Searching across hundreds of databases
Intestinal mesenchymal cells play essential roles in epithelial homeostasis, matrix remodeling, immunity, and inflammation. But the extent of heterogeneity within the colonic mesenchyme in these processes remains unknown. Using unbiased single-cell profiling of over 16,500 colonic mesenchymal cells, we reveal four subsets of fibroblasts expressing divergent transcriptional regulators and functional pathways, in addition to pericytes and myofibroblasts. We identified a niche population located in proximity to epithelial crypts expressing SOX6, F3 (CD142), and WNT genes essential for colonic epithelial stem cell function. In colitis, we observed dysregulation of this niche and emergence of an activated mesenchymal population. This subset expressed TNF superfamily member 14 (TNFSF14), fibroblastic reticular cell-associated genes, IL-33, and Lysyl oxidases. Further, it induced factors that impaired epithelial proliferation and maturation and contributed to oxidative stress and disease severity in vivo. Our work defines how the colonic mesenchyme remodels to fuel inflammation and barrier dysfunction in IBD.
Pubmed ID: 30270042 RIS Download
Publication data is provided by the National Library of Medicine ® and PubMed ®. Data is retrieved from PubMed ® on a weekly schedule. For terms and conditions see the National Library of Medicine Terms and Conditions.
Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.
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 mentionsSoftware package for high-performance read alignment, quantification and mutation discovery.General purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. Subread aligner as fast, accurate and scalable read mapping by seed-and-vote.These programs were also implemented in Bioconductor R package Rsubread.
View all literature mentionsHarvester is a Web-based tool that bulk-collects bioinformatic data on human proteins from various databases and prediction servers. It is a meta search engine for gene and protein information. It searches 16 major databases and prediction servers and combines the results on pregenerated HTML pages. In this way Harvester can provide comprehensive gene-protein information from different servers in a convenient and fast manner. As full text meta search engine, similar to Google trade mark, Harvester allows screening of the whole genome proteome for current protein functions and predictions in a few seconds. With Harvester it is now possible to compare and check the quality of different database entries and prediction algorithms on a single page. Sponsors: This work has been supported by the BMBF with grants 01GR0101 and 01KW0013.
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 mentionsAn Organization portal, Antibody supplier, Service resource,
View all literature mentionsThis monoclonal targets CD45
View all literature mentionsThis polyclonal targets Human LIGHT / TNFSF14
View all literature mentionsThis unknown targets IgG Rabbit
View all literature mentionsThis monoclonal targets Human OSF-2 / Periostin
View all literature mentionsThis unknown targets CD31/PECAM-1
View all literature mentionsThis monoclonal targets Human SOX6
View all literature mentionsThis monoclonal targets Human Clusterin MAb (Clone 350227)
View all literature mentionsThis unknown targets CD45
View all literature mentionsThis polyclonal targets FDCSP antibody
View all literature mentionsThis recombinant monoclonal targets Fibroblast
View all literature mentionsThis monoclonal targets CD74
View all literature mentionsThis monoclonal targets CD326/EpCAM
View all literature mentionsThis monoclonal targets IL-33
View all literature mentionsThis monoclonal targets CD326
View all literature mentionsThis monoclonal targets CD90
View all literature mentionsThis monoclonal targets Podoplanin
View all literature mentionsThis unknown targets IgG
View all literature mentionsThis monoclonal targets Human ZEB1 MAb (Clone 639914)
View all literature mentionsThis monoclonal targets CD45R antibody [RA3-6B2]
View all literature mentionsThis monoclonal targets CD24
View all literature mentionsThis polyclonal targets Human Podoplanin
View all literature mentionsThis polyclonal targets SMAD7 antibody produced in rabbit
View all literature mentionsThis unknown targets Rabbit IgG
View all literature mentionsThis monoclonal targets Human CCL19 / MIP-3 beta
View all literature mentionsThis monoclonal targets CD31
View all literature mentionsThis polyclonal targets Human CCL21 / 6Ckine
View all literature mentionsThis unknown targets
View all literature mentionsThis unknown targets
View all literature mentionsThis unknown targets IgG
View all literature mentionsThis unknown targets IgG
View all literature mentionsThis monoclonal targets 2B11: Isolated neoplastic cells from a case of T-cell lymphoma/leukaemia (1). PD7/26: Human peripheral blood lymphocytes maintained in T-cell growth factor (1).
