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: January 19, 2024
Last Modified: January 22, 2024
Protocol Integer ID: 93827
Abstract
This is a protocol for performing RNAscope® in situ hybridization analysis on fixed-frozen mouse brain tissue using the RNAscope® Multiplex Fluorescent v2 kit (Advanced Cell Diagnostics; ACD). It is similar to the v2 protocol provided by ACD; places where it deviates from ACD's protocol have been indicated. This protocol provides steps for staining sections through dorsal striatum of mouse brain, but can also be applied to other brain areas. It also has steps for sample preparation, including cryosectioning.
Collect sections spaced 20 μm apart between Bregma = +1.0–0.0 in RNase-free PBS.
Immediately mount sections onto Superfrost® plus microscopy slides. Mount sections spaced 120 microns apart 4 per slide (Note that this is different from the ACD protocol, which recommends mounting only 1 section per slide). This amounts to a total of 8 sections between Bregma = +1.0–0.0 mounted onto 2 slides.
Allow slides to dry for 60 minutes at -20°C, then, immediately store at −80°C in a slide box placed inside of a Ziploc bag with drierite desiccant until the day of the RNAscope procedure.
Pretreatment of fixed-frozen tissue samples
Pretreatment of fixed-frozen tissue samples
Baking. Bake slides for 60 min at 60°C in the HybEZ™ oven. Note that this is longer than the time recommended in the ACD v2 protocol.
Post-fixation. Post-fix the slides by immersing them in 4% PFA in 1X PBS for 30 min at 4°C. Note that this post-fixation time is longer than the time recommended in the ACD v2 protocol.
Serial dehydration. Slides are then rinsed once in ddH2O and then serially dehydrated using an ethanol series in the following order: 50%, 70%, two times 100% ethanol (5 min each).
Hydrogen peroxide treatment. Take the dehydrated slides and add ~5–8 drops of RNAscope® Hydrogen Peroxide to cover the sections on each slide. Treat sections with RNAscope® Hydrogen Peroxide for 10 min at RT.
Rinse slides with ddH2O. Repeat with fresh ddH2O water.
Manual target retrieval. Perform manual target retrieval using RNAscope® Target Retrieval Reagents as described in Appendix B of the ACD v2 protocol.
Prepare 700 mL of fresh RNAscope 1X Target Retrieval Reagents by adding 630 mL ddH2O to 1 bottle (70 mL) 10X Target Retrieval Reagents in a clean 1 L beaker. Mix well with stir bar on stir plate.
Place the beaker containing RNAscope 1X Target Retrieval Reagents on the hot plate. Cover the beaker with foil, and turn the hot plate on high until 1X Target Retrieval Reagents reaches 98–102°C.
With a pair of forceps, slowly submerge a Tissue-Tek Slide Rack containing the slides into RNAscope 1X Target Retrieval Reagents solution. Cover the beaker with foil and boil the slides for 5 min.
Wash slides 3–5 times by moving the Tissue-Tek Slide Rack up and down in the distilled water. Then Transfer the slides to 100% ethanol for 3 min.
Slides are then air dried for 5 min and a hydrophobic barrier is drawn around sections using an ImmEdge™ Pen (H-4000; Vector Laboratories, Inc.).
Incubate slides with RNAscope® Protease III reagent for 30 min at 40°C in the HybEZ™ oven.
Wash slides 2x with ddH2O.
Probe hybridization
Probe hybridization
Prepare probe mixture. C1 probes are 1X; C2 and C3 probes come as 50X solutions and therefore must be diluted 1:50 with the C1 probe.
Add probe mixture to slides. Refer to Appendix C. Reagent Volume Guidelines to determine the volume of probe mixture to add to each slide.
Insert into HybEZ™ oven for 2 hrs at 40°C.
(Optional stopping point). You can store the slides in 5X SSC overnight at RT.
Amplification
Amplification
Hybridize AMP 1. Add RNAscope® Multiplex FL v2 AMP 1 to each slide.
Incubate in the HybEZ™ oven for 30 min at 40°C.
Wash slides 2x for 2 min at RT with 1X Wash Buffer.
Hybridize AMP 2. Add RNAscope® Multiplex FL v2 AMP 2 to each slide.
Incubate in the HybEZ™ oven for 30 min at 40°C.
Wash slides 2x for 2 min at RT with 1X Wash Buffer.
Hybridize AMP 3. Add RNAscope® Multiplex FL v2 AMP 3 to each slide Incubate in the HybEZ™ oven for 15 min at 40°C.
Incubate in the HybEZ™ oven for 15 min at 40°C.
Wash slides 2x for 2 min at RT with 1X Wash Buffer.