Question: How do I design a custom targeted assay for Single Cell 3'?
Answer: It is feasible to incorporate targeted amplification of transcripts of interest within the Single Cell 3' workflow although it has not been done internally and we are unable to provide target-specific recommendations.
For targeted enrichment, the cDNA amplification reaction (Protocol Step 2.2) could be modified using the partial R1 forward primer provided in the cDNA Primer Mix (CTACACGACGCTCTTCCGATCT) with a custom pool of gene-specific reverse primers to amplify transcripts of interest. The amplified targets would then be converted to Illumina-ready sequencing constructs by following the remaining steps in the Single Cell 3' v2 User Guide.
Success will depend on the primer pool design and level of expression for the genes of interest. Before optimizing primer design for specific target genes, the user should run whole transcriptome sequencing with the Single Cell 3' v2 assay on typical samples and sequence to saturation. Genes with low levels of expression are not good candidates for targeted sequencing since they are unlikely to be detected at a high enough level to give adequate representation across cells in the sample.
A few notes to be aware of when developing a targeted protocol:
- The number of cDNA amplification cycles, or in this case the number of "enrichment" cycles, may need to be increased by 1-2 cycles, particularly if there is a low relative abundance of the transcript of interest.
- The number of SI-PCR cycles will likely need to be increased by 1-2 cycles since the total initial mass will be significantly less.
- Depending on the length of the transcript(s) of interest, the parameters for fragmentation may need to be optimized to prevent excessive fragmentation. Fragmentation has been optimized for cDNA originating from full-length mammalian transcriptomes and thus fragmentation from a selected group of transcripts may require protocol adjustments. The length of the fragmentation reaction (5 minutes) can be increased or decreased accordingly.
For more detailed information on the Single Cell 3' v2 assay scheme, please see: https://support.10xgenomics.com/single-cell-gene-expression/index/doc/technical-note-assay-scheme-and-configuration-of-chromium-single-cell-3-v2-libraries
Products: Single Cell 3'