Epi Multiome ATAC + Gene Expression

Chromium Single Cell

Epi Multiome ATAC + Gene Expression

Single cell profiling of open chromatin and 3' gene expression from the same nucleus

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10K nuclei/sample or 80K nuclei/chip

Run 8 samples in parallel

Why choose Epi Multiome ATAC + Gene Expression

Direct linkage of gene expression and open chromatin readouts from the same nucleus
Aim to discover new gene regulatory interactions

Assay specifications

Species

Mouse

Human

Rat

Non-human primate

Marine

Plant

Insect

Compatible samples

Cell suspension

Nuclei suspension

Fresh tissue

Frozen tissue

Organoids

Multiomics

Chromatin accessibility

3' gene expression

Compatible instruments

Chromium X

Chromium iX

Singleplex throughput options

10K nuclei/sample

80K nuclei/chip

8 samples/chip

Assay Components

Each experiment requires a chip, index kit, and core reagents. If you're unsure what you need, use the experiment builder to find the custom list of items required for your experiment.

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Consumables

Nuclei Isolation (optional)

REAGENT

1000494

Chromium Nuclei Isolation with RNase Inhibitor Kit, 16rxns

Chip

CHIP

1000230

Chromium Next GEM Chip J Single Cell Kit, 16 rxns

CHIP

1000234

Chromium Next GEM Chip J Single Cell Kit, 48 rxns

Index Kit

REAGENT

1000215

Dual Index Kit TT Set A 96 rxns

REAGENT

1000212

Single Index Kit N Set A, 96 rxn

Core Reagents

REAGENT

1000285

Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 4 rxns

REAGENT

1000283

Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 16 rxns

RNase Inhibitor (Optional)

REAGENT

1000887

Kit, RNase Inhibitor 40x

Compatible Instruments

Chromium X Chromium iX

Build your own Epi Multiome experiment

Design the experiment that's right for you

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Documents and resources

View all technical documentation

Sequencing requirements

Minimum 20,000 read pairs/nucleus for gene expression; 25,000 read pairs per nucleus for ATAC

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Analysis guides

Find software documentation

Grant resources

Create a Letter of Support

Download grant application resources

Research highlight

Enrich single cell studies with a unified view of transcriptomic and epigenomic profiles

Videos

Data analysis

Explore analysis software

Cell Ranger ARC

Cell Ranger is a set of free analysis pipelines for processing Chromium Single Cell Multiome ATAC + Gene Expression data.

Learn more about Cell Ranger ARC

Loupe Browser

Desktop application for Windows and MacOS that allows you to interactively visualize data.

Download Loupe Browser

Cloud Analysis

Cloud Analysis enables quick and easy access to Cell Ranger pipelines from your web browser.

Learn more about Cloud Analysis

Featured publications

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Publications

Mechanisms of action and resistance in histone methylation-targeted therapy

Nature, 2024 Makoto Yamagishi, et al.

Single-cell systems pharmacology identifies development-driven drug response and combination therapy in B cell acute lymphoblastic leukemia

Cancer Cell, 2024 Xin Huang, et al.

Genetic and epigenetic coordination of cortical interneuron development

Nature, 2021 Kathryn C Allaway, et al.

Inferring and perturbing cell fate regulomes in human brain organoids

Nature, 2022 Jonas Simon Fleck, et al.

Cross-lineage potential of Ascl1 uncovered by comparing diverse reprogramming regulatomes

Cell Stem Cell, 2022 Haofei Wang, et al.

Featured datasets

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Datasets

Multiomic Integration Neuroscience Application Note: Single Cell Multiome RNA + ATAC Alzheimer's Disease Mouse Model Brain Coronal Sections from One Hemisphere Over a Time Course

Human Kidney Cancer Nuclei isolated with Chromium Nuclei Isolation Kit, SaltyEZ Protocol, and 10x Complex Tissue DP (CT Sorted and CT Unsorted)

Flash-Frozen Lymph Node with B Cell Lymphoma (14k sorted nuclei)

10k Human PBMCs, Multiome v1.0, Chromium X

Flash-Frozen Human Healthy Brain Tissue (3k)