Lexogen’s QuantSeq technology has become a highly established method for transcriptome analysis by Next Generation Sequencing (NGS). Only one fragment of polyadenylated RNAs is sequenced, allowing the method to accept input down to 100 pg total RNA as well as highly degraded RNA extracted from FFPE and difficult biological samples. Focusing the sequencing effort on the 3’ end significantly reduces read depth when compared to whole transcriptome analysis approaches. 3-5 million reads per sample are sufficient to determine differential gene expression, even for complex eukaryotic transcriptomes. This enables multiplexing of up to 96 QuantSeq libraries in an Illumina NextSeq run and up to 384 libraries on a NovaSeq, reducing sequencing costs per sample tremendously.

The “tag profiling” approach also allows for a straight-forward data evaluation, since genome-mapped QuantSeq reads are counted directly without having to resort to transcript modelling. Incomplete or incorrect transcript annotations have a lower impact, and gene length bias is practically absent. The QuantSeq data analysis pipeline uses transparent, peer-reviewed algorithms, has been cited in more than 200 publications and best of it all, data analysis is free for QuantSeq kit users.

To offer complimentary automated data analysis, Lexogen has partnered with the cloud based BlueBee Genomics Data Analysis Platform, providing an end-to-end solution that includes quality control, mapping, UMI de-duplication (if applicable), genome alignment, gene expression quantification, and differential gene expression evaluation (if applicable). See the detailed data analysis workflow in the Figure 1.

QuantSeq-Data-Analysis-Pipeline

Figure 1. The QuantSeq FWD / REV Data Analysis Pipeline Workflow. Steps in blue represent the data analysis processes, grey bars indicate the results and output files generated. Steps in green indicate the data analysis processes for Differential Expression Pipelines.

A free activation code is included in every QuantSeq kit and can be redeemed at platform.bluebee.com with QuantSeq users benefitting from:

  • User-friendly, pre-configured, and validated workflow designed to be operated also without a bioinformatics background;
  • Certified, secure cloud-based solution;
  • ~40 different genomes, e.g. human, mouse, and rat already available; additional species can easily be added;
  • Time and costs savings on bioinformatics.

To enable users to re-examine QuantSeq reads with different parameters and/or different genomes, the BlueBee QuantSeq data evaluation is now free for also for re-analysis purposes!

For more information on how to obtain extra codes please contact support@lexogen.com. This offer on extra re-analysis codes ends on March 31st, 2020.

Learn more about QuantSeq 3’ mRNA-Seq Library Prep Kits.