Increasing numbers of studies have demonstrated that pathogen and invaded host cell can both exhibit a significant phenotypic heterogeneity during the infection process. We provide a robust microbial single-cell RNA-seq service employing the most advanced methods to reveal gene-expression heterogeneity in a population.
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Microbial transcriptomes are commonly small, with only a few copies of each transcript due to their lack of alternative splicing mechanism. The mRNAs of prokaryotes usually lack polyadenylation (polyA); therefore, traditional eukaryotic single-cell RNA-seq methods relying on polyA tailing protocols are not suitable for prokaryotic transcriptome analysis. Additionally, cell walls of microbes are usually tough, composed of beta-glucan, chitin, and manno-protein. These characteristics of microorganisms make microbial single-cell RNA-seq a challenging task. To solve this problem, we developed and validated a robust microbial single-cell RNA sequencing platform.
Fluorescence-activated cell sorting (FACS), micromanipulation or microfluidic platform are used to harvest single cells. After RNA isolation and quality control, extracted RNAs are reversely transcribed and amplified, and used to construct libraries using improved Smart-seq method or commercial kits. Validated libraries are then subjected to Illumina sequencing (PE100/SE50). Sequenced reads are preprocessed and analyzed by our experienced bioinformatics experts. We help to investigate the gene expression heterogeneity among individual cells, which can be a major determinant of the success in antimicrobial treatment and disease outcome.
Our bioinformatics analyses generally include read QC, transcriptomic mapping, read count, differential gene expression (DGE) analysis and other analyses. Our bioinformatics analysis content is flexible to your needs. Please feel free to contact us.
| Bioinformatics Analysis | Details |
|---|---|
| Read QC | Read quality assessment, sequence trimming and filtering using tools like FastQC and FASTX Toolkit |
| Transcriptomic Mapping | Read alignment using BWA and STAR; read annotation |
| Read Count | Quantification of expression using tools such as RPKM, FPKM and TPM; between-sample normalization using DESeq |
| DGE Analysis | Hierarchical clustering, principal component analysis (PCA), Spearman's correlation analysis, functional annotation, etc. |
| Other Analysis | GO analysis, heatmaps, gene set enrichment analysis, etc. |
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, assembled and annotated sequences, quality-control dashboard, and the customized bioinformatics report.
Please submit a detailed description of your project. We will provide you with a customized project plan to meet your research requests. You can also send emails directly to info@cd-genomics.com for inquiries.
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