scrna-seq results  (Biotechnology Information)

Journal: Frontiers in Molecular Neuroscience

Article Title: Single-Cell RNA-Seq of Cisplatin-Treated Adult Stria Vascularis Identifies Cell Type-Specific Regulatory Networks and Novel Therapeutic Gene Targets

doi: 10.3389/fnmol.2021.718241

Figure Lengend Snippet: scRNA-Seq of cisplatin-treated adult SV demonstrates all the expected cell populations as untreated adult SV. Uniform manifold and projection (UMAP) clusters identified using published markers, showing marginal, intermediate, and basal cells in pink, green, and blue, respectively. Each dot represents a single whole cell. Additional cell types identified were spindle cells, fibrocytes, Reissner’s membrane cells, neutrophils, B-cells, macrophages, and red blood cells (RBCs).

Article Snippet: Following Illumina sequencing of the scRNA-Seq results, three files were created: a list of individually barcoded cells, a list of gene symbols with their Ensembl IDs, and a sparse matrix of the read counts of each gene in each cell.

Techniques:

Journal: Frontiers in Molecular Neuroscience

Article Title: Single-Cell RNA-Seq of Cisplatin-Treated Adult Stria Vascularis Identifies Cell Type-Specific Regulatory Networks and Novel Therapeutic Gene Targets

doi: 10.3389/fnmol.2021.718241

Figure Lengend Snippet: Differential expression analysis reveals the transcriptomic changes in individual cell types of the SV after cisplatin treatment. (A) Volcano plot depicting differential gene expression between the scRNA-Seq data of marginal cells of control and cisplatin-treated mice. Genes are represented by circles, with genes enriched in cisplatin-treated SV cells to the right and genes enriched in control SV cells to the left. Positive and negative fold-change thresholds (FC ± 1.25) in log2 scale are represented by the vertical dotted lines. The p -value threshold ( p -value ± 0.0001) in –log10 scale is represented by the horizontal dotted line. Red circles are genes that exceed both fold change and p -value threshold criteria. Green circles are genes that exceed the fold change threshold but not the p -value threshold. Blue circles are genes that exceed the p -value threshold but not the fold change threshold. Gray circles are genes that do not meet either threshold criteria. (B) Differential gene expression between the scRNA-Seq data of intermediate cells of control and cisplatin-treated mice. (C) Differential gene expression between the scRNA-Seq data of basal cells of control and cisplatin-treated mice.

Article Snippet: Following Illumina sequencing of the scRNA-Seq results, three files were created: a list of individually barcoded cells, a list of gene symbols with their Ensembl IDs, and a sparse matrix of the read counts of each gene in each cell.

Techniques: Expressing