Integration of Viral Short and Long Read RNA Sequencing

In the past years, methodological breakthroughs in sequencing technologies, including next-generation short-read sequencing (SRS) and third-generation long-read sequencing (LRS), have greatly promoted the investigation of transcriptome analysis. SRS excels at generating large amounts of sequencing data at unprecedented rates. However, it cannot sufficiently cover and resolve high-complexity transcriptomes. Compared with LRS, the technique has a lower per-base error rate as well as cost. Although LRS produces lower coverage datasets with a higher error rate, it can address the challenges of SRS, such as the inefficiency in identifying transcripts isoforms and overlapping transcripts. So far, LRS has been used for the investigation of transcriptomic profiling in several organisms, including viruses.

Creative Proteomics has been developing viral RNA sequencing and data analysis methods for many years. Here, we are dedicated to offering viral transcriptomic analysis service using the integrated short- and long-read seq. The combined use of these technologies can generate throughput and high-quality datasets on full-length transcripts. Thanks to our long-term experience, high degree of expertise in virus research, and the application of modern technologies, we can provide high-quality and customized services to greatly accelerate the progress of clients' projects.

Table 1. Comparison of the Various Sequencing Platforms.

Boldogkői, Z., et al. (2019)

Short- and long-read seq integration services Creative Proteomics

In order to provide detailed transcription profiling about the transcription dynamics of viruses, we offer multi-platform sequencing using SRS and LRS techniques. Regarding the SRS techniques, Illumina instruments, such as MiSeq and HiSeq, are employed. As the most widely used method and the standard for transcriptome profiling, the Illumina technology is characterized by high base accuracy and coverage, providing a great tool to identify transcriptional end sites (TESs), transcriptional start sites (TSSs), splice junctions, and RNA editing. Regarding the LRS techniques, we applied two of the most widely used LRS technologies for full-length sequencing, Pacific Creative Proteomics' (PacBio) single-molecule real-time (SMRT) sequencing (PacBio RS-II) and Oxford Nanopore Technologies' (ONT) nanopore sequencing (the MinION portable sequencer).

The combined use of LRS and SRS could avoid the deficiencies of each approach and offer the possibility of a wider range of viral transcriptomc analyses. Our services enable customers to study the transcriptome at different time points after viral infection as well as their effect on the host gene expression. Creative Proteomics' success lies in constantly optimizing our services. We put our heart and soul into supporting our global customers with competitive and professional services. Whatever the scale and complexity of your project for a professional, please feel free to contact us for reliable and highly customized solutions.

References

1. Moldován, N., et al. (2018). "Multi-platform sequencing approach reveals a novel transcriptome profile in pseudorabies virus." Frontiers in microbiology, 8, 2708.
2. Boldogkői, Z., et al. (2019). "Long-read sequencing–a powerful tool in viral transcriptome research." Trends in microbiology, 27(7), 578-592.

* For research use only.