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The challenges of single cell transcriptomics on difficult human tissue: the placenta
Theodoros Xenakis1, George T Hall1, Jose J Moreno-Villena1
1Genetics and Genomic Medicine Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, London WC1N 1DZ, United Kingdom.
NAR Genomics and Bioinformatics
|July 17, 2026
Summary
Sample processing and storage significantly impact single-cell transcriptomics results in challenging tissues like the placenta. Method choice is less critical than sample handling for accurate cell-type identification.
Area of Science:
- Single-cell biology
- Genomics
- Tissue processing
Background:
- Single-cell transcriptomics (scRNA-seq) is increasingly applied to complex tissues.
- The placenta presents unique challenges for scRNA-seq due to its biological complexity and post-collection handling.
- Variability in sample processing and storage can introduce technical noise.
Purpose of the Study:
- To evaluate the impact of different sample processing and storage methods on placental scRNA-seq.
- To compare various scRNA-seq modalities and their suitability for challenging tissues.
- To provide guidance for experimental design in scRNA-seq studies of difficult tissues.
Main Methods:
- Single-cell and single-nucleus transcriptomics were performed on placental samples.
- Multiple tissue processing and storage conditions were tested: fresh, fixed, frozen, and FFPE.
- Different transcript capture chemistries (probe-based, native) and cell isolation methods (droplet, in situ) were employed.
Main Results:
- Sample processing and storage variations had a greater effect on cell-type proportions than scRNA-seq chemistry.
- In situ combinatorial indexing showed high overlap with single-nucleus transcriptomics but limited cytoplasmic RNA capture.
- Technical variance analysis revealed critical considerations for experimental design.
Conclusions:
- Sample handling is a primary driver of technical variation in placental scRNA-seq.
- Careful consideration of processing and storage is essential for reliable scRNA-seq data from challenging tissues.
- The choice of scRNA-seq modality and sample management strategy significantly influences biological interpretation.
