Gut Microbiota Single-cell Transcriptional Profiling

Single-cell transcriptional analysis has already been used in hundreds of fruitful studies through high-throughput sequencing, which has made exciting new biological discoveries. Creative Biolabs offers gut microbiota single-cell transcriptional profiling to precisely and accurately reconstruct the composition of a functional biological unit at the highest resolution, elucidating the networking and dynamic interplay between individual cells.

Background

The single-cell transcriptional profiling, also known as single-cell RNA sequencing (scRNAseq), has changed the field of immunology, revealing an unappreciated complexity of immune cell subsets, identifying new cell types and states, redefining cellular ontogeny and enabling inference of cell fate trajectories and function. ScRNAseq can piece together existing knowledge of cell markers, ontology and interactions into an integrative picture of the building blocks of human tissues. Besides, scRNAseq allows for the hypothesis-generating phase of research and be guided by tissue-specific clues. Targeted experiments in model systems can then be used to support findings and test biological mechanisms.

Single Cell Transcriptional Protocol

Typical single-cell transcriptional protocol consists of three major modular steps: double-stranded complementary DNA (cDNA) synthesis, cDNA amplification and sequencing library preparation (shown in Fig.1).

Fig.1 Single-cell transcriptional experimental pipeline. (Wu, 2017)

Our Service

• ScRNAseq Platforms
  There is a range of scRNAseq methods available, with different benefits for studying gut microbes. The methods include but are not limited to:
• Fluorescence-activated cell sorting (FACS) or microfluidic devices include STRT-seq, CEL2-seq, MARS-seq and SMART-seq2-3.
• High-throughput approaches rely on capture through microfluidic devices of single cells in water droplets in an oil phase (10x Genomics Chromium Gene Expression, Drop-Seq and inDrops) or in microwells (Seq-Well S³ and STRT-seq-2i).
• Genotyping plus transcriptomics (10x Genomics Multiome ATAC + Gene Expression platform) and targeted protein quantification plus transcriptomics available as CITE-seq40 or REAP-seq.
• Spatial transcriptomics (10x Genomics Visium and nanoString GeoMx Digital Spatial Profiler).
• Analysis of scRNAseq data
  Creative Biolabs provides pre-processing and analysis of scRNAseq data from low- and high-throughput platforms:
• Read quality control
• Normalisation of the data and dimensionality reduction
• Lineage tracing
• RNA velocity analyses

Fig.2 ScRNAseq approaches and analysis tools for studying intestinal immunity. (James, 2021)

Advantages of Gut Microbiota Single-cell Transcriptional Profiling

• Unlike microarray or real-time PCR, RNA-seq scans the full length of each transcript.
• RNA-seq does not require probe or primer design.
• Unlike real-time PCR, RNA-seq can easily cover the whole transcriptome.
• Unlike microarrays, a typical next-generation sequencer requires small amounts of library material, typically on the order of nanograms.

With a team of microbiome experts in gut microbiota single-cell transcriptional profiling and complex data analysis, Creative Biolabs provides comprehensive and professional Gut Microbial Biomarker Discovery Services to meet all the needs of our customers. If you are interested in our service, please feel free to contact us for any discussion.

References

1. James, K.R.; et al. Redefining intestinal immunity with single-cell transcriptomics. Mucosal Immunol. 2021.
2. Wu, A.R.; et al. Single-cell transcriptional analysis. Annu Rev Anal Chem. 2017, 10(1): 439-462.

For Research Use Only | Not For Clinical Use