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169 results for “Phagocytes”
Data from: Integrative experimental/computational approach establishes active cellular protrusion as the primary driving force of phagocytic spreading by immune cells
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Deep immunophenotyping reveals endometriosis is marked by dysregulation of the mononuclear phagocytic system in endometrium and peripheral blood
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Data from: Phagocyte chase behaviors—discrimination between Gram-negative and Gram-positive bacteria by amoebae
Phagocytes are cells that pursue, engulf, and kill bacteria. They include macrophages and neutrophils of the mammalian immune system, but also free-living amoebae that hunt and engulf bacteria for food. Phagocytosis can result in diverse outcomes, ranging from sustenance to infection and colonization by either pathogens or beneficial symbionts—and thus, discrimination may be necessary to seek out good bacteria while avoiding bad ones. Here we tested whether the soil amoeba Dictyostelium discoideum can discriminate among different types of bacteria, using behavioral assays where amoebae were presented with paired choices of different bacteria. We observed variation in the extent to which the amoebae pursued different types of bacteria, as well as preferential migration towards Gram-negative over Gram-positive bacteria. Response profiles were similar for amoebae that originated from different geographic locations, suggesting that chase preference is conserved across much of the species range. While prior work has demonstrated that bacteria will use chemotaxis to seek out amoebae they colonize, our work suggests that the opposite also occurs—amoebae can preferentially direct themselves to particular bacteria in the environment. Preferential sensing and response may help to explain why some amoeba-bacterial associations are more common in nature than others.
Single-cell RNA sequencing of CNS-infiltrating HSC-derived phagocytes of Ms4a3Ai14, BM chimeric mice (CD45.2 Csf2rb-/-: CD45.1 Csf2rb+/+ and CD45.2 Ifngr1-/-: CD45.1 Ifngr1+/+) using 10X Genomics platform. IFN-γ and GM-CSF control complementary differentiation programs in the monocyte to phagocyte transition during neuroinflammation.
<p><strong>Single-cell RNA sequencing of CNS-infiltrating HSC-derived phagocytes of <em>Ms4a3</em><sup>Ai14</sup> at onset and peak EAE, BM chimeric mice (CD45.2 <em>Csf2rb</em><sup>-/-</sup>: CD45.1 <em>Csf2rb</em><sup>+/+</sup> and CD45.2 <em>Ifngr1<sup>-/-</sup></em>: CD45.1 <em>Ifngr1<sup>+/+</sup></em>) using 10X Genomics platform.</strong></p> <p>The sorted cells were loaded into 10x Genomics Chromium in parallel. Libraries were prepared as per the manufacturer's protocol (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol) and sequenced on an Illumina NovaSeq sequencer according to 10X Genomics recommendations (paired-end reads, R1=28, i7=8, R2=91) to a depth of around 50,000 reads per cell.</p> <p>Initial processing was done using Cell Ranger (v3.1.0) mkfastq and count (reads were aligned to GENCODE reference build GRCm38.p6 Release M23 with added tdTomato sequence for the dataset from <em>Ms4a3</em><sup>Ai14</sup> mouse and collapse UMIs). Starting from the filtered gene-cell count matrix produced by CellRranger's in-built cell calling algorithms, we proceeded with Seurat v4 workflow.</p>
Single-cell RNA sequencing of Lymph node-infiltrating HSC-derived phagocytes of Ms4a3Ai14 using 10X Genomics platform. IFN-γ and GM-CSF control complementary differentiation programs in the monocyte to phagocyte transition during neuroinflammation.
<p><strong>Single-cell RNA sequencing of Lymph node-infiltrating HSC-derived phagocytes of <em>Ms4a3</em><sup>Ai14</sup> at onset and peak EAE using 10X Genomics platform.</strong></p> <p>The sorted cells were loaded into 10x Genomics Chromium in parallel. Libraries were prepared as per the manufacturer's protocol (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol) and sequenced on an Illumina NovaSeq sequencer according to 10X Genomics recommendations (paired-end reads, R1=28, i7=8, R2=91) to a depth of around 50,000 reads per cell.</p> <p>Initial processing was done using Cell Ranger (v3.1.0) mkfastq and count (reads were aligned to GENCODE reference build GRCm38.p6 Release M23 with added tdTomato sequence for the dataset from <em>Ms4a3</em><sup>Ai14</sup> mouse and collapse UMIs). Starting from the filtered gene-cell count matrix produced by CellRranger's in-built cell calling algorithms, we proceeded with Seurat v4 workflow.</p>
Single-cell RNA sequencing of Bone Marrow-infiltrating HSC-derived phagocytes of Ms4a3Ai14 using 10X Genomics platform. IFN-γ and GM-CSF control complementary differentiation programs in the monocyte to phagocyte transition during neuroinflammation.
<p><strong>Single-cell RNA sequencing of Bone Marrow-infiltrating HSC-derived phagocytes of <em>Ms4a3</em><sup>Ai14</sup> at onset and peak EAE using 10X Genomics platform.</strong></p> <p>The sorted cells were loaded into 10x Genomics Chromium in parallel. Libraries were prepared as per the manufacturer's protocol (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol) and sequenced on an Illumina NovaSeq sequencer according to 10X Genomics recommendations (paired-end reads, R1=28, i7=8, R2=91) to a depth of around 50,000 reads per cell.</p> <p>Initial processing was done using Cell Ranger (v3.1.0) mkfastq and count (reads were aligned to GENCODE reference build GRCm38.p6 Release M23 with added tdTomato sequence for the dataset from <em>Ms4a3</em><sup>Ai14</sup> mouse and collapse UMIs). Starting from the filtered gene-cell count matrix produced by CellRranger's in-built cell calling algorithms, we proceeded with Seurat v4 workflow.</p>
Single-cell RNA sequencing of Blood-infiltrating HSC-derived phagocytes of Ms4a3Ai14 using 10X Genomics platform. IFN-γ and GM-CSF control complementary differentiation programs in the monocyte to phagocyte transition during neuroinflammation.
