RNA-Seq Service

Applications:

A high-quality RNA sequencing service designed to deliver cost-effective and rapid access to meaningful transcriptomics results.

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For more information about any OGT product or service, please contact us.

Overview

Genefficiency RNA-Seq Service includes:

  • Comprehensive interactive report — delivering rapid access to your results
  • Full advice and consultation — saving time and money
  • Enhance your existing gene expression studies — with nucleotide-level data
  • Dedication to quality — providing confidence in your results

Listen to our recent RNA-Seq Webinar: Addressing the challenge of data analysis

Details

Comprehensive interactive report — delivering rapid access to your results

The analysis of RNA-Seq experiments can be challenging due to the sheer volume and complexity of the data generated, as well as the diversity of analysis tools available. Oxford Gene Technology’s (OGT) dedicated bioinformatics team has simplified this demanding process for you, through the rigorous evaluation of leading analysis tools, to provide a bespoke and reliable data analysis pipeline and full RNA-Seq Service that delivers meaningful, publication-ready results. OGT’s bioinformaticians ensure that the pipeline utilises the most stable and up-to-date analysis tools available, saving you time and the need to recruit in-house bioinformatics support and purchase expensive hardware.

Your results will be presented to you in an intuitive interactive reporting tool allowing you to quickly interrogate your data against a number of parameters,including differentially expressed genes (Figure 1). It also provides the facility to instantly view isoforms for specific genes of interest (Figure 2), allowing you to quickly determine which isoforms are contributing to gene-level differential expression.

Figure 1 RNA Sequence

 

 

 

 

 

 

 

 

 

 

Figure 1: OGT’s advanced data analysis pipeline and interactive report allows rapid listing of all differentially expressed genes. Data from Dr Paul Clarke at the Institute of Cancer Research, Sutton, UK shows some of the novel and known genes that are differentially expressed in this investigation. These findings were subsequently compared to legacy microarray data confirming consistency in expression changes of known genes under the experimental conditions.

Figure 2 RNA Sequence

 

 

 

 

 

 

 

 

 

 

Figure 2: Intuitive visualisation of differentially expressed isoforms for a specific gene. Summarised gene level expression of PDE4B is shown in the left-hand bar graph,indicating that the gene is down-regulated in the knockdown condition. The smaller bar charts to the right represent the expression levels of the differentially expressed isoforms and their relative contributions to the overall differential expression of the gene. Numerical data for each transcript is presented in the table below, showing the FPKM values (fragments per kilobase per million sequenced reads) for the isoforms in each condition, the log2 fold changes and p-values from the differential expression tests. Data from Dr Paul Clarke, Institute of Cancer Research, Sutton, UK.

A comprehensive consultation with one of our expert bioinformaticians is provided as standard once your samples have been processed, giving you the chance to experience the full power of the reporting tool. You will also be provided with all of the raw data so that, if required at a later stage, you can add additional sequence data to increase the sequencing depth.

Full advice and consultation — saving time and money

The Genefficiency™ RNA-Seq Service from OGT provides a new level of assay customisation to ensure each experiment is fully optimised to suit your specific study objectives (Figure 3). At OGT we understand the time and effort it takes to generate good quality RNA and how precious your samples are. Whether you are looking for array equivalent output on known specific genes, quantification of novel or known alternative splicing variants for your gene of interest or the detection of a rare transcript, OGT will guide you every step of the way. Our expert team will provide advice on the correct combination of starting material, sequencing depth and the level of bioinformatics required to reach your goals — delivering successful and cost-effective results.

Figure 3 RNA Sequence

 

 

 

Figure 3: A comprehensive and fully integrated RNA-Seq service. The Genefficiency RNA-Seq Service includes full project consultation and support throughout your study to ensure the cost-effective delivery of meaningful results.

Enhance your existing gene expression data — with nucleotide-level data

While microarray-based gene expression analysis is still a popular choice for investigating changes in known transcripts, RNA-Seq allows much broader discoveries at the transcriptome level. For example, variant detection, splice junction analysis, identification of fusion proteins, allele-specific expression and isoform identification can be carried out with confidence at the correct sequencing depth. RNA-Seq provides the experimental freedom to identify unknown genes and isoforms and carry out analysis on other samples without having to wait for updates to exon arrays, development of custom arrays or updates to genome annotation. At OGT there is a complete understanding of the requirements for successful gene expression experiments. Careful planning is essential to ensure that samples are processed consistently to minimise experimental variation. OGT’s experience of RNA-Seq and array-based gene expression studies ensures that we can help you select the most appropriate project design for your specific research objectives.

Dedication to quality — providing confidence in your results

The delivery of high-quality data requires the implementation of high-quality processes. We employ stringent quality control metrics at each stage of the process to ensure your RNA-Seq study will be successful, giving you confidence in the results generated. For example, upon sample receipt and during library preparation, full quality control (QC) metrics are monitored and reported, allowing informed decisions to be made on specific samples before proceeding to the sequencing step. In addition, the interactive report contains detailed QC information on the raw sequence data as well as multiple post-alignment metrics so you can be confident that high-quality, well mapped reads are informing the downstream analysis.

Our industry-leading Laboratory Information Management System (LIMS) has been validated on high-throughput genomic studies, including the Wellcome Trust aCGH population study of >20,000 samples. The OGT managementsystem is also certified to the ISO9001:2008 and ISO27001:2005 international standards for quality and information security management by the British Standards Institute.

Contact us to discuss your project and to request a quote.

 

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