Does SeekSpace support co-localization of H&E staining and gene expression on the same section?
2026-06-23
Answer:
Yes. SeekSpace supports performing both H&E staining and gene expression analysis on the same tissue section.
However, H&E staining may affect AO/PI dye binding efficiency, which can reduce the accuracy of nuclei QC measurements.
For nuclei counting after H&E staining, SeekSpace recommends using:
- SeekMate Tinitan Multifunctional Fluorescence Cell Counter (M002F)
- DRAQ7 dye
- DRAQ counting mode
Important recommendation
Internal testing indicates that performing both H&E staining and gene expression analysis on the same section may reduce median gene counts.
Therefore, the preferred workflow is:
- Use separate adjacent sections for H&E staining and gene expression analysis
- Perform integrated downstream analysis using neighboring sections
This approach generally provides more stable transcriptomic performance while preserving histological correlation.
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