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, drug research and development.
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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.
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 | |
RIN ≥ 7.0, 28s/18s ≥ 1.5, no DNA contamination.
RNA amount ≥ 3 μg, concentration ≥ 30 ng/μL, volume ≥ 30 μL
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.
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