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Comprehensive cellular analysis with single-nucleus RNA-seq of archived PAXgene whole blood samples
Ojasvi Chaudhary1, Mia Steinberg2, Grant Duclos1
1Translational Medicine, Oncology R&D, AstraZeneca, Waltham, MA 02451, USA.
Cell Reports Methods
|March 17, 2026
Summary
Researchers developed a new method for single-cell analysis of preserved blood samples. Cell lysis with globin gene depletion effectively isolates nuclei for RNA sequencing, enabling comprehensive immune cell profiling.
Area of Science:
- Genomics
- Immunology
- Molecular Biology
Background:
- Preserved whole blood samples in PAXgene tubes are valuable but lack single-cell analysis capabilities.
- Existing methods for nuclei isolation are suboptimal for RNA sequencing.
Purpose of the Study:
- To evaluate nuclei isolation techniques for single-nucleus RNA sequencing (snRNA-seq) from PAXgene preserved blood.
- To optimize snRNA-seq for high-yield, low-bias immune cell profiling.
Main Methods:
- Compared mechanical separation (MS) and cell lysis (CL) for nuclei isolation.
- Employed CRISPR-guided globin gene depletion to reduce globin mRNA.
- Analyzed snRNA-seq data for cell-type proportions and gene expression.
Main Results:
- Cell lysis (CL) yielded significantly more nuclei than MS, with less biased immune cell proportions.
- CRISPR globin depletion enhanced gene detection sensitivity and efficiency.
- CL-derived snRNA-seq data mirrored peripheral blood mononuclear cell (PBMC) profiles, including granulocytes.
Conclusions:
- Optimized cell lysis with globin depletion enables comprehensive single-cell analysis of PAXgene whole blood.
- This method unlocks the potential of large archived blood sample repositories.
- Facilitates detailed immune cell profiling and biomarker discovery from preserved samples.
