@ARTICLE{Yang2020-ft,
  title    = "{SMART-Q}: An Integrative Pipeline Quantifying Cell
              {Type-Specific} {RNA} Transcription",
  author   = "Yang, Xiaoyu and Bergenholtz, Seth and Maliskova, Lenka and
              Pebworth, Mark-Phillip and Kriegstein, Arnold R and Li, Yun and
              Shen, Yin",
  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
              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.",
  journal  = "PLoS One",
  volume   =  15,
  number   =  4,
  pages    = "e0228760",
  month    =  apr,
  year     =  2020,
  language = "en"
}

{"_id":"ZG9kLZ6yz55yFrrpQ","bibbaseid":"yang-bergenholtz-maliskova-pebworth-kriegstein-li-shen-smartqanintegrativepipelinequantifyingcelltypespecificrnatranscription-2020","author_short":["Yang, X.","Bergenholtz, S.","Maliskova, L.","Pebworth, M.","Kriegstein, A. R","Li, Y.","Shen, Y."],"bibdata":{"bibtype":"article","type":"article","title":"SMART-Q: An Integrative Pipeline Quantifying Cell Type-Specific RNA Transcription","author":[{"propositions":[],"lastnames":["Yang"],"firstnames":["Xiaoyu"],"suffixes":[]},{"propositions":[],"lastnames":["Bergenholtz"],"firstnames":["Seth"],"suffixes":[]},{"propositions":[],"lastnames":["Maliskova"],"firstnames":["Lenka"],"suffixes":[]},{"propositions":[],"lastnames":["Pebworth"],"firstnames":["Mark-Phillip"],"suffixes":[]},{"propositions":[],"lastnames":["Kriegstein"],"firstnames":["Arnold","R"],"suffixes":[]},{"propositions":[],"lastnames":["Li"],"firstnames":["Yun"],"suffixes":[]},{"propositions":[],"lastnames":["Shen"],"firstnames":["Yin"],"suffixes":[]}],"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 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.","journal":"PLoS One","volume":"15","number":"4","pages":"e0228760","month":"April","year":"2020","language":"en","bibtex":"@ARTICLE{Yang2020-ft,\n title = \"{SMART-Q}: An Integrative Pipeline Quantifying Cell\n {Type-Specific} {RNA} Transcription\",\n author = \"Yang, Xiaoyu and Bergenholtz, Seth and Maliskova, Lenka and\n Pebworth, Mark-Phillip and Kriegstein, Arnold R and Li, Yun and\n Shen, Yin\",\n abstract = \"Accurate RNA quantification at the single-cell level is critical\n for understanding the dynamics of gene expression and regulation\n across space and time. Single molecule FISH (smFISH), such as\n RNAscope, provides spatial and quantitative measurements of\n individual transcripts, therefore, can be used to explore\n differential gene expression among a heterogeneous cell\n population if combined with cell identify information. However,\n such analysis is not straightforward, and existing image analysis\n pipelines cannot integrate both RNA transcripts and cellular\n staining information to automatically output cell type-specific\n gene expression. We developed an efficient and customizable\n analysis method, Single-Molecule Automatic RNA Transcription\n Quantification (SMART-Q), to enable the analysis of gene\n transcripts in a cell type-specific manner. SMART-Q efficiently\n infers cell identity information from multiplexed immuno-staining\n and quantifies cell type-specific transcripts using a 3D Gaussian\n fitting algorithm. Furthermore, we have optimized SMART-Q for\n user experiences, such as flexible parameters specification,\n batch data outputs, and visualization of analysis results.\n SMART-Q meets the demands for efficient quantification of\n single-molecule RNA and can be widely used for cell type-specific\n RNA transcript analysis.\",\n journal = \"PLoS One\",\n volume = 15,\n number = 4,\n pages = \"e0228760\",\n month = apr,\n year = 2020,\n language = \"en\"\n}\n\n","author_short":["Yang, X.","Bergenholtz, S.","Maliskova, L.","Pebworth, M.","Kriegstein, A. R","Li, Y.","Shen, Y."],"key":"Yang2020-ft","id":"Yang2020-ft","bibbaseid":"yang-bergenholtz-maliskova-pebworth-kriegstein-li-shen-smartqanintegrativepipelinequantifyingcelltypespecificrnatranscription-2020","role":"author","urls":{},"metadata":{"authorlinks":{}}},"bibtype":"article","biburl":"https://bibbase.org/f/EJMp3HRuxirjxpcXh/references.bib","dataSources":["sAFYeB74DpbdXM9NN","4zx9n2tbeLTix3Wxr","k3cdWrThyTh5o59Rm","hq9pebjzmsTuyxGGx","h8Atv2SAy4PmShg5j"],"keywords":[],"search_terms":["smart","integrative","pipeline","quantifying","cell","type","specific","rna","transcription","yang","bergenholtz","maliskova","pebworth","kriegstein","li","shen"],"title":"SMART-Q: An Integrative Pipeline Quantifying Cell Type-Specific RNA Transcription","year":2020}