basal and evoked arterial diameter without corresponding changes in population neural activity.</p>
The organophosphate pesticide methamidophos opens the blood-testis barrier and covalently binds to ZO-2 in mice
<p>We studied biological effects and post-translational modifications of proteins after treating mice with the pesticide methamidophos.</p> <p>This data set provides evidence for the modification of ZO-2, indicating that the blood-testis barrier in mouse was crossed.</p>
Physiological trait and genotype data for 1,038 outbred CFW mice
<p>R data set containing physiological trait data and genotype data for 1,038 mice from the Carworth Farms White (CFW) outbred mouse stock. These data were collected as part of a large study to assess the viability of using Carworth Farms White (CFW) mice for mapping genes and genetic loci underlying complex traits relevant to the study of human disease and psychology. The data accompany the following publication:</p> <p>Parker CC, Gopalakrishnan G, Carbonetto P, Gonzales NM, Leung E, Park YJ, Aryee E, Davis J, Blizard DA, Ackert-Bicknell CL, Lionikas A, Pritchard JK, Palmer AA. Genome-wide association study of behavioral, physiological and gene expression traits in commercially available outbred CFW mice. <em>Nature Genetics</em> <strong>48</strong>: 919–926.</p> <p>To use these data for your research, please cite this Zenodo resource, as well as the paper published in <em>Nature Genetics</em>.</p> <p>After loading these data into the R environment, e.g., by running "load(cfw.RData)", you will find R objects including:</p> <p>"pheno"—a 1,038 x 7 matrix containing the quantitative trait, or "phenotype", data. Traits include body weight, tibia length, muscle weights (EDL and soleus), and a binary indicator for abnormal bone health.</p> <p>"map"—a data frame containing information for 79,748 single nucleotide polymorphisms (SNPs) on chromosomes 1–19 genotyped in the CFW mice. All genomic positions are based on Mouse Genome Assembly 38 from the NCBI database (mm10, December 2011).</p> <p>"geno"—a 1,038 x 79,748 matrix containing genotype data for 1,038 mice at 79,748 SNPs.</p> <p>For more information on these data, please refer to the Data Dryad repository: http://dx.doi.org/10.5061/dryad.2rs41</p> <p>For code implementing QTL mapping of physiological, behavioral and gene expression phenotypes, and other analyses of these data, see: http://github.com/pcarbo/cfw</p>
Data from: Spatiotemporal-social association predicts immunological similarity in rewilded mice
<p>Environmental influences on immune phenotypes are well-documented, but our understanding of which elements of the environment affect immune systems, and how, remains vague. Behaviors, including socializing with others, are central to an individual's interaction with its environment. We therefore tracked behavior of rewilded laboratory mice of three inbred strains in outdoor enclosures and examined contributions of behavior, including associations measured from spatiotemporal cooccurrences, to immune phenotypes. We found extensive variation in individual and social behavior among and within mouse strains upon rewilding. And we found that the more associated two individuals were, the more similar their immune phenotypes were. Spatiotemporal association was particularly predictive of similar memory T and B cell profiles and was more influential than sibling relationships or shared infection status. These results highlight the importance of shared spatiotemporal activity patterns and/or social networks for immune phenotype and suggest potential immunological correlates of social life.<span><br></span></p>
Acetylcholine receptor based chemogenetics engineered for neuronal inhibition and seizure control assessed in mice
<p>Analysis scripts and underlying data used to produce the figures in our study entitled "Acetylcholine receptor based chemogenetics engineered for neuronal inhibition and seizure control assessed in mice", in Nature Communications. The listed project leaders can be contacted with any questions.</p>
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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.