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Related Experiment Video

Updated: Apr 15, 2026

Profiling Individual Human Embryonic Stem Cells by Quantitative RT-PCR
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Quantitative single cell gene expression profiling in the avian embryo.

Jason A Morrison1, Andrew C Box1, Mary C McKinney1

  • 1Stowers Institute for Medical Research, Kansas City, Missouri.

Developmental Dynamics : an Official Publication of the American Association of Anatomists
|March 27, 2015
PubMed
Summary
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This study presents a new method for in vivo single cell gene profiling in embryos. Fluorescence-activated cell sorting (FACS) combined with photoconvertible labeling enables accurate transcript preservation for developmental studies.

Area of Science:

  • Developmental Biology
  • Genomics
  • Molecular Biology

Background:

  • Single cell gene profiling is established for cultured cells.
  • Challenges exist in preserving native gene expression from intact embryos.

Purpose of the Study:

  • To develop a method for in vivo single cell profiling in embryos.
  • To optimize cell identification, isolation, and nucleic acid amplification.
  • To compare isolation techniques for preserving native transcripts.

Main Methods:

  • Tested photoconvertible fluorescent proteins for cell marking in chick embryos.
  • Optimized cell isolation and nucleic acid amplification for downstream RNA sequencing or qPCR.
  • Compared fluorescence-activated cell sorting (FACS) with laser capture microdissection (LCM).
Keywords:
FACSLCMRNAseqRT-qPCRavian embryoexpression analysisgene expressionmolecular profilingphotoconversionsingle cellwhole transcriptome amplification

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Related Experiment Videos

Last Updated: Apr 15, 2026

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Main Results:

  • Dual color mDendra2 offered optimal signal/noise for cell identification.
  • Developed protocols to minimize cell death and preserve gene expression.
  • FACS demonstrated higher efficiency in preserving native transcripts than LCM.

Conclusions:

  • Quantitative single cell gene expression profiling is feasible in embryonic development.
  • Combines photoconversion labeling, FACS, and optimized amplification strategies.
  • Enables interrogation of complex cell dynamics during embryogenesis.