How many tissue sections are typically required for a SeekSpace experiment?
2026-06-23
Answer:
A complete SeekSpace workflow generally requires multiple serial tissue sections for RNA QC, histological assessment, nuclei evaluation, and downstream spatial gene expression analysis.
Typical section usage per capture area is summarized below:
Workflow Step | Purpose | Typical Section Usage |
RNA integrity assessment | RNA extraction and RIN/RQN evaluation (recommended RIN >7) | ~6–8 sections |
H&E staining of adjacent sections | Histological evaluation, target region identification, estimation of nuclear size, and section thickness optimization | ~1 section |
Cellularity estimation | CellProfiler-based nuclei quantification from H&E images; recommended total nuclei count >100,000 | Usually performed on the same H&E section |
ssDNA staining | Nuclear visualization and spatial alignment for downstream gene expression analysis | ~1 section |
The ssDNA-stained section is typically the same section subsequently used for formal spatial gene expression analysis. The estimates above do not include additional trimming sections generated during cryosectioning.
Tissue thickness recommendation
Assuming a maximum section thickness of 20 μm per slice, the total thickness of the region of interest within one capture area should generally be at least >200 μm.
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