Integrative Single-cell ATAC and RNA Sequencing Service

Integrative Single-cell ATAC and RNA Sequencing Service

Single-cell RNA sequencing can reveal the transcriptional state of a cell, but this upstream regulatory area, chromatin, has been less studied. Joint analysis of chromatin and RNA within the same cell can help to understand transcriptional regulation and downstream mechanisms of action.

CD Genomics' integrative single-cell ATAC and RNA sequencing service is a new technology for the simultaneous detection of RNA and chromatin accessibility within each of thousands of cells based on the 10X Genomics platform. This technology enables the determination of the impact of regulatory regions on gene expression, enabling the correlation of information within target cells; RNA and chromatin accessibility information allows for in-depth characterization of complex cell populations, capturing cellular heterogeneity, and discovering Gene regulation that drives cell differentiation, development, and disease. Integrative ATAC and RNA analysis is a powerful tool for single-cell multi-omics studies.


Single cell nuclear suspensions are first prepared and then a large number of cells are transposed with transposase, an enzyme that preferentially cleaves nuclear DNA in open chromatin regions. The transposed nuclei are then divided into droplets, also called GEMs, in which individual gel beads (Gel Bead) contain 10x barcodes. The barcodes within the GEM are ligated to mRNA and transposed DNA fragments within individual nuclei. After incubation, the GEM is dissolved and mixed, followed by purification, pre-amplification and library construction. The pooled GEMs prepared two libraries, one for RNA sequencing and the other for ATAC analysis.


1. Ultra-high throughput: 500-10000 nuclei can be captured per sample, 8 samples can be completed at one time.

2. ultra-high capture rate: the capture rate of single sample nuclei is up to 65%, and the transcriptional information and open chromatin information in each nucleus can be obtained efficiently.

3. Single cell multi-omics: detection of mRNA and chromatin accessibility of the same cell in thousands of cells with high sensitivity.

4. Finely define cell subtypes: Single-cell transcript information and chromatin open information jointly define cell subtypes;

5. Digging into transcriptional regulatory mechanisms: comprehensively describe epigenetic mechanisms at the single cell level and discover new gene regulatory relationships.


Stem Cells

❖ Transcriptional regulatory network of cell differentiation

❖ Gene chromatin accessibility validates cell developmental trajectories

❖ Potential transcription factors to define specific cell types


❖ Immunophenotyping research

❖ Understand the impact of epigenetic modifications on T cell activation, differentiation and apoptosis

❖ Peripheral blood biomarker research

❖ Pathogenesis of autoimmune diseases


❖ Cancer pathogenesis pathway

❖ Biomarker identifies different cancer cells

❖ Cancer epigenetic drug and therapeutic development


❖ Subpopulation analysis of neuronal and non-neuronal cell types

❖ Research on brain development in normal and diseased states

Sample Requirements

Type: fresh tissue, primary cells, cell lines, etc.

Source: blood extraction, magnetic bead enrichment, flow enrichment, tissue dissociation, etc.

Sample Type Sample Quality Control Requirements
Cell suspension >105 target cells (min. 10.000 cells)
Viability >80%
Concentration: 500-1000 cells/ul
No intercellular adhesions
No cellular debris or other particles larger than 40μm
Absence of reverse transcription inhibitors and non-cellular nucleic acid molecules
Blood EDTA-anticoagulated whole blood (not heparin-anticoagulated), >5 ml
Tissue 0.3 cm x 0.3 cm (no more than 0.5 cm x 0.5 cm) fresh tissue, 4 to 5 pieces

Integrative analysis of Single-cell multi-omics ATAC and Gene Expression is a commercial solution that allowss high-precision interpretation of the interaction between chromatin accessibility and gene expression, enabling high-resolution understanding of gene regulation in health and disease states.


  1. Single-cell ATAC and RNA sequencing reveal preexisting and persistent cells associated with prostate cancer relapse. Nature Communications volume 12, Article number: 5307 (2021)
For research use only, not intended for any clinical use.

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