Question: Is Single Cell Immune Profiling compatible with nuclei?
Answer: Running the Single Cell Immune Profiling solution with whole cells as input can provide both whole transcriptome gene expression data and paired, full-length V(D)J transcript data. We have recently tested the Single Cell Immune Profiling Solution using nuclei as input on a limited number of sample types and assessed performance on both of these data types.
Based on these tests, we have found that obtaining VDJ data from nuclei is challenging, and we cannot guarantee VDJ assay performance when using nuclei instead of cells. The primary reason for this is the transcript loss that occurs from nuclei isolation. VDJ transcripts tend to be more lowly expressed, even in cells. Isolating only nuclei means that RNA contained in the cytoplasm is lost, which results in reduced transcripts available for capture and analysis. Additionally, increased ambient RNA in the cell suspension resulting from a typical nuclei isolation can make it more challenging for the Cell Ranger VDJ algorithm to accurately assemble contigs and determine which GEMs contain T/B cells which do not.
However, in our hands, the gene expression data generated was comparable to that generated using the Single Cell Gene Expression Solution.
Products: Single Cell Immune Profiling