<p><strong>Single-cell RNA sequencing of Blood-infiltrating HSC-derived phagocytes of <em>Ms4a3</em><sup>Ai14</sup> at onset and peak EAE using 10X Genomics platform.</strong></p> <p>The sorted cells were loaded into 10x Genomics Chromium in parallel. Libraries were prepared as per the manufacturer's protocol (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol) and sequenced on an Illumina NovaSeq sequencer according to 10X Genomics recommendations (paired-end reads, R1=28, i7=8, R2=91) to a depth of around 50,000 reads per cell.</p> <p>Initial processing was done using Cell Ranger (v3.1.0) mkfastq and count (reads were aligned to GENCODE reference build GRCm38.p6 Release M23 with added tdTomato sequence for the dataset from <em>Ms4a3</em><sup>Ai14</sup> mouse and collapse UMIs). Starting from the filtered gene-cell count matrix produced by CellRranger's in-built cell calling algorithms, we proceeded with Seurat v4 workflow.</p>
Images used for Actin nano-architecture of phagocytic podosomes
<p>Images used for Actin nano-architecture of phagocytic podosomes</p>
Molecular Basis of Human Phagocyte Interactions With Bacterial Pathogens
ClinicalTrials.gov study NCT00339287. IPD Sharing: NO. Countries: 1. Publications: 2.
Perioperative Immunonutrition, Phagocytic and Bactericidal Activity of Blood Platelets in Gastric Cancer Patients
ClinicalTrials.gov study NCT01704664. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Data from: Phagocyte chase behaviors—discrimination between Gram-negative and Gram-positive bacteria by amoebae
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Data from: Phagocytic intracellular digestion in amphioxus (Branchiostoma)
The digestive methods employed by amphioxus (Branchiostoma)—both intracellular phagocytic digestion and extracellular digestion—have been discussed since 1937. Recent studies also show that epithelial cells lining the Branchiostoma digestive tract can express many immune genes. Here, in Branchiostoma belcheri, using a special tissue fixation method, we show that some epithelial cells, especially those lining the large diverticulum protruding from the gut tube, phagocytise food particles directly, and Branchiostoma can rely on this kind of phagocytic intracellular digestion to obtain energy throughout all stages of its life. Gene expression profiles suggest that diverticulum epithelial cells have functional features of both digestive cells and phagocytes. In starved Branchiostoma, these cells accumulate endogenous digestive and hydrolytic enzymes, whereas, when sated, they express many kinds of immune genes in response to stimulation by phagocytised food particles. We also found that the distal hindgut epithelium can phagocytise food particles, but not as many. These results illustrate phagocytic intercellular digestion in Branchiostoma, explain why. Branchiostoma digestive tract epithelial cells express typical immune genes, and suggest that the main physiological function of the Branchiostoma diverticulum is different from that of the vertebrate liver.
Alzheimer's disease-induced phagocytic microglia express specific profile of coding and non-coding RNAs
<p>This repository contains the data and the code used in Flavia's project.</p> <p>A folder can contain the starting raw data in "data", the R scripts in order of execution (op1, op2 ..) and the "output" folder that contains the final processed data of each operation.</p> <ul> <li>"BV2_analysis" contains the processing and analysis of the bulk RNA sequencing data with the different miRNAs in study</li> <li>"BV2_fastq_nfcore" contains the results of processing the fasta sequences with nfcore rnaseq workflow</li> <li>"Proinf_analysis" contains the analysis of the external bulk RNA sequencing data with the different studies of proinflammatory microglial cells</li> <li>"Spatial_data_analysis" contains the raw data of the spatial sequencing, the assempbly of the spatial expression profiles starting from the DAPI images and the transcripts coordinates, the analysis performed on the data</li> <li>"Spatial_U_scRNA_analysis" contains the code that integrates the spatial sequencing with the scRNA sequencing, plus the code of the analysis</li> </ul>
Data from: Phagocytic intracellular digestion in amphioxus (Branchiostoma)
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Data from: A method for time-resolved measurements of the mechanics of phagocytic cups
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Enhanced and selective translation expands the lysosome size and promotes antigen presentation during phagocyte activation
GEO Series GSE136470. Mus musculus. 18 samples. Type: Expression profiling by high throughput sequencing.
Secreted phosphoprotein 1 expression in retinal mononuclear phagocytes links murine to human choroidal neovascularization
GEO Series GSE160011. Mus musculus. 19 samples. Type: Expression profiling by high throughput sequencing.
Comparative Single Cell RNA Sequencing of Notch2 and RBPJ-deficient mononuclear phagocyte cells and myeloid progenitors from the spleen and bone marrow
GEO Series GSE289018. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Single-cell mRNA analysis of colon phagocyte heterogeneity identifies two major macrophage developmental pathways
GEO Series GSE137927. Mus musculus. 34 samples. Type: Expression profiling by high throughput sequencing.
Human and murine transcriptome profiling identifies cross-species homology in pulmonary mononuclear phagocytes [DCs and Monocytes]
GEO Series GSE132911. Mus musculus. 15 samples. Type: Expression profiling by high throughput sequencing.
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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.