Question: How do I analyze exogenous RNA transcripts?
Answer: Exogenous RNA transcripts (e.g. mRNA transfection of cells) can be analyzed assuming they have a poly(A) tail.
To map exogenous RNAs with our Cell Ranger pipeline, you must create a custom reference that includes both an annotated genome and the exogenous transcripts using the cellranger mkref tool.
Please be aware that if you inject too many RNA molecules, it may affect downstream processing. The range of total RNA input that we support in the Single Cell 3' application is 0.5-220 ng. In addition, if the number of exogenous transcripts overwhelms endogenous transcripts, you may need to sequence the library to a greater depth to get sufficient coverage of endogenous RNAs.
Finally, a pilot experiment may be required to assess sensitivity of exogenous and endogenous mRNA transcripts.
Products: Single Cell 3', VDJ