Academic Journal
SMART-Q: An Integrative Pipeline Quantifying Cell Type-Specific RNA Transcription.
| العنوان: | SMART-Q: An Integrative Pipeline Quantifying Cell Type-Specific RNA Transcription. |
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| المؤلفون: | Xiaoyu Yang, Seth Bergenholtz, Lenka Maliskova, Mark-Phillip Pebworth, Arnold R Kriegstein, Yun Li, Yin Shen |
| المصدر: | PLoS ONE, Vol 15, Iss 4, p e0228760 (2020) |
| بيانات النشر: | Public Library of Science (PLoS), 2020. |
| سنة النشر: | 2020 |
| المجموعة: | LCC:Medicine LCC:Science |
| مصطلحات موضوعية: | Medicine, Science |
| الوصف: | 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 transcripts in a cell type-specific manner. SMART-Q efficiently infers cell identity information from multiplexed immuno-staining and quantifies cell type-specific transcripts using a 3D Gaussian fitting algorithm. Furthermore, we have optimized SMART-Q for user experiences, such as flexible parameters specification, batch data outputs, and visualization of analysis results. SMART-Q meets the demands for efficient quantification of single-molecule RNA and can be widely used for cell type-specific RNA transcript analysis. |
| نوع الوثيقة: | article |
| وصف الملف: | electronic resource |
| اللغة: | English |
| تدمد: | 1932-6203 |
| Relation: | https://doaj.org/toc/1932-6203 |
| DOI: | 10.1371/journal.pone.0228760 |
| URL الوصول: | https://doaj.org/article/3ea612fd40ed46d1990dabc3c7e1908f |
| رقم الانضمام: | edsdoj.3ea612fd40ed46d1990dabc3c7e1908f |
| قاعدة البيانات: | Directory of Open Access Journals |
Full Text Finder | تدمد: | 19326203 |
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| DOI: | 10.1371/journal.pone.0228760 |