Blogs

23 MAY, 2017

Delivering a seamless end-to-end RNA-seq solution

We are excited to release a new case study that focuses on complete end-to-end solution delivery in partnership with Lexogen, a Vienna-based company, and the provider of innovative RNA transcriptomics solutions for next generation sequencing (NGS) protocols. Not only does this case study highlight the benefits for the end-user of kit solutions that are faced with the challenges related to the complexity of NGS data analysis, but it also demonstrates the value for the provider (Lexogen) by opening a huge market of potential lab customers previously unable to benefit from Lexogen’s products alone.

Besides simplifying the workflow and removing a bioinformatics dependency for Lexogen’s kit users, this partnership further increases Lexogen’s customer reach by enabling direct extended support to labs that do not have the immediate access to bioinformaticians or necessary bioinformatics resources. This independence coming with integrated solutions opens a huge market of labs previously unable to benefit from Lexogen’s products alone.

Dr. Dalia Daujotyte, Head Of Business Development at Lexogen 

Download the full case study.

Below find a summary of a recent discussion with Dr. Dalia Daujotyte, Head of Business Development at Lexogen, on the topic of this valuable partnership.

Bluebee: Lexogen is a leading provider of kit solutions for the analysis of the transcriptome. What are some of the products Lexogen is providing and who is using those products? What differentiates those products from other products currently available on the market?

Dalia: Lexogen’s products cover the entire NGS pipeline from RNA extraction and purification to library preparation, and are used worldwide by thousands of researchers in academia and biotechnology. In addition, Lexogen also provides controls for RNA-seq experiments which are crucial to any experiment.

Our team’s experience and focus is on RNA which made Lexogen an expert in this domain. As such we continuously introduce innovative and novel protocols covering whole NGS experimental pipelines starting from RNA extraction all the way down to library preparation and data analysis.

One important field where this technology will soon be very meaningful is in human diagnostics. DNA-seq is already there, and while RNA-seq is very “young”, we are diligently working on delivering “useable and applicable” RNA-seq type solutions which are expected to soon benefit the diagnostics sector.

Lexogen aims to deliver RNA sequencing as an intuitive, cost-effective research tool, as well as an easily interpretable medical, diagnostics solution.

Bluebee: What do you see as the biggest challenge in the market when it comes to researchers in the NGS sample preparation space?

Dalia: In a recent survey respondents highlighted data analysis and knowledge extraction as a challenge in the whole NGS pipeline besides cost, sample robustness, sensitivity issues for different types of samples, and of course sample preparation.

In striving to improve the overall NGS workflow and to deliver a seamless offering, Lexogen thus needed a cost-effective data analysis solution that was highly secure and robust, yet easy to use.

Rather than asking our users to figure it out themselves and possibly have them struggle with the data analysis aspect, we decided to use Bluebee’s genomics platform and be confident that it’s robust and secure while supplying the necessary data analysis capabilities we needed to offer our customers.

Bluebee: You are in an active collaboration with Bluebee to provide a complete solution for your QuantSeq 3′ mRNA-seq Library kit. What are some of the QuantSeq kit specifics? What are the benefits and values of this partnership to your customers (the kit purchasers/users), and what needs does it address?

Dalia: The QuantSeq 3’ mRNA-Seq Library kit was developed to address the above-noted challenges. As little as 100 pg of total RNA can be processed, and many sample types can be used, including FFPE samples. QuantSeq generates highly strand-specific RNA-seq libraries close to the 3′ end of polyadenylated RNAs within 4.5 hours (and only 2 hours hands-on time). Only one fragment per transcript is produced, directly linking the number of reads mapping to a gene to its specific expression. This means less coverage is needed to gain insight into gene expression values, and hence higher multiplexing in one lane is possible. This in turn results in a more economical study, not just from lower sample preparation costs, but also from the lower costs of sequencing.

Because Bluebee offers the possibility to deploy proprietary analysis tools on the platform, we’re able to provide our own specific analysis for QuantSeq 3’ seq samples, which in turn provides tremendous value to our customers that have little data analysis expertise.

The result is an integrated solution of high quality RNA sample processing kit with the Bluebee platform providing a secure environment for data analysis. Or in other words, the Lexogen QuantSeq kit through this Bluebee solution integration provides immediate and unique access to seamless data analysis capabilities for all users. Furthermore, the secure data analysis and collaboration environment enables rapid and reliable results delivery.

The advantage really lies in the combined offering. Besides, the integration is seamless as the code for logging into the Bluebee platform automatically calls for the correct pipeline to analyze QuantSeq 3’ data. It can’t be simpler than this.

“Bluebee makes validated and well-documented open-access programs accessible while maintaining transparency. It is simple to use and clearly guides you through the steps in the QuantSeq data analysis pipeline.” 

Sheina B. Sim and Scott Geib, University of Hawaii, USDA-ARS Daniel K. Inouye US PBARC, USA

“I found the QuantSeq pipeline on the Bluebee platform to be user-friendly with a step-by-step video guide. I contacted Lexogen to inquire further about the pipeline after I got my results and was readily supplied with very useful explanation and advice.”

Kai Ling Liang, Ghent University, Belgium

Bluebee: Where do you see the market moving towards as more and more complex applications and methodologies are developed? Why is a complete kit solution with an integrated ready-to-use data analysis pipeline useful and most cost-effective for your kit users?

Dalia: The future will encompass various types of samples which in addition to RNA include DNA, protein, and DNA modifications. At one point, all of these samples/data are to be combined into streamlined one sample/one solution approaches. Sample preparation and data analysis will be complex and therefore challenging, including deciphering the interactions between these different entities. For now, we will need to focus on each entity or question separately, but as we learn we should be able to prepare and extract insights from these complex samples. Only such an integrated data analysis approach will enable us to ultimately understand complex diseases or causes of diseases with the hope of leading to impacts on how we prevent or treat disease.

Bluebee: What are the main benefits of working in partnership with Bluebee to provide a “complete kit solution”?

Dalia: By partnering with Bluebee, Lexogen moves closer to its ultimate goal of delivering a “seamless end-to-end” solution. The main aim of the partnership obviously is to provide quality transcriptomic-based data analysis in a streamlined way, so Lexogen’s various customers can quickly and easily extract findings from their unique data.

Besides simplifying the workflow and removing a bioinformatics dependency for Lexogen’s kit users, this partnership further increases Lexogen’s customer reach by enabling direct extended support to labs that do not have the immediate access to bioinformaticians or necessary bioinformatics resources. This independence coming with integrated solutions opens a huge market of labs previously unable to benefit from Lexogen’s products alone.

Within months the project was running and we were able to deliver a complete and integrated data analysis solution. Our experience of working with the Bluebee team was perfect – the company is great to work with, and they definitely are experts in what they do. The collaboration made quick progress and was non-bureaucratic and easy.

Lexogen has received very positive customer feedback. Not only did Bluebee simplify the use of Lexogen’s protocol, it also increased the visibility of our protocols. Now our customers can use our protocols more routinely, and with fewer complications. Today, partnered with Bluebee, we deliver an inexpensive and fast solution that can be accessed in a globally secure environment.

Download the full case study.