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Bacterial RNA Sequencing

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Besides eukaryotic RNA sequencing service, CD Genomics is also dedicated to providing prokaryotic RNA sequencing service to advance your bacterial gene expression profiling needs by utilizing the latest techniques.

The Introduction of Bacterial RNA Sequencing

In recent years, high throughput sequencing of cDNA libraries (RNA-Seq) has emerged as a powerful technology for profiling gene expression, discovering previously unannotated genes, and mapping transcriptome architecture in a wide variety of bacterial species. With the application of RNA-seq derivative approaches, we can gain biological insights into the bacterial world and aspire to uncover the mysteries involving gene expression, organization and other functional genomic features. Bacterial transcriptome and metatranscriptome information is important for predicting resistance to specific antibiotics, understanding host-pathogen immune interactions, quantifying gene expression changes, and tracking disease progression. 

There are obvious differences of cDNA library construction between bacterial RNA-Seq and Eukaryotic RNA-Seq. Bacterial RNA-Seq workflow’s first step is selection of mRNA transcripts. Ribo-Zero ribosomal RNA reduction chemistry is used in place a poly-A tail selection which makes this method particularly suited for bacteria mRNA lack a poly-A tail. Following purification, the mRNA is fragmented into small pieces, and copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity is achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM), followed by second strand cDNA synthesis. Through the use of strand-specific RNA-Seq, a more complete understanding of the transcriptome could be achieved, this has the potential to identify new levels of regulation of gene expression.

Project Workflow

Sample Requirements:

  1. RNA amount: Total RNA≥3 ug (without degradation or DNA contamination)
  2. RNA purity: OD260/280 = 1.8~2.2; OD260/230 ≥1.8
  3. RNA quality: 28S:18S≥1.5,RIN≥7

Sequencing Strategy:

HiSeq X ten, 150 PE, 1~3 G/per sample

Data Analysis

Transcriptome with no Reference

  • Transcriptome Assembly
  • Transcriptome/Unigene Length Statistic
  • Transcriptome Function annotation, including NR, NT, Gene Ontoloy, KEGG pathway, KOG, Swissport, Protein Family
  • Differential expression analysis
  • CDS Predictive Parsing
  • SNP/InDel Analysis
  • … (more upon request)

Transcriptome with Reference

  • Transcriptome Assembly
  • Transcriptome/Unigene Length Statistic
  • Transcriptome Function annotation, including NR, NT, Gene Ontoloy, KEGG pathway, KOG, Swissport, Protein Family
  • Differential expression analysis
  • CDS Predictive Parsing
  • SNP/InDel Analysis
  • … (more upon request)
  • Transcriptome with Reference
  • Reference Genome mapping
  • Transcriptome Function annotation, including NR, NT, Gene Ontoloy, KEGG pathway, KOG, Swissport, Protein Family
  • Differential expression analysis
  • Alternative splicing
  • Antisense Transcript Analysis
  • SNP/InDel Analysis
  • … (more upon request)

CD Genomics provides a fast, one-stop bacterial RNA sequencing solution from the quality control of sample to comprehensive data analysis. Please contact us for more information and a detailed quote.

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