Project description:This submission is a dataset of two modalities, single-nucleus transcriptomics and single-nuclei spatial transcriptomics in the spinal cords of mice. The single-nuclei transcriptomics data is harvested and profiled using 10x Genomics Chromium Single Cell Kit Version. The single-nuclei spatial transcriptomics data is harvested and profiled using Visium Spatial Gene Expression.
Project description:To uncover molecular determinants of motor neuron degeneration and selective vulnerability in amyotrophic lateral sclerosis (ALS), we performed longitudinal single-nucleus RNA sequencing, paired single-nucleus RNA and ATAC sequencing, and MERFISH spatial transcriptomics from control and SOD1-G93A mouse spinal cords. For the final snRNA-seq analysis, control experiments from Blum et al., Nat Neurosci, 2021 (GEO accession: GSE161621) were also used.
Project description:These data were used in the spatial transcriptomics analysis of the article titled \\"Single-Cell and Spatial Transcriptomics Analysis of Human Adrenal Aging\\".
Project description:Identification of cell types in the interphase between muscle and tendon by Visium Spatial Transcriptomics of four human semitendinous muscle-tendon biopsies. Cell types identified by single nuclei RNA seq on similar tissue were localized in situ with the use of Spatial Transcriptomics.
Project description:To uncover molecular determinants of motor neuron degeneration and selective vulnerability in amyotrophic lateral sclerosis (ALS), we performed longitudinal single-nucleus RNA sequencing, paired single-nucleus RNA and ATAC sequencing, and MERFISH spatial transcriptomics from control and SOD1-G93A mouse spinal cords. For the final snRNA-seq analysis, control experiments from Blum et al., Nat Neurosci, 2021 (GEO accession: GSE161621) were also used.
Project description:We profiled 87 primary-recurrentpatient-matched paired GBM specimens with single-nucleus RNA and bulk-DNA sequencing and single-cell open-chromatin and spatial transcriptomics/proteomics assays. We found that recurrent GBMs are characterized by a shift to a mesenchymal phenotype in response to therapy
Project description:Skeletal muscles are complex organs consisting of multiple tissues, including connective tissue, blood vessels, nerves and multinucleated myofibers. Single-nucleus transcriptomics analyses have revealed distinctive myonuclear populations related to myofiber type and to specialized regions, including neuromuscular and myotendinous junctions. However, the use of tissue dissociation methods prevented access to global spatial organization. Here we applied RNA tomography (TOMOseq), a spatial transcriptomics approach, to explore gene expression differences along murine tibialis anterior muscles.
Project description:Animal behavior is linked to the gene regulatory network (GRN) coordinating gene expression in the brain. Eusocial honeybees, with their natural behavioral plasticity, provide an excellent model for exploring the connection between brain activity and behavior. Using single-nucleus RNA sequencing and spatial transcriptomics, we analyze the expression patterns of brain cells associated with the behavioral maturation from nursing to foraging. Integrating spatial and cellular data uncovered cell-type and spatial heterogeneity in GRN organization.
Project description:We applied an integrative single-cell genomics strategy with single nucleus RNA sequencing (snRNA-seq) and single nucleus Assay for Transposase-Accessible Chromatin sequencing (snATAC-seq) together with spatial transcriptomics from the same tissue mapping human cardiac cells in homeostasis and after myocardial infarction (MI) at unprecedented spatial and molecular resolution. We profiled in total 31 samples from 23 patients including four non-transplanted donor hearts as controls and samples from tissues with necrotic tissue areas (ischemic zone, IZ), border zone (BZ), and the non-affected left ventricular myocardium (remote zone, RZ) of patients with acute MI.
