Question: How can I assess whether a tissue sample is a good candidate for Single Cell ATAC or Single Cell Multiome ATAC + Gene Expression assays?
Answer: When isolating nuclei from frozen whole tissue, it is not possible to directly assess cell viability prior to nuclei isolation. Therefore understanding the sample’s source, handling, and storage conditions are critical to determining whether it is of sufficient quality for single cell analysis.
The following table outlines the impact of sample/nuclei quality on several aspects of final data quality:
| RNA Integrity* | Ambient RNA/low GEX data complexity* | Chromatin structure/ ATAC data quality | |
| Is ______ impacted by input sample quality? | Yes - dead/dying cells, RNase activity | Yes - dead/dying cells, RNase activity | Yes - dead/dying cells, prolonged -80°C storage, NETs |
| Is ______ impacted by nuclei quality? | No, as long as recommended RNase inhibitor is used | Yes - overlysed nuclei leak transcripts | Yes - overlysed nuclei can have reduced chromatin structure |
| Can ______ be screened before an assay? | In principle, RIN score (not validated and no recommended cutoff) | Currently no validated method | Currently no validated method |
* RNA integrity and ambient RNA/low GEX data complexity will only impact the Single Cell Multiome ATAC + Gene Expression assay.
It is possible to have high quality GEX data and poor quality ATAC data, or vice versa, and there is not a validated method to assess chromatin structure prior to running an assay. Understanding whether a tissue is of high quality (high expected cell viability, rapid processing from collection to nuclei isolation/snap-freezing, storage in liquid nitrogen, etc.) will best position users to generate high quality data. Tissues of lower or unknown quality have increased risk of poor data quality including reductions in chromatin structure that are not detected before running an assay.
Products: Single Cell Multiome ATAC+GEX, Single Cell ATAC