10x Multiome Sequencing
10x multiome sequencing is a cutting-edge, high-throughput single-cell technology developed on the 10x Genomics platform. It enables the simultaneous profiling of multiple omics layers—such as transcriptomics, epigenomics, TCR/BCR sequences, cell surface protein expression, and spatial localization—at the single-cell or even subcellular level. Initially derived from in-depth studies of single-cell transcriptomics, this technology has evolved in response to increasing recognition of the complexity of cellular function, where single-dimensional data is no longer sufficient to meet the demands of systems biology research. Although single-cell RNA sequencing (scRNA-seq) can reveal differences in gene expression, it falls short in elucidating the underlying regulatory mechanisms or functional outcomes.
By enabling precise alignment of various omics data types—such as RNA plus surface protein, RNA plus ATAC, and RNA plus TCR/BCR—at the single-cell level, 10x multiome sequencing greatly enhances data interpretability. The technology integrates microfluidics, high-throughput sequencing, and multidimensional barcoding systems to overcome the limitations of traditional omics approaches in terms of sample throughput, data resolution, and information connectivity. This allows researchers to capture multiple dimensions of cellular biological states within a single experiment.
Currently, 10x multiome sequencing is being widely applied in diverse research contexts. In cancer research, it enables the characterization of immune cell functional heterogeneity, clonal expansion states, and activation lineages within tumor tissues, as well as the tracking of their dynamic changes before and after treatment. In developmental biology and stem cell research, the technology supports the reconstruction of cell developmental trajectories, identification of transcription factor regulatory networks, and inference of key differentiation events when integrated with epigenomic data. In neuroscience, researchers use this platform to map cell types across brain regions and explore how disease-related mutations are expressed and functionally manifested in different cell types.
The core of 10x multiome sequencing lies in its barcoding system. Each cell, when encapsulated in an oil droplet-based microreactor, is assigned a unique molecular barcode. Captured molecular entities—including mRNA, antibody-tagged oligonucleotides, and fragments of open chromatin—are all labeled with the same cell-specific barcode. This design allows for accurate tracing of each molecular species back to its cell of origin during downstream sequencing analysis, thereby achieving true single-cell multi-omics integration. Compared to conventional approaches, 10x multiome sequencing offers distinct advantages in data throughput, resolution, and systematic integration, significantly improving the efficiency of analyzing complex biological systems.
At the same time, 10x multiome sequencing introduces new challenges and requirements for data analysis. The high-dimensional, high-throughput data necessitate complex computational workflows for normalization, dimensionality reduction, integration, and visualization. Commonly used tools include Seurat, Scanpy, and ArchR, which support joint clustering, differential analysis, and trajectory inference across multiple omics layers. In addition, artificial intelligence and machine learning are increasingly employed for feature recognition and predictive classification in 10x multiome data. As datasets continue to expand, the development of cloud computing infrastructure, distributed storage solutions, and reproducible analysis frameworks is becoming essential for the widespread adoption of this technology.
MtoZ Biolabs offers comprehensive, high-quality multi-omics services, covering the entire workflow from sample preparation and data acquisition to omics integration and bioinformatics analysis.
MtoZ Biolabs, an integrated chromatography and mass spectrometry (MS) services provider.
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