Skip to main content
Addgene
Open Menu

mRNA Expression FlowCode Plasmids

The mRNA FlowCode system is a retroviral barcode platform designed for in vivo multiplexed mRNA expression screens with readout by spectral flow cytometry. Derived from the Pro-Code system (Wroblewska et al., 2018), mRNA FlowCode uses combinatorial triplet arrangements of 11 short linear epitopes (FLAG, VSVg, V5, C, S, HA, AU1, OLLAS, NWS, HAT, and E) fused to histone H2bc3, enabling stable, long-lived barcode detection at single-cell resolution. Each unique triplet combination serves as a barcode corresponding to the specific mRNA expressed from that plasmid, enabling large-scale multiplexed in vivo mRNA expression screens within a single experimental system.

This collection contains 96 unique retroviral plasmids, each encoding a distinct triplet epitope barcode alongside the mRNA of interest. Plasmids carry an ampicillin resistance marker and use EcoRI and XhoI restriction sites for cloning. Retroviral particles produced from these plasmids are used to transduce the target cell population. Any number and combination of plasmids can be used for an experiment, and even a few plasmids provides sorting options.

Note: these plasmids are designed exclusively for mRNA expression.

A three-panel figure. Panel one shows a map of the FlowCode mRNA retroviral vector. It contains that mRNA gene of interest and an IRES driving expression of a downstream H2B-triplet epitope barcode. Plasmids include the resistance gene, the origin of replication, 3’ and 5’ retroviral ITRs, and the psi packaging signal. The second panel shows the 11-epitope palette (see text for list of epitopes). The last panel shows how the FlowCode plasmids can be used. Target cells are retrovirally-transduced, stably expressing the nuclear H2B-epitope barcode, which is detected and deconvoluted by spectral flow cytometry.
Figure 1: The FlowCode mRNA retroviral barcoding system.

Plasmids

ID Plasmid Tags

Additional Resources

Related Items

References

Burton, O.T., Bricard, O., Tareen, S., Gergelits, V., Andrews, S., Biggins, L., Roca, C.P., Whyte, C., Junius, S., Brajic, A., Pasciuto, E., Ali, M., Lemaitre, P., Schlenner, S.M., Ishigame, H., Brown, B.D., Dooley, J., Liston, A. (2024). The tissue-resident regulatory T cell pool is shaped by transient multi-tissue migration and a conserved residency program. Immunity, 57(7), 1586-1602.e10. https://doi.org/10.1016/j.immuni.2024.05.023 PMID: 38897202

Wroblewska, A., Dhainaut, M., Ben-Zvi, B., Rose, S.A., Park, E.S., Amir, E.D., Bektesevic, A., Baccarini, A., Merad, M., Rahman, A.H., Brown, B.D. (2018). Protein Barcodes Enable High-Dimensional Single-Cell CRISPR Screens. Cell, 175(4), 1141-1155.e16. https://doi.org/10.1016/j.cell.2018.09.022 PMID: 30343902

Credits

Contributing Authors
Written by researchers in the Liston group.
Reviewed by the Scientific Curation team at Addgene.
Last Updated
Content last reviewed on 11 August 2026.