RNAscope multiplex in situ hybridization (ISH)
Overview
RNAscope is a commercially developed branched-DNA in situ hybridization assay (Advanced Cell Diagnostics) that enables single-molecule RNA detection in formalin-fixed paraffin-embedded (FFPE) or fresh-frozen tissue sections. The multiplexed fluorescent variant allows simultaneous detection of 2–8 RNA targets at single-molecule resolution while preserving tissue spatial context. It is commonly used to validate transcriptomic findings from bulk or single-cell RNA-seq in situ.
Used by
- PMID:34493726 — RNAscope multiplex fluorescent ISH on postnatal adrenal gland sections (ages 0 y, 4 y, adult) and on high-risk MYCN-amplified and low-risk 4S neuroblastoma tumor sections; confirmed NTRK2+/CLDN11+ double-positive cells in adrenal capsule and medulla, mutually exclusive from TH+ chromaffin cells and SOX10+ SCPs; also validated co-expression of NTRK2/MYCN/NTRK1/ALK and NTRK1/TH/NTRK2 patterns in individual tumor regions PMID:34493726.
- Used in Vhl/HIF conditional mouse model study to validate scRNA-seq findings; RNAscope multiplex ISH confirmed HIF2A-specific downregulation of PT differentiation markers (Slc5a12, Inmt, Cyp2a4) across renal tubule segments PMID:23797736
Notes
- Spatial validation by RNAscope ISH was essential in confirming that hC1 progenitor and nC3 undifferentiated neuroblastoma cells are spatially distinct from canonical SCP and chromaffin populations, which could not be established from bulk or single-nucleus transcriptomics alone PMID:34493726.
- Corpus-grown slug; not present in canonical ontology.
Sources
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