Mapping Single Cells Back to the Tissue

Characterizing the transcriptomic profiles of individual cells by single-cell RNA sequencing (scRNA-Seq) has become a universal tool to identify both known and novel cell types and to understand tissue structure and function, ushering in a new era of single cell biology. This has proven to be especially true in complex organs and tissues with high cellular heterogeneity, such as mammalian brain and tumors. However, scRNA-Seq utilizes dissociated cells and results in the loss of spatial organization of the cell population being analyzed. It is therefore essential to complement scRNA-seq analysis with methods such as RNA in situ hybridization (ISH) in order to obtain visual confirmation of both single cell and spatial gene expression.

RNAscopeTM assays are robust, highly specific and sensitive multiplex RNA ISH assays that allow you to visualize high throughput single cell transcriptomic results. Multiplex up to four assays to co-localize up to four specific markers at the single cell level (can combine with IHC). These assays allow you to visually confirm individual gene and gene signature expression profiles within a single cell, thereby validating transcriptomic findings. They also allow you to spatially localize cell types and states in their intact tissue environment, thus mapping cell type-specific gene expression profiles back to the tissue context of complex and heterogeneous organs and tumors.

The Power of In Situ Transcriptomics

Single Cell Analysis - Detection of glutamatergic and GABAergic neurons in mouse brain

Watch scientists describe the power of in situ transcriptomics and discuss the application of this technology to large-scale tissue mapping in the mouse brain. They explain how RNAscope Multiplex Fluorescence assays complement single cell RNA sequencing. 

Science Webinar Series: Harnessing in situ transcriptomics to reveal complex tissue architecture at single-cell resolution.
Omer Bayraktar, Ph.D., Wellcome Sanger Institute, Hinxton, U.K.

Knowledge Resource Series: Spatial Mapping and Confirmation of Diverse Gene Signatures Using the Multiplexed Single-Cell Approach of RNAscope Assay.

Jyoti Phatak-Sheldon, MS
Associate Scientist - Applications, Advanced Cell Diagnostics


Complement Single Cell RNA Sequencing with RNAscope Assays

A rapidly increasing number of researchers are publishing in prominent journals using RNAscope assays to spatially map scRNA-Seq results. Some recent examples of key publications are listed below:

