ABSTRACT
BACKGROUND: Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of transcriptomes, arising as a powerful tool for discovering and characterizing cell types and their developmental trajectories. However, scRNA-seq analysis is complex, requiring a continuous, iterative process to refine the data and uncover relevant biological information. A diversity of tools has been developed to address the multiple aspects of scRNA-seq data analysis. However, an easy-to-use web application capable of conducting all critical steps of scRNA-seq data analysis is still lacking. We present Asc-Seurat, a feature-rich workbench, providing an user-friendly and easy-to-install web application encapsulating tools for an all-encompassing and fluid scRNA-seq data analysis. Asc-Seurat implements functions from the Seurat package for quality control, clustering, and genes differential expression. In addition, Asc-Seurat provides a pseudotime module containing dozens of models for the trajectory inference and a functional annotation module that allows recovering gene annotation and detecting gene ontology enriched terms. We showcase Asc-Seurat's capabilities by analyzing a peripheral blood mononuclear cell dataset. CONCLUSIONS: Asc-Seurat is a comprehensive workbench providing an accessible graphical interface for scRNA-seq analysis by biologists. Asc-Seurat significantly reduces the time and effort required to analyze and interpret the information in scRNA-seq datasets.
Subject(s)
Single-Cell Analysis , Software , Cluster Analysis , Gene Expression Profiling , Leukocytes, Mononuclear , Sequence Analysis, RNAABSTRACT
We have isolated two cDNAs from geranium, PhETR1 and PhETR2. The deduced amino acid sequences of PhETR1 anti PhETR2 share 78% and 79% identity with ETR1 from Arabidopsis thaliana respectively. These genes are members of a multigene family and are expressed at moderate levels in leaves, pedicels, sepals, pistils and petals, and at very low levels in roots. PhETR1 and PhETR2 mRNAs are expressed in geranium florets long before they are receptive to pollination and transcript levels remain constant throughout floral development. Message levels of PhETR1 and PhETR2 in pistils and receptacles are unaffected by self-pollination or treatment with 1 micro/l ethylene that induces petal abscission. Our results indicate that the amount of PhETR1 and PHETR2 mRNA is not indicative of the level of sensitivity of geranium florets to ethylene.
