Question: Do I need to dissociate tissues into single cells first before isolating nuclei, or can I isolate nuclei directly from the whole tissue?
Answer: Nuclei can be isolated from tissues using the Chromium Nuclei Isolation Kit or the Nuclei Isolation from Mouse Brain Tissue for Single Cell ATAC Sequencing (CG000212) demonstrated protocol for Single Cell ATAC assays.
The Chromium Nuclei Isolation Kit was optimized with many frozen human and mouse samples and is expected to be compatible with most mammalian tissues using the default workflow.
Alternatively, the demonstrated protocol outlines workflows for isolating nuclei from fresh dissociated tissues, frozen tissue homogenate, and whole frozen tissue. When deciding which workflow guidelines to choose, it's important to keep a few considerations in mind such as the nature of the sample (fresh, frozen) as well as any other assays to be done in parallel.
For example, if the tissue is fresh and can be easily dissociated into a single cell suspension, dissociation is recommended as it will provide the user with more control as to the number of input cells that go into the cell lysis and nuclei isolation. Additionally, if there will be other assays that require single-cells (i.e. transcriptional assays, flow cytometry, bead selection), dissociating a tissue would allow the user to run these assays in parallel.
However, if the tissue is hard to dissociate, such as fibrous or frozen tissue, isolating nuclei directly from the tissue is recommended.
Products: Single Cell ATAC