Stellaris Custom RNA FISH Probe Sets

Design your own Custom Stellaris™ RNA FISH Probe Set to detect your RNA of interest. Stellaris RNA FISH is a RNA visualization method that allows simultaneous detection, localisation and quantification of individual RNA molecules at the cellular level in fixed samples using fluorescence microscopy. A set of Stellaris RNA FISH Probes is comprised of a pool of up to 48 unique probes, each labelled with a fluorophore, that collectively bind along an RNA target transcript to produce a diffraction limited spot.

Before you consider designing a Custom Stellaris RNA FISH Probe Set, check out our DesignReady Stellaris RNA FISH Probe Sets for a large selection of professionally designed targets. We also recommend selecting a control ShipReady Stellaris RNA FISH Probe set to complement your experiment. Stellaris Buffers are the perfect accompaniment to your experiment, allowing for even more robust RNA detection and analysis through reduced background signal.

Stellaris RNA FISH Probe Designer

If you have the sequences ready to order, or wish to order a set with different length oligos, please use the:

Stellaris Probes Excel Form

Design Considerations

Please read our tech article titled, “Designing Stellaris RNA FISH Probes” before designing your custom assay. You can also use Chroma’s Spectra Viewer to check your microscope’s dye filter set compatibility. Use our Stellaris Dyes and Modifications page to select the right dye for your microscope and multiplexing recommendations.

Viral detection and identification in 20 min by rapid single-particle fluorescence in-situ hybridisation of viral RNA

In this paper, the researchers from University of Oxford introduced a rapid viral FISH protocol (rvFISH) for the detection of viral particles using probes designed by Stellaris online probe designer. With the high-quality probes provided by LGC, Biosearch Technologies, the scientists were able to detect SARS-CoV-2 particles in nasopharyngeal swabs in a 20-minute assay. This study indicated the potential of Stellaris RNA FISH probes to be used as a powerful tool for quick and easy viral detection in both research and clinical applications.

Note I: Due to the variable autofluorescence in the green channel inherent to some cells and tissues, it is not recommended to use FAM for some Stellaris RNA FISH assays. We recommend testing your sample for green channel autofluorescence before ordering FAM labelled sets or ordering an alternative dye that is compatible with your experiment.

Note II: The success rate of Custom Probe Sets depend on many variables, such as imaging platform, operator use of optics, target sequence, transcript number, subcellular localization of transcript, number of probes in the set, space between probes, masking level, sample identity whether cultured cells or fresh or frozen tissue, preparation and handling of sample, and customer's design of probe sets with or without the Stellaris Probe Designer. The customer is responsible for designing a probe set that is compatible with all of the variables mentioned above unique to their platform technologies and model system, and therefore we cannot guarantee the success of Customer Probe Sets, or troubleshoot the designs.

Product information: One set of Stellaris™ FISH probes contain a blend of up to 48 oligos labeled with a fluorophore. Probes arrive lyophilised and ready to use.

Delivered amount: 5 nmol of pooled oligos (200-400 hybridization experiments depending on optimal working dilutions for each target)

Turnaround time: 5 to 7 business days to ship, delivery time depends on the region.

Storage guidelines: Stellaris RNA FISH Probes are shipped dry at ambient temperature and can be stored at +2 to +8 °C in this state. Dissolved probe mix should be subjected to a minimum number of freeze-thaw cycles. For daily and short-term use of dissolved probe mix, storage at +2 to +8 °C in the dark for up to a month is recommended. For storage lasting longer than a month, we recommend aliquoting and freezing probes in the dark at -15 to -30 °C.

Reconstituting the dried probe stock: A Custom Probe Set can provide up to 400 hybridizations. Re-dissolve the dried oligonucleotide probe blend in 400 μL of TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0) to create a probe stock of 12.5 μM. Mix well by pipetting up and down, and then vortex and centrifuge briefly.

Note: When performing Stellaris RNA FISH, it is imperative to limit RNA degradation. Please ensure that all consumables and reagents are RNase-free. Recipe above is for set volumes. Please adjust accordingly.

Protocols: Please visit our Stellaris RNA FISH Protocols page.

Absorption and emission spectral charts: Please visit our Calibration dyes page.

