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.
Reagent Kits
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)