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Prokaryotic RNA Sequencing


Prokaryotic RNA sequencing refers to the use of next-generation high-throughput sequencing technology to sequence the transcriptome of prokaryotes (bacteria and archeae), and comprehensively and rapidly obtain all transcripts information (mRNA and non-coding RNA) of a single microbial colony or a microbial community. It has been widely used in various fields, such as basic science research, clinical use and drug research and development.

Our Advantages:
  • Powerful supercomputing platform with experienced team of biometric analysis experts.
  • Flexibly conducted custom bioinformatics analysis according to clients’ requirements.
  • Provide collection kits for oral and feces samples.
  • Validated and automated experimental process.
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Introduction to Our Prokaryotic RNA Sequencing Platform

The prokaryotic RNA sequencing platform enables us to effectively study the transcript information of a bacterial sample in a specific time and space to find key functional genes by using Illumina HiSeq (PE150) or PacBio SMRT systems. Before sequencing, it should be noted that prokaryotic sequencing libraries are prepared based on rRNA depletion methods since prokaryotic mRNA does not have a poly(A) tail. This platform can be used for a variety of purposes: (i) accurate determination of the number of each transcript type and discovery of novel transcripts; (ii) determination of regions that show significant levels of antisense transcription; (iii) determination of gene structure and expression regulation; (iv) gene functional annotation via differentially expressed gene (DEG) analysis; (v) on a microbial community level or a prokaryotic strain level.

Our prokaryotic RNA sequencing platform is suitable for strains with/without the reference genome. Our scientists utilize this platform to explore both non-coding RNA and RNA information, which provides an important tool for the screening of functional genes, molecular markers, and drug targets, biological metabolic regulation research, strain typing, and disease typing. The sequencing technology can be applied to many aspects of our lives, including environmental protection, clinical practice and research.

  • Environmental protection: super-bacteria that degrade benzene, petroleum, and heavy metals.
  • Clinical practice: taxonomic composition analysis of human microbiomes from tissues, oral cavity, intestinal tract, and feces.
  • Medical research: screening of microbial strains with activities of interest.

Prokaryotic RNA Sequencing Workflow

Analysis Content

Our bioinformatics analysis includes these parts: read QC and assembly, expression analysis, structure analysis, and advanced analysis. For more detailed bioinformatics analysis, please refer to the following table.

Read QC & Assembly
Quality assessment of raw data Contamination detection
Mapping to the reference genome De novo assembly
Structure analysis
Prediction of novel transcripts UTR analysis and annotation
SNP and indel analysis Operon analysis
sRNA analysis Prediction of antisense transcripts
Gene fusion discovery
Expression analysis
GO/KEGG enrichment analysis Cluster analysis
Gene expression quantification New gene sequence annotation
PCA Alternative splicing analysis
Advanced analysis
Metabolic pathway integration analysis Gene co-expression network analysis
Protein interaction network analysis mRNA-sRNA co-expression network analysis
Correlation analysis

Sample Requirement

Deliverables: Raw sequencing data (FASTQ), clean data, trimmed and stitched sequences (FASTA), quality-control dashboard, sample contamination report, statistic data, and your designated bioinformatics result report.

Areas of Interest

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