You can find the most up-to-date protocols for Stellaris™ RNA FISH Probes by visiting the Stellaris RNA FISH Protocols page. For answers to specific questions please visit our Stellaris RNA FISH FAQ section. The protocols and FAQs apply to imaging on a widefield fluorescence microscope with at least a 60X-oil, 1.4 NA objective, mercury or metal halide lamps, and cooled CCD camera. We do not recommend confocal applications as an entry point, although we have many successful experienced confocal users.

See Stellaris RNA FISH Probes at work by viewing our Stellaris image gallery. Images are contributed by customers and by scientists from LGC Biosearch Technologies.

Comprehensive Stellaris Education and Links Page

Dyes and Modifications for Stellaris

Stellaris Citation Center

Stellaris Getting Started Guide

Related Products

The following peer-reviewed customer publications cite Stellaris RNA FISH products and/or services. Over 33% of publications citing Stellaris RNA FISH publish in Cell, Nature, or Science speaking volumes about the quality of our product and the thought leadership of our customers.

424

Publications

148

Nature, Cell or Science

How to Cite Stellaris RNA FISH

The following Publications include citations of all Stellaris® RNA FISH product types.

Stellaris Citations Papers labeled as Nature, Science, or Cell include sub-groups of these publishing groups such as communications, letters, methods etc.
*Updated August 2016

Stellaris Scoop Research Highlights

Stellaris® RNA FISH DesignReady probe sets take the guesswork out of designing custom assays

Programmable RNA Tracking in Live Cells with CRISPR/Cas9
Nelles et al. Cell. 2016.

Stellaris® RNA Fluorescence In Situ Hybridization for the Simultaneous Detection of Immature and Mature Long Noncoding RNAs in Adherent Cells
Orjalo et al. Methods in Molecular Biology. 2016.

Simultaneous Detection of Nuclear and Cytoplasmic RNA Variants Utilizing Stellaris® RNA Fluorescence In Situ Hybridization in Adherent Cells
Coassin et al. Methods in Molecular Biology. 2014.

Published using professionally designed DesignReady probe sets.

Stellaris Custom RNA FISH Probe Sets

Design Considerations

Related Products

424

Publications

148

Nature, Cell or Science

Research Focus

Organism

Application

RNA Target Type

Multiplexing

Publications citing Custom Stellaris Probe Sets

Dyes

Stellaris Scoop Research Highlights

Custom Probe Sets

Nanoscale imaging of RNA with expansion microscopy

Absolute quantitative measurement of transcriptional kinetic parameters in vivo

Altered RNA processing and export leads to retention of mRNAs near transcription sites, nuclear pore complexes, or within the nucleolus

Memory of cell shape biases stochastic fate decision-making despite mitotic rounding

Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways

An Epstein-Barr Virus-Encoded Protein Complex Requires an Origin of Lytic Replication In Cis to Mediate Late Gene Transcription

The Wnt pathway limits BMP signaling outside of the germline stem cell niche in Drosophila ovaries

Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing

Soluble calcium-binding proteins (SCBPs) of the earthworm Lumbricus terrestris: molecular characterization and localization by FISH in muscle and neuronal tissue

Perturbing HIV-1 genomic RNA subcellular location inhibits virus particle production

Transcriptional enhancement of Smn levels in motoneurons is crucial for proper axon morphology in zebrafish

Feedback modulation of cholesterol metabolism by the lipid-responsive non-coding RNA LeXis

Ebola virus does not induce stress granule formation during infection and sequesters stress granule proteins within viral inclusions

lnc-β-Catm elicits EZH2-dependent β-catenin stabilization and sustains liver CSC self-renewal

Nuclear speckles are detention centers for transcripts containing expanded CAG repeats

A system to study mechanisms of neuromuscular junction development and maintenance

Centromeric Transcription Regulates Aurora-B Localization and Activation

Single-molecule detection and tracking of RNA transcripts in living cells using phosphorothioate-optimized 2'-O-methyl RNA molecular beacons

Spatial organization shapes the turnover of a bacterial transcriptome

Clustered nuclei maintain autonomy and nucleocytoplasmic ratio control in a syncytium

Phenotypic heterogeneity driven by nutrient limitation promotes growth in fluctuating environments

