Gene Expression Array Service
A gene expression array is a compact, massively parallel, and semi-automated method for monitoring gene product concentrations (or mRNA or transcripts), which can be widely used to diagnose the presence of an illness.
Gene Expression
The DNA in an organism's cells contains a set of instructions for the organism's continued existence. Usually, a genetic message is first transcribed from DNA to mRNA (also known as messenger RNA) before being translated into a protein. Measuring the quantities of mRNA provides an indirect perspective on the activity of the cell. Expressions are the absolute and relative levels of the transcripts, and the expression profile is an instantaneous collection of expressions.
Fig.1 The central dogma of molecular biology. (Wikipedia)
Published Data
| Paper Title | Direct RNA sequencing on nanopore arrays redefines the transcriptional complexity of a viral pathogen |
| Journal | Nature Communications |
| Published | 2019 |
| Abstract | High gene density, overlapping reading frames, and complex splicing make it difficult to characterize complex viral transcriptomes with conventional RNA sequencing techniques. Direct RNA sequencing (direct RNA-seq) utilizing nanopore arrays is an exciting alternative for sequencing individual polyadenylated RNAs without the recording and amplification biases inherent to other sequencing techniques. Here, the herpes simplex virus type 1 (HSV-1) transcriptome during productive infection of primary cells is profiled using direct RNA-seq. They demonstrate that direct RNA-seq data can be utilized to define transcription initiation and RNA cleavage sites associated with all polyadenylated viral RNAs and that low-level read-through transcription generates a novel class of chimeric HSV-1 transcripts, including a functional mRNA encoding a fusion of the viral E3 ubiquitin ligase ICP0 and viral membrane glycoprotein L. Therefore, direct RNA-seq is a potent method for characterizing the dynamic transcriptional landscape of viruses with complex genomes. |
| Result |
Using the same starting material, they sequence the polyadenylated portion of the HSV-1 transcriptome. Here, profiling the genome-wide depths of coverage produced a visual profile with peaks corresponding to previously annotated transcription units. Using a 100nt sliding-window approach, the authors compared changes in mean read depth (MRD) between genic and intergenic regions and found that MRDs in genic regions were about 7~12-fold higher than in intergenic regions in both normalized Illumina (6.8-fold) and nanopore (12.1-fold) datasets. This difference is likely due to mispriming from internal adenosine-rich tracts during the poly(A) selection step of standard Illumina protocols, as well as intrinsic biases in reverse transcription and amplification steps. In direct RNA-seq, on the other hand, the requirement for ligation of an adaptor-coupled motor protein to the poly(T) adaptor means that only polyadenylated RNAs will pass through the pore complex.
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Fig.2 Comparison of direct RNA nanopore sequencing to Illumina sequencing. (Depledge, 2019)
Features and Benefits of Our Gene Expression Array Service
Creative Biolabs offers high-resolution array scanning and automation services to enhance gene expression efficiency significantly. We have experience in processing microarrays from manufacturers on a standard slide format. In order to provide genome-wide expression profiles of people, model organisms, plants, and animals, these various microarrays are created using the most recent genome content.
- Accurate and simultaneous analysis of the entire transcriptome's expression.
- Adaptable, customized solutions for any project.
- Available for numerous species.
- Cost-effective analysis.
- Outstanding study design, data analysis options, and assistance.
- Complete sample tracking and quality assurance.
- Automated sample processing provides a rapid delivery of high-quality results.
We offer a comprehensive selection of arrays for whole-, transcriptome–, gene–, exon–, and short noncoding RNA–level investigation to suit diverse research objectives. They are compatible with many sample types and have a low RNA input requirement. Single-sample array cartridges and multi-sample array plate variants are available for varying throughput requirements. For any information, please contact us.
Fig.3 A schematic of gene expression array analysis. (Staudt, 2000)
References
- Depledge, D.P.; et al. Direct RNA sequencing on nanopore arrays redefines the transcriptional complexity of a viral pathogen. Nature Communications. 2019, 10: 754.
- Staudt, L.; Brown, P. Genomic Views of the Immune System. Annual Review of Immunology. 2000, 18(1): 829-59.
