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Nuclear Staining (DAPI)

Morphology staining performed after signal readout (PRISM imaging or SPRINTseq sequencing). DAPI labels cell nuclei for segmentation and structural context.

Reagents

Reagent Working Conc. Notes
DAPI 5 μg/ml in PBS Nuclear DNA intercalator; Ex/Em 358/461 nm

Manual Staining (Off Flow Cell)

  1. Wash: PBS, 2 x 2 min.
  2. Stain: Apply DAPI (5 μg/ml in PBS), incubate RT for 10--15 min, protected from light.
  3. Wash: PBS, 2 x 2 min.
  4. Image: DAPI channel (405 nm excitation).

Automated Staining (In Flow Cell)

For SPRINTseq workflows using a flow cell and pump system:

  1. Wash (pre-clean): Pump PBS-T (0.05% Tween), flush 2 min to remove residual sequencing reagents.
  2. Stain: Pump DAPI (5 μg/ml in PBS) until Flow Cell is filled. Stop flow. Incubate RT for 15 min.
  3. Wash (post-clean): Pump PBS, flush 2 min.
  4. Image: Full slide scan in DAPI channel.

See also: Cell Membrane Staining (WGA) | H&E Staining