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ViewRNA® In Situ Hybridization Overview

In Situ Hybridization (ISH) is a powerful technique that allows for specific localization of nucleic acid targets in fixed tissues, cells and circulating tumor cells (CTCs).  The principle of ISH is that nucleic acids, when preserved adequately in a histologic specimen and when fixed appropriately, can be detected by using a nucleic acid probe, allowing you to obtain gene expression information in the context of tissue/cell morphology. In the past, quantitation of in situ gene expression, at the RNA (mRNAs or non-coding RNAs) level, had limited utility due to low sensitivity (e.g. non-radioactive formats), long complicated workflows (e.g. radioactive formats) and/or the inability to simultaneously multiplex.

ViewRNA Assays are possibly the most powerful and innovative tools you can bring to your pathology work. At Affymetrix, we are experts in designing assays that unlock the mysteries of the impact of coding and non-coding RNA on human development and disease. We can design and manufacture probes for any transcript you seek, including secreted proteins and non-coding sequences.Probes are manufactured to our quality consistency standards to ensure quantitative and reproducible results that you can trust time after time. Unique branched DNA detection technology delivers ultra-sensitive and highly specific signal. With ViewRNA Assays you can get the results you want.

We offer two basic ways to visualize your RNA targets in situ: chromogenic (CISH) and fluorescence (FISH) detection.

Chromogenic RNA in situ hybridization

CISH RNA in situ hybridization - colon Multiplex chromogenic in situ hybridization (CISH) enables you to visualize up to two RNA and lncRNA targets in the context of tissue morphology.

RNA in situ hybridization assays for FFPE and frozen tissue sections

Fluorescence RNA in situ hybridization

CISH/FISH RNA in situ hybridization - tissues and cells Multiplex fluorescence in situ hybridization (FISH) allows you to visualize up to four RNA and lncRNA targets in the context of tissue/cell morphology. You can analyze up to two RNA targets per tissue section and up to four RNA targets in cell samples.

RNA in situ hybridization assays for FFPE and frozen tissue sections

RNA in situ hybridization assays for CTCs and cells

With ViewRNA Assays for RNA in situ hybridization you can enjoy

  • Sensitive single-molecule detection of RNA
  • High specificity using simultaneous branched DNA (bDNA) signal amplification and background suppression
  • Flexible probe design to target any sequence within a gene
  • “By request” probe synthesis to any target gene are delivered in less than 1 week

RNA in situ hybridization applications

  • Transcriptional profiling of individual cells within a population
  • Heterogeneity of gene expression in cells or tissues
  • Stem cell pluripotency & differentiation
  • Signaling pathways – cell to cell variability
  • Quantifying gene expression in cancer biopsies
  • A companion to antibody based in situ immunofluorescent and immunohistochemistry or DNA FISH assay

Criteria for selecting the appropriate RNA in situ hybridization assay format:


ViewRNATM Assay Formats

ISH Tissue
ISH Cell
miRNA ISH Cell
HC Screening
Cell Samples
Cultured cells (adherent or suspension), CTCs*
Cultured cells (adherent or suspension)
Cultured cells (adherent or suspension)
Tissue Samples
FFPE & OCT-frozen tissue sections, TMAs, FNAs
 2 RNA targets
Up to 4 RNA targets
1 miRNA and up to 2 mRNA targets
Up to 4 RNA targets
Detection Signal
Chromogenic & fluorescence
Automation Compatible
Brightfield or fluorescence microscope or slide scanner
Fluorescence microscopy or high content imaging system
Fluorescence microscopy or high content imaging system
High content imaging system

*Part of the ViewRNA CTC Platform.

**Full automation on Leica BOND RX - coming soon. Batch automation of the assay procedures can be achieved using the Little Dipper® Processor from SciGene