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Methodologies for Following EMT In Vivo at Single Cell Resolution.

Publication ,  Journal Article
Massri, AJ; Schiebinger, GR; Berrio, A; Wang, L; Wray, GA; McClay, DR
Published in: Methods in molecular biology (Clifton, N.J.)
January 2021

An epithelial-mesenchymal transition (EMT) occurs in almost every metazoan embryo at the time mesoderm begins to differentiate. Several embryos have a long record as models for studying an EMT given that a known population of cells enters the EMT at a known time thereby enabling a detailed study of the process. Often, however, it is difficult to learn the molecular details of these model EMT systems because the transitioning cells are a minority of the population of cells in the embryo and in most cases there is an inability to isolate that population. Here we provide a method that enables an examination of genes expressed before, during, and after the EMT with a focus on just the cells that undergo the transition. Single cell RNA-seq (scRNA-seq) has advanced as a technology making it feasible to study the trajectory of gene expression specifically in the cells of interest, in vivo, and without the background noise of other cell populations. The sea urchin skeletogenic cells constitute only 5% of the total number of cells in the embryo yet with scRNA-seq it is possible to study the genes expressed by these cells without background noise. This approach, though not perfect, adds a new tool for uncovering the mechanism of EMT in this cell type.

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Published In

Methods in molecular biology (Clifton, N.J.)

DOI

EISSN

1940-6029

ISSN

1064-3745

Publication Date

January 2021

Volume

2179

Start / End Page

303 / 314

Related Subject Headings

  • Single-Cell Analysis
  • Sea Urchins
  • RNA-Seq
  • Epithelial-Mesenchymal Transition
  • Embryo, Nonmammalian
  • Developmental Biology
  • Computational Biology
  • Animals
  • 3404 Medicinal and biomolecular chemistry
  • 3101 Biochemistry and cell biology
 

Citation

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Massri, A. J., Schiebinger, G. R., Berrio, A., Wang, L., Wray, G. A., & McClay, D. R. (2021). Methodologies for Following EMT In Vivo at Single Cell Resolution. Methods in Molecular Biology (Clifton, N.J.), 2179, 303–314. https://doi.org/10.1007/978-1-0716-0779-4_23
Massri, Abdull J., Geoffrey R. Schiebinger, Alejandro Berrio, Lingyu Wang, Gregory A. Wray, and David R. McClay. “Methodologies for Following EMT In Vivo at Single Cell Resolution.Methods in Molecular Biology (Clifton, N.J.) 2179 (January 2021): 303–14. https://doi.org/10.1007/978-1-0716-0779-4_23.
Massri AJ, Schiebinger GR, Berrio A, Wang L, Wray GA, McClay DR. Methodologies for Following EMT In Vivo at Single Cell Resolution. Methods in molecular biology (Clifton, NJ). 2021 Jan;2179:303–14.
Massri, Abdull J., et al. “Methodologies for Following EMT In Vivo at Single Cell Resolution.Methods in Molecular Biology (Clifton, N.J.), vol. 2179, Jan. 2021, pp. 303–14. Epmc, doi:10.1007/978-1-0716-0779-4_23.
Massri AJ, Schiebinger GR, Berrio A, Wang L, Wray GA, McClay DR. Methodologies for Following EMT In Vivo at Single Cell Resolution. Methods in molecular biology (Clifton, NJ). 2021 Jan;2179:303–314.

Published In

Methods in molecular biology (Clifton, N.J.)

DOI

EISSN

1940-6029

ISSN

1064-3745

Publication Date

January 2021

Volume

2179

Start / End Page

303 / 314

Related Subject Headings

  • Single-Cell Analysis
  • Sea Urchins
  • RNA-Seq
  • Epithelial-Mesenchymal Transition
  • Embryo, Nonmammalian
  • Developmental Biology
  • Computational Biology
  • Animals
  • 3404 Medicinal and biomolecular chemistry
  • 3101 Biochemistry and cell biology