Spatial CUT&Tag

Spatial CUT&Tag

Chromatin state determines genomic function and is regulated in a cell type-specific manner. Although single-cell sequencing enables the analysis of epigenomes in single cells, integrating spatial information from individual cells in primary tissues remains challenging. Spatial epigenomics has emerged as a new field of biology and biomedical research. Among the various spatial epigenomics technologies, spatial-CUT&Tag has received much attention for its ability to provide high-resolution, spatially resolved information about chromatin modifications. It is a technology for spatial histone modification analysis that adds a new dimension to spatial biology by mapping epigenetic regulation broadly related to development and disease.

Technical Principle of Spatial CUT&Tag

Spatial CUT&Tag is used for spatially resolved genome-wide analysis of histone modifications by combining in situ target and tag (CUT&Tag) chemistry, microfluidic deterministic barcoding, and next-generation sequencing. This approach helps us understand the larger picture of chromatin modification profiles and provides a new way to explore epigenetic regulation, cell function, and fate determination under physiological and pathogenic conditions.

Fig. 1. Chemistry workflow of spatial-ATAC-seq.Fig. 1. Spatial-CUT&Tag: design and validation. (Deng Y, et al, 2022)

Workflow of the Spatial CUT&Tag Technique

(1) Adding histone modification-specific antibodies to the fixed tissue.

(2) Adding a secondary antibody to enhance the tethering of a transposome.

(3) Activating the transposome by inserting a junction containing a ligand into the histone modification antibody recognition site in the genomic DNA.

(4) Flowing DNA barcodes through microchannel-guided delivery on the tissue to allow in situ ligation to the adapter.

(5) Passing a second set of barcodes on the same tissue through a microchannel perpendicular to the first barcode step.

(6) Tissue imaging to correlate morphology with spatial epigenomics.

(7) Collecting DNA fragments to complete library construction.

(8) Perform next-generation sequencing.

Our Spatial CUT&Tag Analysis Service

CD Genomics offers a comprehensive spatial CUT&Tag analysis service to perform genome-wide protein modification analysis on frozen tissue sections on a pixel-by-pixel basis, helping clients gain insight into the spatial correlation and regulatory mechanisms of different levels of genetic information. Our state-of-the-art laboratory facilities combined with a team of experienced scientists ensure accurate and reliable results. With advanced technology and meticulous workflows, we enable researchers to reveal the spatial epigenomic landscape with unprecedented resolution and detail.

Advantages of Our Service

  1. Allows differentiation of major cell types in tissues while examining cell type-specific marker gene expression
  2. Supports the examination of developmental processes ranging from radial glia to excitatory neurons to premature post-mitotic neurons.
  3. Allows selection of regions containing monocyte or histone modification patterns, thus supporting the extraction of single-cell epigenomic data without first dissociating the tissue.
  4. Also helps to identify other cell types and supports the prediction of regions for cell type localization.

Sample Requirements

Tissue samples: Fresh frozen tissue samples are preferred for Spatial CUT&Tag. Samples should be properly collected, preserved, and stored to maintain the integrity of chromatin modifications. Our experts can provide detailed instructions on sample collection protocols and shipping guidelines to ensure that sample quality is maintained during shipping.

Sample size: The amount of sample required depends on the specific experimental design and complexity of the tissue. We recommend using a sufficient amount of tissue to obtain reliable results.

Application Areas

Developmental biology

Our spatial CUT&Tag service provides the mapping of chromatin modifications at high resolution, which can reveal spatial patterns of cell types and the dynamics of epigenetic regulation during development.

Disease Research

Our spatial CUT&Tag service provides valuable information on epigenetic alterations associated with disease, helping you gain insight into disease progression, heterogeneity, and treatment response.


By analyzing chromatin modifications in specific brain regions and cell types, we help you uncover the epigenetic mechanisms behind neurodevelopment, synaptic plasticity, and neurological disorders.

CD Genomics offers specialized spatial CUT&Tag services to comprehensively analyze chromatin modifications at high resolution and is dedicated to helping clients unlock the spatial epigenomic landscape. By leveraging the power of spatial CUT&Tag, we unlock new dimensions of knowledge in developmental biology, disease research, and neuroscience. Together we advance scientific discovery and improve our understanding of the complex world of epigenomics. If you are interested in our services, please contact us now.


  1. Deng Y, Bartosovic M, Kukanja P, et al. Spatial-CUT&Tag: spatially resolved chromatin modification profiling at the cellular level[J]. Science, 2022, 375(6581): 681-686.
For research use only, not intended for any clinical use.

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