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"Add More Life to Your Data: Optimizing Single-Cell RNA-Seq with Dead Cell Removal"

Low cell viability can lead to unreliable cell recovery and increased background noise from dead or apoptotic cells, compromising data quality.

This technical note from Azenta Life Sciences discusses a case in which a group of scientists studying T cells in mouse tumors submitted samples with low cell viability and were unable to improve sample quality due to experimental constraints. The note addresses the challenge of obtaining both a high quantity and high concentration of healthy cells for single-cell RNA sequencing, which is essential for accurate results.

To overcome this challenge, Azenta Life Sciences developed a standardized workflow incorporating dead cell removal (DCR) to enrich viable cells. The procedure uses magnetic beads conjugated to antibodies directed against annexin V, a marker for dead and apoptotic cells. By applying DCR to the low-viability T-cell samples, Azenta increased average cell viability from 65 percent to 94 percent, resulting in slightly higher quality scores for DCR-treated samples compared to untreated samples. This approach demonstrates the potential to improve sample quality and maximize data richness for single-cell projects.

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