View all literature mentionsThis polyclonal targets Human PDGF R alpha
View all literature mentionsThis monoclonal targets Actin, alpha, Smooth Muscle
View all literature mentionsThis monoclonal targets ZEB2/SIP1
View all literature mentionsThis monoclonal targets Human CD55 / DAF
View all literature mentionsThis polyclonal targets Mouse Bcl-6, aa 522-696
View all literature mentionsThis monoclonal targets SOX6
View all literature mentionsThis polyclonal targets Human Coagulation Factor III / Tissue Factor
View all literature mentionsThis polyclonal targets Human/Mouse COX-2 Affinity Purified Ab
View all literature mentionsSoftware package for classification and regression based on a forest of trees using random inputs.
View all literature mentionsSoftware R package for weighted correlation network analysis. WGCNA is also available as point-and-click application. Unfortunately this application is not maintained anymore. It is known to have compatibility problems with R-2.8.x and newer, and the methods it implements are not all state of the art.
View all literature mentionsSoftware as R wrapper for Van der Maaten's Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding. Used for high-dimentional data visualisation.
View all literature mentionsSoftware program for adapter trimming that is specially designed for processing Illumina paired-end sequences.
View all literature mentionsSoftware toolkit for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control. This package facilitates pre-processing, quality control, normalization and visualization of scRNA-seq data.
View all literature mentionsSoftware package that implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.
View all literature mentionsJava toolset for working with next generation sequencing data in the BAM format.
View all literature mentionsData aggregate that compiles results from bioinformatics analyses across multiple samples into a single report. It is written in Python.
View all literature mentionsGraph-based alignment of next generation sequencing reads to a population of genomes.
View all literature mentionsA read summarization program, which counts mapped reads for the genomic features such as genes and exons.
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 mentionsCollection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.
View all literature mentionsSoftware as R package designed for QC, analysis, and exploration of single cell RNA-seq data. Enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data.
View all literature mentionsContains functions for removing batch effects and other unwanted variation in high-throughput experiment.
View all literature mentionsCell line RAW 264.7 is a Cancer cell line with a species of origin Mus musculus
View all literature mentionsCell line L Wnt-3A is a Spontaneously immortalized cell line with a species of origin Mus musculus (Mouse)
View all literature mentionsSoftware package for classification and regression based on a forest of trees using random inputs.
View all literature mentionsSoftware R package for weighted correlation network analysis. WGCNA is also available as point-and-click application. Unfortunately this application is not maintained anymore. It is known to have compatibility problems with R-2.8.x and newer, and the methods it implements are not all state of the art.
View all literature mentionsSoftware as R wrapper for Van der Maaten's Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding. Used for high-dimentional data visualisation.
View all literature mentionsSoftware program for adapter trimming that is specially designed for processing Illumina paired-end sequences.
View all literature mentionsSoftware toolkit for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control. This package facilitates pre-processing, quality control, normalization and visualization of scRNA-seq data.
View all literature mentionsSoftware package that implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.
View all literature mentionsJava toolset for working with next generation sequencing data in the BAM format.
View all literature mentionsData aggregate that compiles results from bioinformatics analyses across multiple samples into a single report. It is written in Python.
View all literature mentionsGraph-based alignment of next generation sequencing reads to a population of genomes.
View all literature mentionsA read summarization program, which counts mapped reads for the genomic features such as genes and exons.
