Single-cell RNA sequencing (scRNA-seq) is a powerful tool for understanding gene expression at the individual cell level. However, analyzing the data generated from these experiments can be a prohibitive challenge for labs without in-house bioinformatics expertise.
Customer Challenge
A research laboratory specializing in viral vector-mediated gene therapy research generated a scRNA-seq dataset by Multiplexed Fixed RNA Profiling, a probe-based assay that captures transcripts derived from the coding genes.
The lab transduced target cells with a viral vector carrying a transgene which was hypothesized to rescue the biological function of a native gene implicated in a disease phenotype. The dataset consisted of a single multiplexed pair of FASTQ files containing reads derived from an untransduced (control) and two transduced (treatment) samples at different multiplicity of infections (MOIs).
Although the lab had the biological expertise to execute the assays, they needed more bioinformatics expertise and resources to generate meaningful insights from the data.
The Solution
Almaden Genomics supplied the partner with the bioinformatics support necessary to build an analysis pipeline for their unique experiment, the computational infrastructure and resources required to execute the pipeline on large NGS datasets, and the analytical support to interpret and communicate the results.
Deliverables were provided via the g.nome platform, a consolidated cloud-based platform to store and organize large raw data files, run analyses, and view results.
The Results
The Almaden bioinformatics team first provided a QC report, visualizing metrics like genes per cell and mitochondrial DNA content to demonstrate the quality of the data.
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The Almaden bioinformatics team then validated the lab’s hypothesis by verifying the absence of transgene expression in the untransduced condition and increased transgene expression in the two transduced conditions.
Conclusion
Almaden Genomics services eliminated barriers for the research lab by serving as a trusted bioinformatics partner. By delivering custom pipelines, comprehensive analyses, and results interpretation, we helped the lab glean actionable insights from their data and the confidence to advance their research.