Nanopore-Based Microbial Transcriptomics

Overview

Our nanopore-based microbial transcriptomics uses standardized analysis pipeline to capture the complexity of the entire transcriptome analysis and to generate accurate transcriptome assemblies ready for functional annotation based on a relatively simple workflow. Nanopore sequencing is a long-read technology that can sequence full-length transcripts without the need for transcript assembly.

Our Advantages:

Experienced staff assist you with experimental design.
Fast turnaround times and full bioinformatics analysis.
Avoid amplification biases without reverse transcription and PCR amplification steps.
Real-time, long-read, and low-cost.

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Nanopore-based microbial transcriptomics platform

The study of microbial transcriptome and metatranscriptome is important for detecting RNA isoforms, quantifying gene expression levels, predicting resistance to specific antibiotics, understanding host-pathogen immune interactions, and tracking disease progression. Our nanopore-based microbial transcriptomics enables a relatively simple workflow and provides full-length, highly accurate transcriptome data of bacteria, archeae, fungi, and viruses, so as to reveal the complete set of mRNAs, circular RNA (circRNA), long non-coding RNA (lncRNA), microRNA (miRNA), and other non-coding RNAs in a sample under specific conditions. Nanopore sequencing enables direct RNA sequencing and simultaneous detection of epigenetic RNA modifications.

Microbial transcriptomics analysis can provide a snapshot of actively expressed genes and transcripts under specific conditions. It plays an importance role in gene annotation, isoform identification, identification of fusion transcripts, and lncRNA identification. It can also be used to elucidate the molecular mechanisms and biological pathways that regulate microbial activities, and to study host-microbe interactions like the effects of host environments on microbial gene expression and metabolic pathways.

Nanopore-based microbial transcriptomics workflow

Bioinformatics analysis

And we have fast turnaround times and full bioinformatics analysis to handle diverse datasets and generate best results, including raw data processing, gene annotation, gene structure analysis and gene expression analysis.

Pipeline	Details
Raw data processing	Correction, classification, reduced redundancy, etc.
Genome annotation	Gene ontology, KEGG pathway, MAKER2, BRAKER1, KOG or COG, Swissport, etc.
Gene structure analysis	Prediction of transcription iniation, alternative polyadenylation, and alternative splicing; identification of lncRNAs, novel transcript discovery, identification of fusion genes, etc.
Gene expression analysis	Gene expression level analysis, differential expression gene analysis, etc.
Custom analysis	We provide custom data analysis according to your needs.

Sample requirement

1. RNA amount: Total RNA ≥ 5 ug
2. RNA purity: 1.8 < OD_260/280 < 2.2; OD_260/230 ≥ 1.5 (without RNA degradation or DNA contamination)
3. RNA quality: 28S:18S ≥ 1.5，RIN ≥ 7

Sampling kits: We provide a range of microbial sampling kits for clients, including MicroCollect™ oral sample microbial collection products and MicroCollect™ stool sample collection products.

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

References

Rohan Lowe, et al. Transcriptomics technologies. PLOS Computational Biology. 2017, 13(5): e1005457.
Cook, D. E., et al. Long-read annotation: automated eukaryotic genome annotation based on long-read cDNA sequencing. Plant Physiol. 2019, 179: 38–54.
Liangzhen Zhao, et al. Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing. Frontiers in Genetics. 2019, 253(10):1-14.

* For Research Use Only. Not for use in diagnostic procedures or other clinical purposes.