10X Genomics - Single Cell ATAC-Seq

The 10X Genomics Single Cell ATAC-Seq Workflow is a workflow that analyses the chromatin structure in individual cells. In this case, a suspension of isolated nuclei is first digested with a transposase and then the individual nuclei are packed in tiny water-in-oil droplets together with a gel bead, which containing a mixture of different barcodes, using the Chromium Controller. In this reaction volume of about 1 nl, the DNA fragments generated after the transposase digestion are barcoded and serve as the basis for creating an Illumina-compatible Library.

This workflow can also be combined with the analysis of cellular gene expression ("multiome") to obtain information about the cellular transcriptome and chromatin structure from the same cell.

As input material, a suspension of single nuclei is required. This suspension has to meet two key criteria in order to deliver high-quality data.

On the one hand only truly single nuclei may be present in the suspension. If aggregates of nuclei are present in the suspension, they have to be removed. On the other hand, the nuclei should have the highest possible vitality. The suspension should not contain more than about 20% of dead nuclei. An excessive amount of dead nuclei leads to a high background signal. If your samples does contain a higher proportion of dead nuclei it may be necessary to remove the dead cells.

After receiving the samples in our laboratory, a quality control is routinely performed determining both nuclei count and vitality of your sample.

Since for this type of analysis the input material is cell material, please clarify in advance with us whether your material may be processed in our laboratory!