Prokaryotic mRNA Sequencing

Prokaryotic mRNA sequencing uses the second-generation high-throughput sequencing technology to sequence the transcripts (mRNA) of prokaryotes, comprehensively and quickly obtains the information of all transcripts of a specific microorganism in a specific state, so as to find out the key functional genes for expression. Analysis and structural analysis.


Analyzing the transcriptome information of biological samples is helpful to study the situation of gene transcription and the law of transcriptional regulation in cells. The vast majority of RNA in prokaryotes is rRNA, and mRNA only accounts for 1% to 5% of all RNAs. Therefore, to sequence the prokaryotic transcriptome, the mRNA must be purified first. In addition, prokaryotic mRNA does not have a poly A structure like eukaryotic mRNA, so it cannot be directly purified by oligo T. Generally, rRNA-removing methods need to be used to construct libraries when performing prokaryotic transcriptome sequencing. CD Genomics takes effective methods to remove rRNA for different research species to ensure data quality.

CD Genomics's prokaryotic mRNA sequencing service is based on the Illumina high-throughput sequencing platform, capable of detecting the overall transcript level of any species at the single nucleotide level. While analyzing the structure and expression level of transcripts, unknown transcripts and rare transcripts can also be found, and alternative splicing sites and coding sequence single nucleotide polymorphisms (cSNPs) can be accurately identified, providing the most comprehensive transcriptome information.


Good Fidelity & Reliability Experienced Scientist Team Fast and Efficient Professional Bioinformatics
Profiling gene expression more realistically; Transcripts of different abundances can be accurately quantified. Can provide a full set of professional services from experimental design, sample testing, data analysis, etc. Mature process reduces unnecessary waste of samples and time, and the turn-around time is short. Strong bioinformatic team provides conventional analysis and in-depth data analysis.

Project Workflow

Sample Preparation

1. Sample Preparation

RNA purification; quality assessment and quantification.

Library Preparation

2. Library Preparation

RNA fragmentation; crosslinking reaction; PCR amplification.


3. Sequencing Platform

Illumina HiSeq; PE 50/75/100/150.

Data Analysis

4. Data Analysis

Preprocess and visualize results, and perform custom bioinformatics analysis.

Prokaryotic mRNA Sequencing

Bioinformatics Analysis Pipeline

In-depth data analysis:

  • Read mapping and statistical data analysis
  • Sequencing quality assessment (QC)
  • Transcriptome expression level analysis
  • Differential analysis of gene expression
  • Differential gene pathway analysis
  • Differential gene GO functional analysis
  • SNP and Indel analysis
  • New transcript prediction and operon prediction
  • sRNA analysis

Sample Requirements

RNA sample: RNA quantity: 30-300 μg; RNA purity: OD260/280 = 1.6~2.3; OD260/230 ≥ 1.5; RNA quality: 28S:18S ≥ 1.5 or RIN ≥ 7

Please make sure that the RNA is not significantly degraded.

Sample storage: RNA samples can be dissolved in ethanol or RNA-free ultrapure water, and stored at -80°C. Avoid repeated freezing and thawing during sample storage.

Shipping Method: When shipping RNA samples, the RNA sample is stored in a 1.5 mL Eppendorf tube, sealed with sealing film. Shipments are generally recommended to contain 5-10 pounds of dry ice per 24 hours.

Deliverable: FastQ, BAM, coverage summary, QC report, custom bioinformatics analysis.


  1. Sorek R, Cossart P. Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nature Reviews Genetics. 2010 Jan;11(1).
  2. Kozak M. Regulation of translation via mRNA structure in prokaryotes and eukaryotes. Gene. 2005 Nov 21;361.
* For Research Use Only. Not for use in diagnostic procedures.

Research Areas
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