Question: What is the recommended sequencing depth for nuclei data when compared with cellular data?
Answer: The number of recommended sequencing reads is the same for nuclei or cells i.e. minimum of 20,000 read pairs per nuclei or a total of 40,000 reads per nucleus for Single Cell GEX while ATAC needs 25000 read pairs/nuclei. However as the sequencing depth increases, more genes are detected, but this reaches saturation at different sequencing depths and is highly dependent on the tissue and sample types.
In general, if the sequencing is done at our minimum sequencing depth recommendations, it is still possible to get a good sense of the transcriptome and this applies to nuclei data too. Our internal tests have shown the recovery of Single Cell populations between whole cells and nuclei is comparable. In some cases, there are advantages to using single nuclei for RNA-seq, including reducing biases in cell populations and this is explained here.
Please also read the technote on resolving cell types as a function of Read Depth and Cell Number here.
Related KB articles: Can I perform shallow sequencing to assess the quality of Single Cell 3' Gene Expression libraries?
Product: Single Cell Gene Expression, Single Cell ATAC, Single Cell Multiome ATAC + Gene Expression