Expression analysis: Every gene, all at once.

Instantly know the relative expression level of every gene in your SAGEspeed custom model with RNA-seq provided by SAGE Labs and Cofactor Genomics.

SAGE Labs has partnered with Cofactor Genomics to offer RNA-seq expression analysis in your SAGE research model. This service focuses on characterizing the transcriptome of your custom animal model as compared to wild-type control. Following delivery of your animal model, you’ll receive an in-depth representation of expressed loci, differential expression of genes, and the opportunity for gene discovery and alternative splicing characterization.

Expression profiling, also known as transcriptomics or RNA-seq, is an application of next generation sequencing where an entire set of mRNA is sequenced. Normalized “read counts”, or the number of times a certain mRNA transcript molecule is sequenced, are calculated. This is directly proportional to the number of copies of RNA present in the original sample, allowing the comparison of relative expression levels between samples. Cofactor’s analysis pipeline allows users to either look at their data from a transcript view (including well-curated splice variants), or a wider whole-genome view including intergenic regions that may be of interest. At the end of the experiment, a researcher will have a set of candidate genes of interest and the relative expression levels in hand.

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Included in your RNA-seq expression profiling:

  • RNA-seq analysis of one tissue from 3 custom model animals and 3 control animals
  • Tissue extraction and total RNA isolation and preparation
  • Sample quality control and library preparation
  • Approximately 25 million reads/sample during sequencing
  • Standard differential expression analysis, including normalized expression of known genes, expression of unannotated genes, comparative expression and fold change
  • Access to ActiveSite Expression Viewer for data sorting and refinement
  • Analysis consultation with our team of experts for support
  • Ready for publication Materials & Methods

See just how easy it is to analyze your RNA-seq experiment with SAGE Labs and Cofactor Genomics.

Figure 1. Representative expression data. In this plot, each dot represents the mean expression value for a specific loci. The mean expression value for one set of samples (Group 1, x-axis) are compared to the mean values for another set of samples (Group 2, y-axis). Each dot is colored to represent the degree of differential expression, or fold-change in expression. Black indicates the change in differential expression is less than 2-fold, red indicates at least a 2 fold change, blue indicates at least a 5-fold change, and green indicates a 10-fold change or greater.

Additional information:

Fast Turnaround Time

We recognize that researchers need interpretable, accurate results to move their research forward. Expression analysis data will be delivered to you within 8 weeks of sample preparation. Please note that a period of 5-7 months may be required to breed your model to homozygosity for analysis. Follow-up projects have access to our average turnaround time of 8 weeks from sample arrival to data delivery.

ActiveSite Expression Viewer

Our ActiveSite Viewer is a web-based home for all of the information associated with your project including data quality, alignment information, and characterization. ActiveSite enables researchers to examine, sort, and discover patterns in their data that may not be visible when working with just text files or in classical expression applications. Researchers are easily able to share their data with their team and download their refined data set for further exploration in the laboratory, or publication.

See just how easy it is to analyze your RNA-seq experiment with SAGE Labs and Cofactor Genomics.

Coverage Stats

We provide coverage statistics on both annotated and unannotated regions of the genome. In this way, researchers interested in discovery may explore these regions of differential expression that may not have yet been identified as coding.

Analysis Consultation

Following the delivery of your results, you will have the opportunity to schedule an analysis consultation with a member of our bioinformatics team. This consultation allows you to obtain answers to questions and receive expert feedback on your project.

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