SMART-Q:  An Integrative Pipeline Quantifying Cell Type-Specific RNA Transcription.

ABSTRACT: Accurate RNA quantification at the single-cell level is critical for understanding the dynamics of gene expression and regulation across space and time. Single molecule FISH (smFISH), such as RNAscope, provides spatial and quantitative measurements of individual transcripts, therefore, can be used to explore differential gene expression among a heterogeneous cell population if combined with cell identify information. However, such analysis is not straightforward, and existing image analysis pipelines cannot integrate both RNA transcripts and cellular staining information to automatically output cell type-specific gene expression. We developed an efficient and customizable analysis method, Single-Molecule Automatic RNA Transcription Quantification (SMART-Q), to enable the analysis of gene t

SUBMITTER: Yang X 

PROVIDER: S-EPMC7190163 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature