In situ capturing technologies add tissue context to gene expression data, with the potential of providing a greater understanding of complex biological systems. However, splicing variants and full-length...
Read More »Analysis of single-cell rna-seq data
As single-cell RNA sequencing experiments continue to advance scientific discoveries across biological disciplines, an increasing number of analysis tools and workflows for analyzing the data have been developed. In this chapter, University of Florida...
Read More »AllenDigger – spatial expression data visualization, spatial heterogeneity delineation, and single-cell registration based on the Allen Brain Atlas
Spatial transcriptomics can be used to capture cellular spatial organization and has facilitated new insights into different biological contexts, including developmental biology, cancer, and neuroscience. However, its wide application is still hindered by...
Read More »New research identifies an inaccuracy in the single cell GENCODE gene model
Correction of the single cell RNA sequencing GENCODE gene model enables accurate detection and study of the novel target PVRIG, advancing...
Read More »Femtosecond laser microdissection for isolation of regenerating C. elegans neurons for single-cell RNA sequencing
Our understanding of nerve regeneration can be enhanced by delineating its underlying molecular activities at single-neuron resolution in model organisms such as Caenorhabditis elegans. Existing cell...
Read More »Spatial epigenome–transcriptome co-profiling of mammalian tissues
Emerging spatial technologies, including spatial transcriptomics and spatial epigenomics, are becoming powerful tools for profiling of cellular states in the tissue context1-5. However, current...
Read More »A protocol for single nucleus RNA-seq from frozen skeletal muscle
Single-cell technologies are a method of choice to obtain vast amounts of cell-specific transcriptional information under physiological and diseased states. Myogenic cells are resistant to single-cell RNA...
Read More »Single-nucleus transcriptomics reveals new understanding of how androgen therapy affects breast tissue
Insights from the study of transgender men undergoing androgen therapy may help scientists learn how to use the hormone to prevent or fight a type of breast cancer that is fueled by estrogen...
Read More »The power of scRNA-seq in guiding the development of CAR-T cell therapy
Acute myeloid leukemia (AML) is a type of cancer that affects the bone marrow and blood. It is a very aggressive cancer and has a high mortality rate...
Read More »scAnnotate – an automated cell type annotation tool for single-cell RNA-sequencing data
Single-cell RNA-sequencing (scRNA-seq) technology enables researchers to investigate a genome at the cellular level with unprecedented resolution...
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