In-situ Sequencing & Post-Sequencing Staining¶
This page is retired — it has been split by stain
This page bundled sequencing and all three post-readout stains together. Each part now has its own protocol, and each is independently optional:
- Sequencing cycles → SPRINTseq Sequencing
- DAPI → Nuclear Staining (DAPI)
- WGA (including the critical flow-cell line cleaning) → Cell Membrane Staining (WGA)
- Flow-cell and on-slide H&E → H&E Staining
Nothing was lost — each successor page is a superset of what was here (the H&E section, for instance, gained an on-slide variant and a reagent table).
Do not use the concentrations that were on this page
It specified DAPI at 5 μg/mL, which is now known to crosstalk into the 480 nm channel and will contaminate the WGA/FITC signal in multiplexed imaging. The current working concentration is 10 ng/mL — see DAPI Stock.
Post-readout workflow: SPRINTseq Sequencing → DAPI + WGA → H&E.
Changelog¶
- retired -- 2026-07-30 -- Split into sprintseq-seq.md, morphology-dapi.md, morphology-membrane.md and morphology-he.md. Had fallen out of the site navigation and carried the superseded 5 μg/mL DAPI concentration. See git history for the original text.