  • Li DQ, Kim S, Li JM, Gao Q, Choi J, Bian F, Hu J, Zhang Y, Li J, Lu R, Li Y, Pflugfelder SC, Miao H, Chen R. Single-cell transcriptomics identifies limbal stem cell population and cell types mapping its differentiation trajectory in limbal basal epithelium of human cornea. Ocul Surf. 2021 Apr;20:20-32. doi: 10.1016/j.jtos.2020.12.004. Epub 2021 Jan 1. PMID: 33388438.
  • Kupari J, Usoskin D, Parisien M, Lou D, Hu Y, Fatt M, Lönnerberg P, Spångberg M, Eriksson B, Barkas N, Kharchenko PV, Loré K, Khoury S, Diatchenko L, Ernfors P. Single cell transcriptomics of primate sensory neurons identifies cell types associated with chronic pain. Nat Commun. 2021 Mar 8;12(1):1510. doi: 10.1038/s41467-021-21725-z. PMID: 33686078; PMCID: PMC7940623.
  • Jansky S, Sharma AK, Körber V, Quintero A, Toprak UH, Wecht EM, Gartlgruber M, Greco A, Chomsky E, Grünewald TGP, Henrich KO, Tanay A, Herrmann C, Höfer T, Westermann F. Single-cell transcriptomic analyses provide insights into the developmental origins of neuroblastoma. Nat Genet. 2021 May;53(5):683-693. doi: 10.1038/s41588-021-00806-1. Epub 2021 Mar 25. PMID: 33767450.
  • De Micheli AJ, Swanson JB, Disser NP, Martinez LM, Walker NR, Oliver DJ, Cosgrove BD, Mendias CL. Single-cell transcriptomic analysis identifies extensive heterogeneity in the cellular composition of mouse Achilles tendons. Am J Physiol Cell Physiol. 2020 Nov 1;319(5):C885-C894. doi: 10.1152/ajpcell.00372.2020. Epub 2020 Sep 2. PMID: 32877217; PMCID: PMC7701267.
  • Solé-Boldo L, Raddatz G, Schütz S, Mallm JP, Rippe K, Lonsdorf AS, Rodríguez-Paredes M, Lyko F. Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming. Commun Biol. 2020 Apr 23;3(1):188. doi: 10.1038/s42003-020-0922-4. PMID: 32327715; PMCID: PMC7181753.
  • Hashikawa Y, Hashikawa K, Rossi MA, Basiri ML, Liu Y, Johnston NL, Ahmad OR, Stuber GD. Transcriptional and Spatial Resolution of Cell Types in the Mammalian Habenula. Neuron. 2020 Jun 3;106(5):743-758.e5. doi: 10.1016/j.neuron.2020.03.011. Epub 2020 Apr 8. PMID: 32272058; PMCID: PMC7285796.
  • Menon R, Otto EA, Hoover P, Eddy S, Mariani L, Godfrey B, Berthier CC, Eichinger F, Subramanian L, Harder J, Ju W, Nair V, Larkina M, Naik AS, Luo J, Jain S, Sealfon R, Troyanskaya O, Hacohen N, Hodgin JB, Kretzler M, Kpmp KPMP; Nephrotic Syndrome Study Network (NEPTUNE). Single cell transcriptomics identifies focal segmental glomerulosclerosis remission endothelial biomarker. JCI Insight. 2020 Mar 26;5(6):e133267. doi: 10.1172/jci.insight.133267. PMID: 32107344; PMCID: PMC7213795. 
  • Travaglini KJ, Nabhan AN, Penland L, Sinha R, Gillich A, Sit RV, Chang S, Conley SD, Mori Y, Seita J, Berry GJ, Shrager JB, Metzger RJ, Kuo CS, Neff N, Weissman IL, Quake SR, Krasnow MA. A molecular cell atlas of the human lung from single-cell RNA sequencing. Nature. 2020 Nov;587(7835):619-625. doi: 10.1038/s41586-020-2922-4. Epub 2020 Nov 18. PMID: 33208946; PMCID: PMC7704697.


Download publication list here:



Recent Single Cell Articles


Application Note

Download eBook


Easy to Start with the RNAscope Assay Intro Packs

New to RNAscope assays? You can visualize any RNA target from any species in any tissue in just one day. Start by selecting a RNAscope Assay Intro Pack that has everything you need to run your first assay. Then select the RNAscope Probe that is specific to your RNA target of interest. These intro packs can also be used for multiplex assays, detecting more than one RNA target at a time. Contact one of our RNAscope assay scientist to help address your research needs.

Get Intro PackSpeak with a Scientist


Promotions for New Users

New User Program – FREE!

For first-time users, we offer the opportunity for a RNAscope Assay scientist to personally assist you with setting up your first assay. Our team of scientists are ready to support you in getting superior results from our RNAscope™ assays.

Learn More

Contact Us

Complete one of the three forms below and we will get back to you.

For Quote Requests, please provide more details in the Contact Sales form below

Advanced Cell Diagnostics

Our new headquarters office starting May 2016:

7707 Gateway Blvd.  
Newark, CA 94560
Toll Free: 1 (877) 576-3636
Phone: (510) 576-8800
Fax: (510) 576-8798



19 Barton Lane  
Abingdon Science Park
OX14 3NB
United Kingdom
Phone 2: +44 1235 529449
Fax: +44 1235 533420


Advanced Cell Diagnostics China

20F, Tower 3,
Raffles City Changning Office,
1193 Changning Road, Shanghai 200051


For general information:
For place an order:
For product support:
For career opportunities: