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Updated: Apr 18, 2026

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Does FACS perturb gene expression?

Graham M Richardson1, Joanne Lannigan, Ian G Macara

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Summary

Fluorescence activated cell sorting (FACS) minimally impacts gene expression. However, mammary cell isolation steps before FACS significantly alter miRNA and target transcript levels, affecting transcriptional profiles.

Keywords:
FACSmammary epithelial cellsmiRNA

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Area of Science:

  • Cell Biology
  • Molecular Biology
  • Genomics

Background:

  • Fluorescence activated cell sorting (FACS) is crucial for isolating mammary epithelial sub-populations for gene expression analysis.
  • The impact of FACS and preceding isolation steps on short-term transcriptional profiles remains largely unexamined.

Purpose of the Study:

  • To investigate the effects of mammary cell isolation and FACS on gene expression.
  • To assess the short-term transcriptional consequences of these procedures.

Main Methods:

  • RNA was harvested from mouse mammary gland cells at three stages: before enzymatic digestion, after enzymatic digestion, and after a mock FACS sort.
  • Microarray analysis was employed to compare gene expression profiles across these stages.

Main Results:

  • FACS itself induced minimal disruption to overall gene expression patterns.
  • Mammary cell isolation steps preceding FACS led to the upregulation of 18 miRNAs.
  • These miRNA changes were associated with rapid decreases in their predicted target transcripts.

Conclusions:

  • While FACS is a low-impact technique for mammary cell sorting, the initial isolation process significantly influences transcriptional profiles.
  • Pre-FACS isolation steps cause notable miRNA dysregulation and subsequent changes in target gene expression.