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Macrophages are strongly adapted to their tissue of residence. Yet, little is known about the cell-cell interactions that imprint the tissue-specific identities of macrophages in their respective niches. Using conditional depletion of liver Kupffer cells, we traced the developmental stages of monocytes differentiating into Kupffer cells and mapped the cellular interactions imprinting the Kupffer cell identity. Kupffer cell loss induced tumor necrosis factor (TNF)- and interleukin-1 (IL-1) receptor-dependent activation of stellate cells and endothelial cells, resulting in the transient production of chemokines and adhesion molecules orchestrating monocyte engraftment. Engrafted circulating monocytes transmigrated into the perisinusoidal space and acquired the liver-associated transcription factors inhibitor of DNA 3 (ID3) and liver X receptor-α (LXR-α). Coordinated interactions with hepatocytes induced ID3 expression, whereas endothelial cells and stellate cells induced LXR-α via a synergistic NOTCH-BMP pathway. This study shows that the Kupffer cell niche is composed of stellate cells, hepatocytes, and endothelial cells that together imprint the liver-specific macrophage identity.
Pubmed ID: 31561945 RIS Download
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Software package that implements and enhances circular visualization in R. Due to natural born feature of R to draw statistical graphics, this package can provide more general and flexible way to visualize huge information in circular style.
View all literature mentionsStatistical analysis software that combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. Designed for biological research applications in pharmacology, physiology, and other biological fields for data analysis, hypothesis testing, and modeling.
View all literature mentionsCommercial supplier and developer of in vivo antibodies. Provides antibodies and antibody production services.
View all literature mentionsImaris provides range of capabilities for working with three dimensional images. Uses flexible editing and processing functions, such as interactive surface rendering and object slicing capabilities. And output to standard TIFF, Quicktime and AVI formats. Imaris accepts virtually all image formats that are used in confocal microscopy and many of those used in wide-field image acquisition.
View all literature mentionsSoftware for single-cell flow cytometry analysis. Its functions include management, display, manipulation, analysis and publication of the data stream produced by flow and mass cytometers.
View all literature mentionsA commercial organization which provides assay technologies to isolate DNA, RNA, and proteins from any biological sample. Assay technologies are then used to make specific target biomolecules, such as the DNA of a specific virus, visible for subsequent analysis.
View all literature mentionsA web-based software application that enables users to analyze, integrate, and understand data derived from gene expression, microRNA, and SNP microarrays, metabolomics, proteomics, and RNA-Seq experiments, and small-scale experiments that generate gene and chemical lists. Users can search for targeted information on genes, proteins, chemicals, and drugs, and build interactive models of experimental systems. IPA allows exploration of molecular, chemical, gene, protein and miRNA interactions, creation of custom molecular pathways, and the ability to view and modify metabolic, signaling, and toxicological canonical pathways. In addition to the networks and pathways that can be created, IPA can provide multiple layering of additional information, such as drugs, disease genes, expression data, cellular functions and processes, or a researchers own genes or chemicals of interest.
View all literature mentionsSoftware application that carries out single-point and multipoint analyses of pedigree data, including IBD and kinship calculations, nonparametric and variance component linkage analyses, error detection and information content mapping. For multipoint analyses in dense maps, Merlin allows the user to impose constraints on the number of recombinants between consecutive markers. Merlin estimates haplotypes by finding the most likely path of gene flow or by sampling paths of gene flow at all markers jointly. It can also list all possible nonrecombinant haplotypes within short regions. Finally, Merlin provides swap-file support for handling very large numbers of markers as well as gene-dropping simulations for estimating empirical significance levels. (entry from Genetic Analysis Software)
View all literature mentionsAn open community platform for bioimage informatics providing the software resources to visualize, annotate and quantify bioimaging data. To bridge the gap between developers and users, it combines: a) an open-source image analysis software, offering a powerful and flexible environment for developers such as applied mathematicians to write algorithms fast and efficiently; b) a common set of tools to view and manipulate data, and a set of plugins to perform specific quantification or analysis on images; c) a community-based website centralizing all plugins and resources to facilitate their management and maximize their visibility towards users. Workspaces are virtual groups of plugins dedicated to a specific application or image processing domain. By downloading a workspace, ICY automatically installs all corresponding plugins. The workspaces are enabled, but the editing section is not ready yet. If you want to publish a plugin on this website, its code has to be GPL. Source code is available and provided in each application download.
View all literature mentionsSoftware package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression.
