Question: Can I salvage my experiment if I did not use the recommended Feature cDNA primers for Cell Surface Protein during cDNA amplification?
Answer: Unfortunately, we have not tested whether it is possible to recover Feature Barcode Cell Surface Protein libraries when the incorrect cDNA primer is used during the cDNA amplification step (Step 2.2A). We recommend repeating the experiment with new samples using the recommended Feature cDNA primers to ensure assay performance.
However, if this is a precious sample, you may be able to rescue the libraries. To perform this unsupported and untested workflow modification, the Transferred Supernatant Cleanup sample from Step 2.3B-xiv can be amplified again using the correct Feature cDNA Primer (Step 2.2A). Following re-amplification, Step 2.3B should be repeated before Cell Surface Protein Library Construction. Although there will be significant sample loss, recovering some of the Cell Surface Protein libraries for downstream analysis may be possible. These Cell Surface Protein libraries will likely have lower yields and contain additional non-specific peaks not typically observed with the standard workflow protocol.
Please note: These workflow modifications are untested and not supported on the 10x Single Cell 3’ or 5’ workflows.
Products: Single Cell Gene Expression, Single Cell Immune Profiling