Parkinson-associated risk variant in distal enhancer of α-synuclein modulates target gene expression

IF-combined smRNA FISH reveals interaction of MCPIP1 protein with IER3 mRNA

Wnt Ligands Secreted by Subepithelial Mesenchymal Cells Are Essential for the Survival of Intestinal Stem Cells and Gut Homeostasis

The Caenorhabditis elegans Protein FIC-1 Is an AMPylase That Covalently Modifies Heat-Shock 70 Family Proteins, Translation Elongation Factors and Histones

CRISPR-Cas9 targeted deletion of the C9orf72 repeat expansion mutation corrects cellular phenotypes in patient-derived iPS cells

A simple and rapid method for combining fluorescent in situ RNA hybridization (FISH) and immunofluorescence in the C. elegans germline

Viral genome imaging of hepatitis C virus to probe heterogeneous viral infection and responses to antiviral therapies

Dissecting Transcriptional Heterogeneity in Pluripotency: Single Cell Analysis of Mouse Embryonic Stem Cells

Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

Th17 Cells Are Preferentially Infected Very Early after Vaginal Transmission of SIV in Macaques

Single-Gene Dual-Color Reporter Cell Line to Analyze RNA Synthesis in vivo

Characterization of a Novel Orthomyxo-like Virus Causing Mass Die-Offs of Tilapia

DDX3 Interacts with Influenza A Virus NS1 and NP Proteins and Exerts Antiviral Function through Regulation of Stress Granule Formation

Long non-coding RNA C2dat1 regulates CaMKIIδ expression to promote neuronal survival through the NF-κB signaling pathway following cerebral ischemia

Deficiency of the Survival of Motor Neuron Protein Impairs mRNA Localization and Local Translation in the Growth Cone of Motor Neurons

Transposon Dysregulation Modulates dWnt4 Signaling to Control Germline Stem Cell Differentiation in Drosophila

Regulation of cell-to-cell variability in divergent gene expression

Localized Translation of gurken/TGF-a mRNA during Axis Specification Is Controlled by Access to Orb/ CPEB on Processing Bodies

CD133 does not enrich for the stem cell activity in vivo in adult mouse prostates

cAMP/CREB-regulated LINC00473 marks LKB1- inactivated lung cancer and mediates tumor growth

Topologically associated domains enriched for lineage specific genes reveal expression-dependent nuclear topologies during myogenesis

Single-cell differences in matrix gene expression do not predict matrix deposition

Fezf2 Expression in Layer 5 Projection Neurons of Mature Mouse Motor Cortex

Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss-of-imprinting mutant

Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells

Overlapping cell population expression profiling and regulatory inference in C. elegans

A continuum model of transcriptional bursting

Mutagenesis of GATA motifs controlling the endoderm regulator elt-2 reveals distinct dominant and secondary cis-regulatory elements

Germ Plasm Biogenesis—An Oskar-Centric Perspective

Replacement of Lost Lgr5-Positive Stem Cells through Plasticity of Their Enterocyte-Lineage Daughters

RNase P Protein Subunit, Rpp29, Represses Histone H3.3 Nucleosome Deposition

Natural antisense RNA promotes 3 end processing and maturation of MALAT1 lncRNA

Fixed and live visualization of RNAs in Drosophila oocytes and embryos

RNase P protein subunit Rpp29 represses histone H3.3 nucleosome deposition

DDX3 interacts with influenza A NS1 and NP proteins and exerts antiviral function through regulation of stress granule formation

Rapid evolutionary turnover underlies conserved lncRNA–genome interactions

Brain regions and molecular pathways responding to food reward type and value in honey bees

Microstructural heterogeneity directs micromechanics and mechanobiology in native and engineered fibrocartilage

Long Non-Coding RNAs

Stellaris® RNA Fluorescence In Situ Hybridization for the Simultaneous Detection of Immature and Mature Long Noncoding RNAs in Adherent Cells

Post-transcriptional Modifications Contribute to the Upregulation of Cyclin D2 in Multiple Myeloma

Unequal distribution of 16S mtrRNA at the 2-cell stage regulates cell lineage allocations in mouse embryos

Identifying Centromeric RNAs Involved in Histone Dynamics In Vivo