RNA FISH for stem cell research

Stem cells hold great promise for the treatment of various diseases due to their capacity for self-renewal and ability to differentiate. Stellaris™ RNA fluorescence in situ hybridisation offers a unique insight into the expression patterns of embryonic and adult stem cells.

Visualisation, quantification, and localization of individual RNA molecules provide insight into the unique expression patterns of embryonic and adult stem cells. Though stem cells hold great promise for the treatment of various diseases due to their capacity for self-renewal and ability to differentiate, a basic understanding of stemness remains elusive. Advanced methods of analysis are required for the complex gene expression present in stem cells.

Custom or DesignReady Probe sets

LGC, Biosearch Technologies‘ free, online Stellaris Probe designer allows you to craft Stellaris RNA FISH probes with optimal binding properties for your target RNA sequence. A custom Stellaris RNA FISH probe set is a blend of up to 48 oligos labelled with a fluorophore.

We also offer DesignReady probe sets which are professionally designed and go through rigorous bioinformatics analysis to ensure specificity. These made-to-order probe sets include stem cell-specific targets across a wide range of model organisms. More information and current protocols are available online.

Example DesignReady Probe sets


Detect, localise, and quantify RNA molecules in cells or intact tissue

Biosearch Technologies’ Stellaris RNA FISH probes, can quantify and localise RNA within cells, tissue sections, or whole mount tissue where the morphology is preserved. A Stellaris FISH probe set comprises multiple oligonucleotides targeting a single RNA target. The fluorescently labeled probes bind along the target transcript, and combine to produce a punctate signal for an individual RNA molecule.

Stellaris XIST and GFAP

Image of Stellaris RNA FISH with Immunofluorescence. XIST (red), GFAP protein (green). Photo credit: N. Khoury

Publication highlights

Over 33% of publications citing Stellaris RNA FISH publish in Cell, Nature, or Science

Visit our Citation Center for the complete list.

Stem cell publication highlights

High Impact, Triplex

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

Valentaet al. Cell Reports. 2016. url: https://dx.doi.org/10.1016/j.celrep.2016.03.088

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

Guedeset al. Methods in Molecular Biology. 2016. url: https://dx.doi.org/10.1007/7651_2016_356

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

Upadhyayet al. PLOS Genetics. 2016. url: https://dx.doi.org/10.1371/journal.pgen.1005918

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

Weiet al. Stem Cell Research. 2016. url: https://dx.doi.org/10.1016/j.scr.2016.03.003

High Impact

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

Coteet al. Nature Communications. 2016. url: https://dx.doi.org/10.1038/ncomms10865

High Impact

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

Tettehet al. Cell Stem Cell. 2016. url: https://dx.doi.org/10.1016/j.stem.2016.01.001

X chromosome inactivation in human parthenogenetic embryonic stem cells following prolonged passaging

Qi et al. International Journal of Molecular Medicine. 2015. url: http://www.spandidos-publications.com/10.3892/ijmm.2014.2044

High Impact

Proteostatic Control of Telomerase Function through TRiC-Mediated Folding of TCAB1

Freund et al. Cell. 2014. url: https://dx.doi.org/10.1016/j.cell.2014.10.059

High Impact

Stochastic promoter activation affects Nanog expression variability in mouse embryonic stem cells

Ochiai et al. Nature Scientific Reports. 2014. url: https://dx.doi.org/10.1038/srep07125

High Impact

Luminal signalling links cell communication to tissue architecture during organogenesis

Durdu et al. Nature Letter. 2014. url: https://dx.doi.org/10.1038/nature13852

Defined Human Pluripotent Stem Cell Culture Enables Highly Efficient Neuroepithelium Derivation Without Small Molecule Inhibitors

Lippmann et al. Stem Cells. 2013. url: https://dx.doi.org/10.1002/stem.1622

A dynamic population of stromal cells contributes to the follicle stem cell niche in the Drosophila ovary

Sahai-Hernandez et al. The Company of Biologists Ltd., Development. 2013. url: https://dx.doi.org/10.1242/dev.098558

Identifying Division Symmetry of Mouse Embryonic Stem Cells: Negative Impact of DNA Methyltransferases on Symmetric Self-Renewal

Jasnos et al. Stem Cell Reports. 2013. url: https://dx.doi.org/10.1016/j.stemcr.2013.08.005

SNP-FISH, High Impact

Allele-specific detection of single mRNA molecules in situ

Hansen et al. Nature Communications. 2013. url: https://dx.doi.org/10.1038/nmeth.2601

linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in cis

Maamar et al. Genes & Development. 2013. url: https://dx.doi.org/10.1101/gad.217018.113

Single-cell gene expression profiling reveals functional heterogeneity of undifferentiated human epidermal cells

Tan et al. Development and Stem Cells. 2013. url: https://dx.doi.org/10.1242/dev.087551

High Impact

Asymmetric Segregation of the Double-Stranded RNA Binding Protein Staufen2 during Mammalian Neural Stem Cell Divisions Promotes Lineage Progression

Kuseket al. Cell Stem Cell. 2012. url: https://dx.doi.org/10.1016/j.stem.2012.06.006

High Impact

TPP1 OB-Fold Domain Controls Telomere Maintenance by Recruiting Telomerase to Chromosome Ends

Zhonget al. Cell. 2012. url: https://dx.doi.org/10.1016/j.cell.2012.07.012

The P granule component PGL-1 promotes the localization and silencing activity of the PUF protein FBF-2 in germline stem cells

Voronina et al. Development and Stem Cells. 2012. url: https://dx.doi.org/10.1242/dev.083980

High Impact

EGFR/Ras/MAPK Signaling Mediates Adult Midgut Epithelial Homeostasis and Regeneration in Drosophila

Jiang et al. Cell Stem Cell. 2011. url: https://dx.doi.org/10.1016/j.stem.2010.11.026

The Stellaris RNA FISH method

The Stellaris Method