Question: How can the poly-A based cDNA synthesis work on RNA from isolated nuclei?
Answer: Since transcription happens so quickly, most RNA in the nucleus (both pre-mRNA and mature mRNA) is immediately poly-adenylated. There is a small portion of transcripts that are being transcribed at the time of cell capture and therefore have not yet received the poly-A tail. These will not be captured.
Data from nuclei may have a higher percentage of intronic mapping data due to the presence of pre-mRNA. For nuclei samples, you can create a custom "pre-mRNA" transcriptome reference. For more information on this, please see the support site: Making pre-MRNA references.
Products: Single Cell Gene Expression