bone marrow datasets  (Matek Inc)

Journal: Communications Biology

Article Title: Cluster-independent multiscale marker identification in single-cell RNA-seq data using localized marker detector (LMD)

doi: 10.1038/s42003-025-08485-y

Figure Lengend Snippet: A , B Gene modules associated with the cell cycle. Gene modules were identified from the Tabula Muris bone marrow FACS dataset, and their function was classified by Reactome pathway analysis. Modules 22, 20, and 19 were associated with S phase, S/G2/M and G2/M phases, respectively. A Bubble plot of the top 5 significantly enriched Reactome pathways (Benjamini-Hochberg adjusted p -value < 0.05) for each module. Bubble color indicates -log 10 -adjusted p -value, and the size represents the fraction of module genes associated with the pathway. B Module scores in two Tabula Muris bone marrow datasets, and reference cell-cycle annotation from Seurat (left). C Gene modules associated with B cells at different stages of maturation. Module 7 is associated with pro-B cells, module 6 with pre-pro-B cell, module 2 with immature and mature B cells, and module 3 with naive B cells. D Gene modules associated with the production of granulocytes. Module 8 contains genes expressed during granulocytopoiesis, module 15 contains genes common for granulocytopoietic cells and granulocytes, module 11 contains genes involved in granulocyte maturation, and module 10 may represent a rare granulocyte subgroup.

Article Snippet: We demonstrate the flexibility of LMD markers in characterizing functional cell groups using the Tabula Muris bone marrow FACS dataset, ranging from broad gene expression across multiple regions to fine-grained expression within a single cluster.

Techniques:

Journal: Communications Biology

Article Title: Cluster-independent multiscale marker identification in single-cell RNA-seq data using localized marker detector (LMD)

doi: 10.1038/s42003-025-08485-y

Figure Lengend Snippet: A , B Gene modules associated with the cell cycle. Gene modules were identified from the Tabula Muris bone marrow FACS dataset, and their function was classified by Reactome pathway analysis. Modules 22, 20, and 19 were associated with S phase, S/G2/M and G2/M phases, respectively. A Bubble plot of the top 5 significantly enriched Reactome pathways (Benjamini-Hochberg adjusted p -value < 0.05) for each module. Bubble color indicates -log 10 -adjusted p -value, and the size represents the fraction of module genes associated with the pathway. B Module scores in two Tabula Muris bone marrow datasets, and reference cell-cycle annotation from Seurat (left). C Gene modules associated with B cells at different stages of maturation. Module 7 is associated with pro-B cells, module 6 with pre-pro-B cell, module 2 with immature and mature B cells, and module 3 with naive B cells. D Gene modules associated with the production of granulocytes. Module 8 contains genes expressed during granulocytopoiesis, module 15 contains genes common for granulocytopoietic cells and granulocytes, module 11 contains genes involved in granulocyte maturation, and module 10 may represent a rare granulocyte subgroup.

Article Snippet: The processed Seurat data objects (Tabula Muris bone marrow dataset and mouse embryonic skin dataset) are available at Figshare: 10.6084/m9.figshare.26507098.

Techniques:

Journal: Communications Biology

Article Title: Cluster-independent multiscale marker identification in single-cell RNA-seq data using localized marker detector (LMD)

doi: 10.1038/s42003-025-08485-y

Figure Lengend Snippet: A , B Gene modules associated with the cell cycle. Gene modules were identified from the Tabula Muris bone marrow FACS dataset, and their function was classified by Reactome pathway analysis. Modules 22, 20, and 19 were associated with S phase, S/G2/M and G2/M phases, respectively. A Bubble plot of the top 5 significantly enriched Reactome pathways (Benjamini-Hochberg adjusted p -value < 0.05) for each module. Bubble color indicates -log 10 -adjusted p -value, and the size represents the fraction of module genes associated with the pathway. B Module scores in two Tabula Muris bone marrow datasets, and reference cell-cycle annotation from Seurat (left). C Gene modules associated with B cells at different stages of maturation. Module 7 is associated with pro-B cells, module 6 with pre-pro-B cell, module 2 with immature and mature B cells, and module 3 with naive B cells. D Gene modules associated with the production of granulocytes. Module 8 contains genes expressed during granulocytopoiesis, module 15 contains genes common for granulocytopoietic cells and granulocytes, module 11 contains genes involved in granulocyte maturation, and module 10 may represent a rare granulocyte subgroup.

Article Snippet: To assess the effect of expression scaling, we tested binarizing expression values by setting all non-zero entries to one, using the Tabula Muris bone marrow FACS dataset (Supplementary Fig. ).

Techniques: