The single cell ATAC approach provides for simultaneously profiling of open chromatin regions across thousands of nuclei. The Next GEM Single Cell Multiome ATAC kit from 10x Genomics captures nuclei which have been incubated with a transposase to preferentially fragment open regions of chromatin. Nuclei are partitioned into nanoliter-scale Gel Beads-in-emulsion (GEMs) to capture the DNA fragments and incorporate a 10x barcode allowing for DNA fragments to be associated with specific cells.
Key features of the service:
- Joint consultation available with Genomics Core and Bioinformatics Core.
- Cell counting with K2 Cellometer and cell suspension loading.
- Chromium X instrument to process cells with latest GEM-X reagents.
- 10x library construction and rigorous library QC.
- Sequence generation performed on a NovaSeq X Plus platform providing economical sequencing and project scalability.
- Biosafety level 2 containment available for cell collection.
Additional documentation and resources are available on the 10x Genomics support site
A meeting is required with core staff to initiate a single cell project. The meeting will discuss experimental goals as well as project turnaround times, collection scheduling, cell concentration requirements, and cell/nuclei quality requirements. Arrangements for a meeting to discuss a project can be made by sending an email to Nathan Bivens, Genomics Core director.
All projects must be initiated with a quote, and quote accepted, before a collection can be scheduled. .
The 10x Genomics Single Cell Calculator may be used to estimate the amount of sequence required for a project.
General Considerations:
- Submit cells in Eppendorf DNA Lo Bind Tubes, 2.0 ml (Cat. No. 022431048)
- Must minimize presence of cellular aggregates, dead cells, non-cellular nucleic acids and reverse transcription inhibitors.
- On the scheduled day of submission, core staff should be notified 1 hour prior to cells/nuclei being delived. It is best practice to provide periodic updates to core staff on the day of collection.
Submission Requirements:
| Nuclei Concentration | Volume | Required Buffer | Special Instructions |
| 3,200 - 8,000 nuclei/ul | 30 - 100 ul | Diluted Nuclei Buffer *provided in kit |
Review the 10x article on how to assess nuclei quality. |
| Sequence Depth/Coverage* | Read Type | Index Type | Read Length | ||
| 25,000 read pairs/nucleus | Paired end | unique dual-index | 50 bases | ||
* minimum read count recommended by MUGTC; increased sequencing depth may be desired for some studies