Project description:We report a series of spatial transcriptomics datasets of regenerating mouse muscle tissue generated with the 10x Genomics Visium platform.
Project description:Spatial transcriptomics reveals the spatial context of gene expression, but current methods are limited to assaying endogenously polyadenylated (A-tailed) RNA transcripts. Here we demonstrate that enzymatic in situ polyadenylation of RNAs enables detection of the full spectrum of RNAs, expanding the scope of sequencing-based spatial transcriptomics to the total transcriptome. We apply this Spatial Total RNA-Sequencing (STRS) approach to spatially map noncoding RNAs, newly transcribed RNAs, and non-host RNAs at the tissue-scale in the study skeletal muscle regeneration and viral-induced myocarditis. Our analyses reveal the spatial patterns of noncoding RNA expression with near-cellular resolution, identify noncoding transcripts which exhibit zonal variation in skeletal muscle regeneration, and highlight host transcriptional responses highly associated with local viral RNA abundance. Our in situ polyadenylation strategy relies on a brief, low-cost add-on to a widely used protocol for spatial RNA-sequencing, and thus could be broadly and quickly adopted. Spatial RNA-sequencing of the total transcriptome will enable new insights into spatial gene regulation and biology.
Project description:We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium platform.
Project description:Conserved and muscle group-specific gene expression patterns shape postnatal development of the novel extraocular muscle phenotype. Comparison of postnatal development of extraocular and hindlimb muscle between birth and P45. Keywords: parallel sample
Project description:Muscle injury was elicited by cardiotoxin injection into the tibialis anterior muscle. Macrophages were isolated 2 days post-injury from the regenerating muscle. We used microarray to obtain global gene expression data of muscle-derived tissue macrophage subsets. Tissue macrophages were collected from regenerating muscle samples of three animals, Ly6C+ F4/80low and Ly6C- F4/80high macrophage subsets were sorted. The global gene expression patterns of distinct macrophage subsets were analyzed on Affymetrix microarrays.
Project description:To investigate the molecular mechanisms governing the transition of skeletal muscle from atrophy to compensatory regeneration and hypertrophy, we employed a mouse model involving hindlimb unloading and subsequent reloading, conducting a comprehensive analysis of global gene expression using RNA-sequencing (RNA-seq). Gastrocnemius muscle samples were obtained from three groups: control mice, mice subjected to 10 days of hindlimb unloading-induced muscle atrophy, and mice reintroduced to normal cage activity for 1 day following the unloading period (reloading).
Project description:We report a series of single-cell transcriptomic datasets of regenerating mouse muscle tissue generated with the 10x Genomics Chromium v3 platform.