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 mentionsCollection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.
View all literature mentionsSoftware as R package designed for QC, analysis, and exploration of single cell RNA-seq data. Enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data.
View all literature mentionsContains functions for removing batch effects and other unwanted variation in high-throughput experiment.
View all literature mentionsMus musculus with name C57BL/6J from IMSR.
View all literature mentionsCell line RAW 264.7 is a Cancer cell line with a species of origin Mus musculus
View all literature mentionsCell line L Wnt-3A is a Spontaneously immortalized cell line with a species of origin Mus musculus (Mouse)
View all literature mentionsThis unknown targets
View all literature mentionsThis unknown targets
View all literature mentionsThis unknown targets IgG
View all literature mentionsThis unknown targets IgG
View all literature mentionsThis unknown targets IgG Rabbit
View all literature mentionsThis unknown targets CD31/PECAM-1
View all literature mentionsThis unknown targets CD45
View all literature mentionsThis monoclonal targets CD326/EpCAM
View all literature mentionsThis monoclonal targets CD90
View all literature mentionsThis monoclonal targets CD45R antibody [RA3-6B2]
View all literature mentionsThis polyclonal targets SMAD7 antibody produced in rabbit
View all literature mentionsThis monoclonal targets Human OSF-2 / Periostin
View all literature mentionsThis monoclonal targets Human Clusterin MAb (Clone 350227)
View all literature mentionsThis monoclonal targets IL-33
View all literature mentionsThis monoclonal targets Human ZEB1 MAb (Clone 639914)
View all literature mentionsThis polyclonal targets Human Podoplanin
View all literature mentionsThis monoclonal targets Human CCL19 / MIP-3 beta
View all literature mentionsThis polyclonal targets Human CCL21 / 6Ckine
View all literature mentionsThis polyclonal targets Human LIGHT / TNFSF14
View all literature mentionsThis monoclonal targets Human SOX6
View all literature mentionsThis polyclonal targets FDCSP antibody
View all literature mentionsThis recombinant monoclonal targets Fibroblast
View all literature mentionsThis monoclonal targets CD74
View all literature mentionsThis monoclonal targets CD326
View all literature mentionsThis monoclonal targets Podoplanin
View all literature mentionsThis unknown targets IgG
View all literature mentionsThis monoclonal targets CD24
View all literature mentionsThis unknown targets Rabbit IgG
View all literature mentionsThis monoclonal targets CD31
View all literature mentionsThis monoclonal targets CD45
View all literature mentionsThis monoclonal targets 2B11: Isolated neoplastic cells from a case of T-cell lymphoma/leukaemia (1). PD7/26: Human peripheral blood lymphocytes maintained in T-cell growth factor (1).
View all literature mentionsThis polyclonal targets Human PDGF R alpha
View all literature mentionsThis monoclonal targets Human CD55 / DAF
View all literature mentionsThis polyclonal targets Mouse Bcl-6, aa 522-696
View all literature mentionsThis monoclonal targets SOX6
View all literature mentionsThis polyclonal targets Human Coagulation Factor III / Tissue Factor
View all literature mentionsThis polyclonal targets Human/Mouse COX-2 Affinity Purified Ab
View all literature mentionsThis unknown targets IgG
View all literature mentionsThis polyclonal targets FDCSP antibody
View all literature mentionsThis monoclonal targets CD45
View all literature mentionsThis unknown targets Rabbit IgG
View all literature mentionsThis monoclonal targets CD31
View all literature mentionsThis monoclonal targets CD24
View all literature mentionsThis polyclonal targets SMAD7 antibody produced in rabbit
View all literature mentionsThis unknown targets CD45
View all literature mentionsThis monoclonal targets SOX6
View all literature mentionsThis monoclonal targets Human CD55 / DAF
View all literature mentionsThis polyclonal targets Human Coagulation Factor III / Tissue Factor
View all literature mentionsThis polyclonal targets Mouse Bcl-6, aa 522-696
View all literature mentionsThis polyclonal targets Human CCL21 / 6Ckine
View all literature mentionsThis polyclonal targets Human LIGHT / TNFSF14
View all literature mentionsThis monoclonal targets Human SOX6
