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Targeted Single-Cell Sequencing

Recent advances in single-cell sequencing based technologies allow the assignment of functional roles to members of mixed microbiome samples. We provide a robust targeted single-cell sequencing to prioritize individual cells from complex samples for genome sequencing. This approach can be applied to targeted studies of relevant microorganisms in disease or environments.

Our Advantages:
  • Standardized laboratory methods and quality assurance processes.
  • Streamlined single-cell sorting and lysis, PCR screening, and whole genome sequencing.
  • The most advanced microbial single-cell sequencing technologies and methods.
Tell Us About Your Project

We are dedicated to providing outstanding customer service, listening to customer requests and being reachable at all times.

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Introduction to our targeted single-cell sequencing

Microorganisms found in the environments can significantly affect the ecosystem. Similarly, the human body is inhabited by a collection of diverse microorganisms. They are increasingly found to have critical roles in human health and disease. Single-cell genomics of mixed microbiome samples has greatly accelerated the human microbiome research, and it provides access to individual microbial genomes without the requirement of microbial cultivation. It has led to the discovery of microorganisms with novel metabolic features, or even an alternative genetic code. To better determine which cells are to sequence, targeted cell capture is becoming a highly attractive alternative for studying environmental microbes and human microbiome.

There are several methods for identity-based targeting of populations, such as FACS, PCR screening and function-driven or activity-driven approaches. For example, PCR screening of amplified single cell genomes by targeting marker genes (e.g. 16S/18S rRNAs or customer-specified protein-coding genes) enables to prioritize individual cells form complex environmental or clinical samples for further analysis. Antibodies are also generally used to isolate cells of interest based on cell-surface markers. We can design the optimal targeted call capture scheme for your specific microbial single-cell sequencing projects.

Targeted single-cell sequencing workflow

Bioinformatics Analysis

Our bioinformatics analyses generally include Data preprocessing, genome assembly, genome quality control and comparative genomics analysis, which can be customized to your specific needs. Please feel free to contact us.

Bioinformatics Analysis Details
Data Pre-processing Read quality assessment, sequence trimming and filtering using tools like Trim and Quality Filter
Genome Assembly Genome assembly using tools like SPAdes and IDBA-UD
Genome Quality Control Assessing the quality and continuity of assembled genome using tools like CheckM and Anvi’o
Comparative Genomics Analysis Phylogenetic analysis, variant calling (SNP/InDel/SV) and annotation, developmental genetics, etc.

Sample requirement

Sampling kits: we provide a range of microbial sampling kits for clients, including MicroCollect™ oral sample microbial collection products and MicroCollect™ stool sample collection products.

Deliverables: raw sequencing data, PCR screening results, assembled and annotated sequences, quality-control dashboard, and the customized bioinformatics report.


  1. Woyke T, Doud D F R, Schulz F. The trajectory of microbial single-cell sequencing. Nature Methods, 2017, 14(11): 1045.
  2. Tolonen A C, Xavier R J. Dissecting the human microbiome with single-cell genomics. Genome medicine, 2017, 9(1): 56.
  3. Bowers R M, Doud D F R, Woyke T. Analysis of single-cell genome sequences of bacteria and archaea. Emerging Topics in Life Sciences, 2017, 1(3): 249-255.


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