Multiple, unique options are available for RNA fluorescent in situ hybridization assays (RNA FISH). Two types of detection chemistries are available depending on your research requirements, preferred manual or automated workflow, and your preferred imaging platform. Imaging mass cytometry (IMC™) compatible workflow is also included in this page for ease of assay comparison and selection.
Product Line Features
Multiplexing Capability
Multiplexing Capability
- Options for 3-plex to 12-plex RNA detection on FFPE tissues
- 48-plex RNA detection compatible option for frozen tissues
- Options compatible with multiplex immunofluorescence
Same Section Multiomics
Same Section Multiomics
- Protease-free assay options ideal for RNA and protein co-detection
- Capability for detection of smRNA and RNA with RNAscope Plus
- Simultaneous spatial detection of RNA and protein using RNAscope™ HiPlex Pro and seqIF™ on COMET™
Flexible Workflows
Flexible Workflows
- Manual assay kits for benchtop use.
- Assay kits for automated platforms.
- TSA-based assays for maximum signal:noise or HiPlex assays for direct detection.
RNAscope Multiplex Assays with TSA Detection
RNAscope assays utilizing a tyramide signal amplification (TSA) system gain signal from the RNAscope HRP-labeled amplification tree to provide excellent signal : noise. All assays offer use of titratable fluorophores, flexible fluorophore assignment, and simultaneous detection/imaging of all targets.
- RNAscope Multiplex (Fluorescent) assays offer 3 to 4 plex RNA target detection
- RNAscope LS Multiomic assay enables up to 6 plex target detection of RNA and/or protein using a protease-free workflow
- RNAscope Plus smRNA-RNA assays enable co-detection of 1 smRNA and up to 3 RNAs
RNAscope HiPlex Assays with Direct Detection
RNAscope HiPlex assays utilize cleavable fluorophores with a cyclic workflow that enables higher plex target detection. The assays improve S:N using a quencher or background subtraction methods. IMC is not fluorescent detection, but it is included here for easy comparison.
- RNAscope HiPlex Pro for COMET enables a protease-free, fully automated spatial multiomics workflow, combining RNA detection with seqIF (sequential immunofluorescence) on hyperplex COMET platform.
- RNAscope HiPlex v2 offers 12-plex RNA detection in FFPE tissues and up to 48-plex RNA detection in frozen tissues with use of HiPlex Up.
- RNAscope HiPlex v2 for IMC uses a metal-labeled detection probes (instead of fluorophore-labeled probes) and is compatible with protein detection for Standard Biotools IMC on Hyperion.
Find RNAscope Probes
Find probes below or request a custom design if you don’t see your target.
Assay Selection Guidance
Step 1: Review the assay selection guide for RNAscope Multiplex with TSA (Table 1) or RNAscope HiPlex (Table 2) technologies to understand more about the assays.
Step 2: Select manual benchtop assays or automated assays to fit your platform.
Step 3: Search our probe catalog or contact us to speak with an expert.
| RNAscope Multiplex | RNAscope Multiomic | RNAscope Plus smRNA-RNA | |
|---|---|---|---|
| Platform/Workflow | BOND RX: RNAscope 2.5 LS Fluorescent Multiplex Assay | ||
| Compatible Tissue Type | FFPE and Frozen | FFPE (RNA/protein) Fixed Frozen (RNA only) | FFPE and Frozen |
| Total Plex Capability | 3-4-plex Detect 3 RNA targets (4 with ancillary kit) | 6-plex Detect combinations of up to 6 total RNA/protein targets | 4-plex Detect up to 3 RNAs and 1 smRNA (miRNA) target |
| Protease-free Pretreatment Compatible† See the benefits | Contact us | Yes, included with kit | Contact us |
| Compatible Probe Channels†† | C1-C3 RNAscope probes (C4 RNAscope probes with ancillary kit) | C1-C6 probes | C2-C4 RNAscope probes S1 miRNAscope probe |
| Imaging System | All assays require ability to image and reliably separate signals from selected fluorophore options. Please refer to guidance for individual assay | ||
†Protease-free pretreatment streamlines compatibility with downstream IHC or IF.
††Probe formulations are platform-specific and this is denoted by LS (compatible with LS kits). Probes compatible with manual workflow do not have a distinction.
| RNAscope HiPlex v2 Assay | RNAscope HiPlex Pro for COMET | RNAscope HiPlex-IMC Co-Detection* | |
|---|---|---|---|
| Platform/Workflow | Manual Learn More | COMET Learn More | Manual Learn More |
| Compatible Tissue Type | FFPE and frozen | FFPE | FFPE |
| Total Plex Capability | 12 RNA targets (FFPE) 48 RNA targets (frozen tissue) | 12 RNA targets and 24 protein targets | 12 RNA targets and 28 protein targets |
| Protease-free Pretreatment Compatible† See the benefits | Contact us | Yes, included with kit | Contact us |
| Compatible Probe Channels†† | T1-T12 RNAscope HiPlex probes | T1-T12 RNAscope HiPlex CS probes | T1-T12 RNAscope HiPlex probes |
| Imaging System | Preferred system meeting requirements listed in USM | COMET | Hyperion IMC |
†Protease-free pretreatment streamlines compatibility with downstream IHC or IF.
††Probe formulations are platform-specific. Probes compatible with RNAscope HiPlex Pro for COMET contain “CS” denotation . Probes compatible with manual workflow do not have a distinction.
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