Single Cell ATAC

Single Cell ATAC Workflow

The single cell ATAC assay allows for determination of the accessibility of chromatin on a single cell level. A sample of hundreds to thousands of nuclei undergoes a transposition reaction and the transposed nuclei are then partitioned into GEMs which uniquely barcode accessible DNA fragments. For more information about this assay, please visit 10xGenomics.

ATAC workflow

Reagent Kits

For staff-run experiments, the core will provide all required reagents. For self-run experiments, use this guide to determine what to purchase and what the core provides.

Sequencing for Single-cell Assays

Libraries generated with 10x kits are compatible with any of the core's Illumina Sequencers. Sequencing depth is dependent the particular kit used, number of cells captured & experimental design. Here are our standard recommendations for read lengths and # of reads/cell:

1. Single cell 3' v3 expression sample: 20-50K reads/cell; Read 1: 28bp, Index: 8bp, Read 2: 91bp (may truncate Read 2 to 58bp)

2. Single cell 3' v3 Feature Barcoding sample: 5K reads/cell; Read 1: 28bp, Index: 8bp, Read 2: 91bp (may truncate Read 2 to 25bp)

3. Single cell 5' v1 expression sample: 20-50K reads/cell; Read 1: 26bp, Index: 8bp, Read 2: 91bp (may truncate Read 2 to 58bp)

4. Single cell 5' v1 VDJ enrichment sample: 5K reads/cell; Read 1: 150bp, Index: 8bp, Read 2: 150bp

5. Single cell 5' v1 Feature Barcoding sample: 5K reads/cell; Read 1: 26bp, Index: 8bp, Read 2: 25bp 

6. Single Cell ATAC v1: 25K reads/nucleus; Read 1: 50bp, Index 1: 8bp, index 2: 16 bp, Read 2: 50bp (may truncate Read 2 to 49bp)