Case Study Highlight: Differential Expression of Splicing Factor Genes

Dr. Miriam Bucheli, an instructor at Harvard University, is this month’s use case focus. She demonstrates in an elegant way that one can analyze differential expression of splicing factor genes by using DNAnexus to determine the expression profiles in undifferentiated mouse embryonic stem cells (MeS) and differentiated neurons in a senataxin (SETX) knockdown compared to wild type control. During her research-intensive class, Miriam together with her students are beginning to characterize the transcription and RNA processing activities of SETX which is associated with Amyotrophic Lateral Sclerosis (ALS), a disease which affects nerve cells in the brain and spine and leads to progressive loss of motor control.

They used DNAnexus to analyze, visualize and compare the different samples. RPKM values were computed for each gene of interest and an analysis was run to compare the differential expression of splicing factors in SETX knockdown compared to a wild type control. Using this approach, they confirmed that SETX expression is significantly reduced in the knockdown samples (see Figure 1). “The straightforward features and tools made available at DNAnexus helped us complete the project within the deadlines for the students’ presentations,” said Miriam Bucheli, “DNAnexus is a powerful and efficient cloud-based web solution for the analysis of NGS data”.

Figure 1: SETX expression in normal vs. knockdown sample as visualized in the DNAnexus Genome Browser.

In their user case study, Miriam shared additional data which was presented while visiting Columbia Medical School and will be shared at a future Keystone Meeting.

Figure 2: Differential expression of splicing factors in SETX knockdown compared to normal control. Values calculated from RPKM ratios of cells non-induced or induced for neuronal differentiation by SAG.

Miriam shared her experience with us by submitting to our “Tell us how you use DNAnexus” contest and was selected as January’s winner. View Miriam Bucheli’s complete submission.