Microbial Iso-Seq

Service Overview

Bacterial, fungal, viral, and other microbial RNA-Seq can provide unbiased strand-specific information on novel and known transcripts and help annotate and quantify microbial transcripts. Microbial isoform sequencing (Iso-Seq) is an ideal method to analyze microbial transcriptomes and gene fusion events, and characterize gene isoforms and alternative splicing events. Our microbial iso-seq service can provide full-length reads with no assembly needed, spanning entire transcript isoforms from the polyA-tail to the 5' end using PacBio Single Molecular and Real-Time (SMRT) technologies.

Our Advantages:
  • An efficient standard workflow, fast turnaround time, and comprehensive bioinformatics analyses in a cost-effective way.
  • Large sequencing capacity and effective methodology: advanced PacBio and Illumina sequencing platforms.
  • Provide comprehensive data analysis by using widely accepted mainstream software and mature in-house pipeline for discovery of novel transcripts, function annotations and differential expressions.
  • Keep up with the frontiers of bioinformatics analysis, evolutionary genomics and molecular epidemiology.
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Introduction to Our Microbial Iso-Seq

Our fungal iso-seq or bacterial iso-seq can offer complete solutions for full-length transcript sequencing. It is a powerful technique using combined Illumina and PacBio SMRT sequencing platforms to identify both high and low expressors in a single bacterial or microbial population. PacBio SMRT sequencing enables the sequencing of contiguous full-length transcripts and captures each transcript's start, splice sites, and polyadenylation from a single read. Illumina short reads are further mapped to the PacBio SMRT full-length transcripts for more accurate quantification analysis and error correction.

Microbial iso-seq is becoming increasingly important for basic research. It accurately characterizes the diverse landscape of transcript isoforms, further providing key information on the functional biology of genomes for developing potential applications of these abundant microbes in disease, medicine, agriculture, and environment, for example, predicting resistance to specific antibiotics, quantifying gene expression changes, understanding host-pathogen immune interactions, and tracking disease progression.

Microbial Iso-Seq Workflow

Bioinformatics Analysis

Our bioinformatics analysis includes transcriptome analysis, structure analysis, expression correlation and differential expression analysis, which is flexible to your needs. Please feel free to contact us to discuss your project.

Bioinformatics Pipelines Details
Transcriptome Assembly Mapping to reference; de novo assembly, transcript classification
Transcriptome Analysis Novel genes, novel isoforms, structural category, length distribution, spice junction, transcriptome diversity
Structure Analysis Gene ontology, Swissport, lncRNA prediction, transcription factor, fusion transcript, alternative splicing, alternative polyA adenylation
Expression Correlation Expression boxplot, expression heatCluster
Differential Expression Go enrichment analysis, KEGG enrichment analysis

Sample requirements

    1. RNA amount ≥ 5 µg, RNA concentration ≥ 300 ng/µL.
    2. 1.8< OD260/280 < 2.2，OD260/230 ≥ 1.8, 28S/18S ≥1.5.
    3. RNA integrity number (Agilent 2100) ≥ 9. No degradation, no contamination.
    4. 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.
    5. Deliverables: raw sequencing data (FASTQ), assembled and annotated sequences, quality-control dashboard, and the customized bioinformatics report.

References

  1. Philippot L, Abbate C, Bispo A, et al. Soil microbial diversity: an ISO standard for soil DNA extraction. J Soils Sediments. 2010, 10:1344–1345.
  2. Rhoads A, Au KF. PacBio Sequencing and Its Applications. Genomics Proteomics Bioinformatics. 2015,13(5): 278–289.
  3. Sahlin K, Tomaszkiewicz M, Makova KD, et al. Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon. Nat Commun. 2018, 9: 4601.
* For research purposes only, not intended for clinical diagnosis, treatment, or individual health assessments.