View all literature mentionsThis polyclonal targets Human/Mouse COX-2 Affinity Purified Ab
View all literature mentionsThis monoclonal targets CD326
View all literature mentionsThis recombinant monoclonal targets Fibroblast
View all literature mentionsThis monoclonal targets Podoplanin
View all literature mentionsThis monoclonal targets CD74
View all literature mentionsThis unknown targets IgG Rabbit
View all literature mentionsThis unknown targets IgG
View all literature mentionsThis monoclonal targets Human CCL19 / MIP-3 beta
View all literature mentionsThis unknown targets IgG
View all literature mentionsThis unknown targets CD31/PECAM-1
View all literature mentionsThis unknown targets
View all literature mentionsThis monoclonal targets 2B11: Isolated neoplastic cells from a case of T-cell lymphoma/leukaemia (1). PD7/26: Human peripheral blood lymphocytes maintained in T-cell growth factor (1).
View all literature mentionsThis monoclonal targets CD326/EpCAM
View all literature mentionsThis monoclonal targets CD45R antibody [RA3-6B2]
View all literature mentionsThis monoclonal targets CD90
View all literature mentionsThis monoclonal targets Human ZEB1 MAb (Clone 639914)
View all literature mentionsThis monoclonal targets Human Clusterin MAb (Clone 350227)
View all literature mentionsCell line L Wnt-3A is a Spontaneously immortalized cell line with a species of origin Mus musculus (Mouse)
View all literature mentionsCell line RAW 264.7 is a Cancer cell line with a species of origin Mus musculus
View all literature mentionsThis monoclonal targets Actin, alpha, Smooth Muscle
View all literature mentionsThis unknown targets
View all literature mentionsSoftware package for classification and regression based on a forest of trees using random inputs.
View all literature mentionsData aggregate that compiles results from bioinformatics analyses across multiple samples into a single report. It is written in Python.
View all literature mentionsA read summarization program, which counts mapped reads for the genomic features such as genes and exons.
View all literature mentionsGraph-based alignment of next generation sequencing reads to a population of genomes.
View all literature mentionsJava toolset for working with next generation sequencing data in the BAM format.
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 mentionsCollection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.
View all literature mentionsContains functions for removing batch effects and other unwanted variation in high-throughput experiment.
View all literature mentionsSoftware as R package designed for QC, analysis, and exploration of single cell RNA-seq data. Enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data.
View all literature mentionsMus musculus with name C57BL/6J from IMSR.
View all literature mentionsSoftware program for adapter trimming that is specially designed for processing Illumina paired-end sequences.
View all literature mentionsSoftware R package for weighted correlation network analysis. WGCNA is also available as point-and-click application. Unfortunately this application is not maintained anymore. It is known to have compatibility problems with R-2.8.x and newer, and the methods it implements are not all state of the art.
View all literature mentionsSoftware toolkit for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control. This package facilitates pre-processing, quality control, normalization and visualization of scRNA-seq data.
View all literature mentionsSoftware as R wrapper for Van der Maaten's Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding. Used for high-dimentional data visualisation.
View all literature mentionsSoftware package that implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.
View all literature mentionsThis monoclonal targets Human OSF-2 / Periostin
View all literature mentionsThis polyclonal targets Human PDGF R alpha
View all literature mentionsThis monoclonal targets IL-33
View all literature mentionsThis monoclonal targets ZEB2/SIP1
View all literature mentionsThis polyclonal targets Human Podoplanin
View all literature mentionsThe SciCrunch Infrastructure was developed as a cooperative data platform to be used by diverse communities in making data more FAIR.
scicrunch.org
