nicheView

A resource of gene expression, signaling and intercellular interactions in the bone marrow
Reference: C. Baccin, J. Al-Sabah, L. Velten, et al.: Combined single-cell and spatial transcriptomics reveals the molecular, cellular and spatial organization of bone marrow niches.
Contact: Lars Velten , EMBL Heidelberg and Simon Haas , DKFZ

To download our complete dataset as a Seurat object, containing all clustering and dimensionality reduction results click here

Single cell transcriptomics dataset 

            

            

              Spatial transcriptomics dataset
              

              Gene expression on various features of the image is estimated from a linear model. Deatils of the model and raw data are given in the right-hand side plots. Asterisk indicate significance of factor, in a model accounting for batch (limma/voom).
              *: p<0.05, **: p<0.01, ***: p<0.001
            

          

          

            

              

              

            

            

              

              

            

            

              

              

              

            

          

        

        

          
            In the network displayed below, cell types with a high number of potential signaling interactions are connected. To see what signaling receptors and ligands mediate the interaction select any two cell types in the drop down menus below. For the algorithm used, see
            the RNAMagnet R package
          
          

            

              

              Select any two cell types:
              

                
                

                  
                  
                

              

              

                
                

                  
                  
                

              

            

            

              

              Select a ligand-receptor pair below to display their expression
              

              

              

            

          

        

        

          
            In the t-SNE below,
            the RNAMagnet algorithm
            was used to, for each cell, estimate the anchor population it is most likely to bind to. To see what cell-cell adhesion receptors mediate the interaction, click on a point.