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Updated: Jan 10, 2026
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Determining Genome-wide Transcript Decay Rates in Proliferating and Quiescent Human Fibroblasts
Published on: January 2, 2018
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Cell passage number drives transcriptomic drift as an overlooked factor in experimental reproducibility
Shuai Liu1, Hailun Peng2, Junyan Meng2
1Department of Laboratory, The Fourth People's Hospital of Shenzhen (Shenzhen Samii Medical Center), Shenzhen, 518118, Guangdong, China.
Scientific Reports
|November 22, 2025
Summary
Cell passage number significantly alters gene expression, impacting research reproducibility. Controlling and reporting passage numbers are crucial for reliable scientific findings.
Area of Science:
- Cell Biology
- Genomics
- Scientific Reproducibility
Background:
- Scientific research reproducibility is a growing concern.
- Extrinsic factors affecting reproducibility are well-studied, but intrinsic factors like cell passage number are underexplored.
Purpose of the Study:
- To investigate the impact of cell passage number on transcriptomic profiles.
- To determine how passage number influences experimental reproducibility in cell lines.
Main Methods:
- RNA sequencing was used to analyze transcriptomic dynamics.
- Two tumor cell lines (ACHN and Renca) were studied across multiple passages (P3 to P39).
Main Results:
- A nonlinear transcriptomic shift was observed with passage number.
- Mid-passage cells showed increased activity in cell cycle, metabolism, and stress response pathways.
- Low and high passage cells exhibited stable and similar transcriptomic profiles, with significant pathway alterations during passaging.
Conclusions:
- Cell passage number is a critical intrinsic factor that shapes transcriptional landscapes.
- Strict passage number control and reporting are essential for enhancing the reliability and reproducibility of scientific research.
- Standardized cell culture practices are needed to improve research reproducibility.
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