Jun 24, 2025
Molecular Cartography for FF-OCT (Resolve Biosciences)
- 1Stanford University
- Human BioMolecular Atlas Program (HuBMAP) Method Development CommunityTech. support email: [email protected]
Protocol Citation: Joanna Bi 2025. Molecular Cartography for FF-OCT (Resolve Biosciences). protocols.io https://dx.doi.org/10.17504/protocols.io.n92ldnoqnv5b/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: June 24, 2025
Last Modified: June 24, 2025
Protocol Integer ID: 220935
Keywords: molecular cartography protocol for ff, molecular cartography for ff, molecular cartography protocol, molecular cartography, intestine tissue, resolve bioscience, oct, tissue
Abstract
Molecular Cartography protocol for FF-OCT (Resolve Biosciences), used for intestine tissue.
FF-OCT samples were sectioned into 10 µm sections with a Cryostat (Leica, CM1850UV), placed within the imageable area on the Resolve observation slides, and stored at -80˚C until use.
Upon retrieval from the freezer, the slide was heated at 37˚C for 5 minutes. Sticky wells were assembled using an aligner and adaptor.
The sections were fixed with MF1 at 4˚C for 30 minutes, followed by washes with PBS and ethanol.
They were subsequently rehydrated in a sequential series of isopropanol, 95% ethanol, and 70% ethanol.
DST1 was applied to stain the sections at room temperature for 5 minutes, followed by washes with 50% ethanol and Wash Buffer 1.
To prepare for probe hybridization, the sections were incubated in Priming Solution at 37˚C for 30 minutes.
A custom probe mix of 100 genes was then added to each section and incubated at 37˚C on a thermal cycler for 16–24 hours.
Excess probe mix was removed by three washes with Wash Buffer 2, and the sections were stored in Wash Buffer 1.
For imaging, the slides were loaded onto the Molecular Cartography Workflow, following the manual (Workflow Setup v2.2, Resolve Biosciences).
The sample preparator unit, tray handler, imager, and PC were set up according to the manual.
The imager captured a brightfield overview scan, where regions of interest (ROIs) were selected for each section. ROIs were scanned to detect signals from target transcripts.