10X Chromium Epi Multiome ATAC + Gene Expression

Profiling of 3´gene expression and chromatin accessibility in the same cell.

We offer single cell transcriptome and chromatin accessibility profiling using the Chromium Epi Multiome kit. The Epi Multiome kit combines single nuclei RNA-seq with single cell Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) within the same cell.

Compatible sample types

The 10X Epi Multiome kit is only compatible with nuclei suspensions.

Sample requirements

In order to obtain high quality data from the experiment the sample should have:

• No observable debris or aggregates.
• No inhibitors of reverse transcription or GEM generation.  
• A viability of the cell suspension of more than 90% (before nuclei isolation) 
• Intact nuclei of more than 90%
• Intact nuclei with high-quality nuclear membranes and less than 5% of intact cells. (nuclear membranes are well resolved and nuclei show no visible sign of blebbing)
• A concentration of 160-8060 nuclei/μl (concentration depends on targeted nuclei recovery; see table in user guidelines)
• Only use RNase inhibitors that are recommended by 10X Genomics!

We recommend performing a trial prep and assessing nuclei quality at 60x in a microscope. The quality of the nuclei suspension to be used with the Multiome kit plays a crucial role in obtaining high quality sequencing data. Please visit the 10X Genomics webpage for “Demonstrated Protocols’‘ for guidance on how to obtain high quality single nuclei suspensions.

Starting a single-cell Epi Multiome project with NGI

• Contact us at support@ngisweden.se to discuss your project.
• Read our current user guidelines here (v5).
• If possible – run a pilot for the sample preparation to ensure that it yields high quality cell suspensions/nuclei.
• Submit an order via the NGI order portal, using the “Single-cell library preparation and sequencing” order form (you’ll need to make an account first, if you do not have one already).
• Book a day/days to bring your samples to us.

Information we need prior to sample delivery

• A signed agreement and filled-in sample information sheet (both provided to you when we have processed your submitted order).
• A filled-in safety declaration that is sent to you along with the user agreement (if applicable).

Sample reception at NGI

Upon delivery of the samples to NGI, the responsible lab staff will count the nuclei and check that the nuclei suspension is free of aggregates and debris before you leave. It is your responsibility to ensure that the nuclei are of high-quality.

Should the sample be sub-optimal and you still wish to continue with the experiment, we will ask you to confirm this in writing. In such a situation you will be charged the cost of the 10x reactions regardless of the outcome. If you decide not to continue, there will be no charge unless a kit was purchased specifically for you (communicated to you before setting up your project).  

All custom sample manipulation such as labeling, multiplexing etc must be performed by the researcher prior to delivery of the sample. The delivered sample should be ready to load on the 10X Chromium instrument. 

Library preparation

1. Transposition

A transposition mix, containing a transposase, is added to the nuclei suspension. The transposase inserts its adapters preferentially into open chromatin regions which can later be amplified and sequenced. 

2. GEM generation and barcoding

The samples are loaded on the Chromium X controller for GEM generation. Fragments containing a transposase-added adapter receive a 10x Barcode and are amplified inside the GEMs. During cDNA synthesis a cell-specific barcode is incorporated into the full-length cDNA inside the GEMs. The barcodes will be used to bioinformatically assign fragments to single nuclei.

3. Post-GEM Clean-up & Pre-Amplification PCR

The emulsion is broken by addition of a recovery agent and the amplified fragments are purified, after which a pre-amplification PCR is performed. The product is used to generate both the ATAC library and for cDNA generation to make a gene expression (GE) library. 

4. ATAC Library preparation

Illumina indexes are added during PCR in bulk.

5. cDNA amplification and library construction

Full-length cDNA is amplified before library construction. Sample Indexes are added in the next step via PCR. The GE libraries are QC-checked through BioAnalyzer, Qubit and qPCR before pooling and sequencing.

6. Library QC and Sequencing

The ATAC and GE libraries are QCed by Qubit, BioAnalyzer and qPCR before pooling for sequencing.

Bioinformatics

Basic bioinformatic analysis using the CellRanger software from 10X Genomics. Your data will be delivered to you through the DDS online delivery system.

Last Updated: 24th February 2026