View all literature mentionsSoftware Java pipeline for trimming tasks for Illumina paired end and single ended data. Flexible Trimmer for Illumina Sequence Data. Pair aware preprocessing tool optimized for Illumina next generation sequencing data. Includes several processing steps for read trimming and filtering. Operating systems Unix/Linux, Mac OS, Windows.
View all literature mentionsQuality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis.
View all literature mentionsSoftware package for advanced image processing, analysis, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets.
View all literature mentionsMus musculus with name B6(C)-Ccr2tm1.1Cln/J from IMSR.
View all literature mentionsAllele Detail: Targeted, Transgenic This is a legacy resource.
View all literature mentionsMus musculus with name C57BL/6J from IMSR.
View all literature mentionsThis polyclonal secondary targets IgG (H+L)
View all literature mentionsThis polyclonal secondary targets IgG (H+L)
View all literature mentionsThis unknown targets Rabbit IgG (H+L)
View all literature mentionsThis unknown targets Rat IgG (H+L)
View all literature mentionsThis monoclonal targets TIM-4
View all literature mentionsThis monoclonal targets Siglec-F
View all literature mentionsThis monoclonal targets TNFα
View all literature mentionsThis monoclonal targets LYVE1
View all literature mentionsThis polyclonal targets Mouse M-CSF Affinity Purified Ab
View all literature mentionsThis monoclonal targets LYVE1
View all literature mentionsThis monoclonal targets Ly-6G
View all literature mentionsThis monoclonal targets Mouse Ly-6C
View all literature mentionsThis polyclonal targets Mouse LYVE-1
View all literature mentionsThis monoclonal targets Ki-67
View all literature mentionsThis monoclonal targets Mki67
View all literature mentionsThis polyclonal targets Mouse IL-34
View all literature mentionsThis monoclonal targets Ly-6C
View all literature mentionsThis polyclonal targets IL1 alpha
View all literature mentionsThis polyclonal targets Mouse IL-1 beta / IL-1F2
View all literature mentionsThis monoclonal targets MHC Class II (I-A/I-E)
View all literature mentionsThis monoclonal targets I-A/I-E
View all literature mentionsThis monoclonal targets I-A/I-E
View all literature mentionsThis monoclonal targets MHC Class II (I-A/I-E)
View all literature mentionsThis polyclonal targets GFP-1010
View all literature mentionsThis monoclonal targets F4/80
View all literature mentionsThis monoclonal targets F4/80
View all literature mentionsThis monoclonal targets Delta-like protein 4 (DLL4)
View all literature mentionsThis monoclonal targets Delta-like protein 1 (DLL1)
View all literature mentionsThis polyclonal targets Human/Mouse Desmin Affinity Purified Ab
View all literature mentionsThis polyclonal targets Desmin
View all literature mentionsThis polyclonal targets Mouse CLECSF13 / CLEC4F
View all literature mentionsThis monoclonal targets CD207 / Langerin
View all literature mentionsThis monoclonal targets CD140b (PDGFRB)
View all literature mentionsThis monoclonal targets CD146
View all literature mentionsThis monoclonal targets CD115 (c-fms)
View all literature mentionsThis monoclonal targets CD172a
View all literature mentionsThis monoclonal targets CD106
View all literature mentionsThis unknown targets IgG (H+L)
View all literature mentionsThis monoclonal targets CD62E (E-Selectin)
View all literature mentionsThis monoclonal targets CD64
View all literature mentionsThis monoclonal targets CD54
View all literature mentionsThis monoclonal targets CD45
View all literature mentionsThis monoclonal targets CD45
View all literature mentionsThis monoclonal targets CD61
View all literature mentionsThis monoclonal targets CD38
View all literature mentionsThis monoclonal targets CD41
View all literature mentionsThis monoclonal targets CD45
View all literature mentionsThis monoclonal targets CD11c
View all literature mentionsThis monoclonal targets CD31 (PECAM-1)
View all literature mentionsThis monoclonal targets CD11b
View all literature mentionsThis monoclonal targets CD11b
View all literature mentionsThis unknown targets Goat IgG (H+L)
View all literature mentionsThis unknown targets Goat IgG (H+L)
View all literature mentionsThis isotype control targets GST
View all literature mentionsThis unknown targets Armenian Hamster IgG (H+L)
View all literature mentionsThis polyclonal secondary targets IgG (H+L)
View all literature mentionsThis unknown targets IgG (H+L)
View all literature mentionsThis unknown targets IgG (H+L)
View all literature mentionsThis unknown targets IgG (H+L)
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