Epigenetics
The Chromium Epi Multiome ATAC + Gene Expression platform enables direct, simultaneous measurement of 3' gene expression and chromatin accessibility within single cells. This multiomic technique provides a detailed view of gene regulation by profiling both the epigenomic and transcriptomic landscapes from the same nuclei. It leverages bulk transposition of nuclei for efficient data collection.
The current information pertains to Next GEM versions, and it's expected that 10x Genomics will release the new Gem-X Multiome protocol by 2026.
Epi Multiome ATAC and Gene Expression from 10X Genomics
Epi ATAC from 10X Genomics
Min and max load: 500-10k nuclei
Recovery rate: 60%
Sequencing depth: 50.000 – 100.000 reads/cell, based on cell type and scientific questions
✅ Tip: It is recommended to perform a pilot experiment with a well-characterized sample and optimize the sample preparation protocol for your specific cell type/tissue.
Single Nuclei Suspensions
Quality Requirements:
- Measurements of <5% live input cells indicate proper cell lysis.
- High-quality nuclei improve downstream data accuracy and reproducibility. Always, check nuclei quality to ensure optimal results. Figure A provides an example of the best outcome.
A: High-quality nuclei have well-resolved edges. Optimal quality for single-cell ATAC libraries.
B: Mostly intact nuclei with minor evidence of blebbing. Quality single-cell ATAC libraries can still be produced.
C: Nuclei with strong evidence of blebbing. Proceed at your own risk.
D: Nuclei are no longer intact. Do not proceed!
Resuspension Buffers
Provide us nuclei in 5 µl of chilled Diluted Nuclei Buffer (follow nuclei isolation protocol)
Diluted Nuclei Buffer Preparation: Prepare fresh and maintain at 4°C
| Stock | Final | 1 ml Preparation | |
| Nuclei Buffer (20X) | 1X | 50 µl | |
| DTT (1000 mM) | 1mM | 1 µl | |
| RNase Inhibitor (40 U/µl) | 1 U/µl | 25 µl | |
| Nuclease-free Water |
|
Concentration Guidelines: please check page 29 of user guide
Example for Target Recovery
| Nuclei | Concentration(nuclei/µL) |
| 500 | 160-400 |
| 5,000 | 1,610-4,030 |
| 10,000 | 3,230-8,060 |
Labeling and Storage
- Use Low-bind microcentrifuge tubes (e.g. Eppendorf)
- Clearly label tubes/plates with sample names (matching the Excel submission file)
- Keep samples on ice (store up to 30 minutes)
Protocols by 10x Genomics:
General Guidelines by 10x Genomics
- Nozzle: 100 μm and up
- Sheath fluid: no EDTA or excessive magnesium
- Collection Buffer: 5-20% FBS in 1X PBS or 100% FBS for fragile cells
- Resuspending: Centrifuge at 200 rpm for 10 min at 4°C; remove supernatant, 1X PBS with 0.04% BSA
- Precision Sorting: Use a 96-well plate for lower volumes.
- Timing: Process samples within 30 minutes of sorting.
- Viability Staining: Consider DAPI exclusion.
✅ Tip: Do a test run, let samples sit on ice for 30 min and remeasure viability. This will likely reflect the viability at the start of sample processing.
Lead times: 6-8 weeks
Request service via iLab
For questions, book a consultation in iLab
Our Process:
- nuclei suspension quality assessment (optional)
- Transposition
- GEM generation and barcoding using Chromium X
- Post GEM Incubation Cleanup
- Library Pre-Amplification PCR
- Single Cell ATAC Library Construction
- Gene Expression Library Construction
- cDNA amplification (QC)
- Library construction (QC)
- Pooling and Sequencing on NovaSeq X
- Data analysis using Cell Ranger software
- Data delivery through DDS