In recent years, single-cell RNA sequencing (scRNA-seq) has revolutionized our ability to study gene expression at the single-cell level, allowing for the identification of cell subpopulations and the discovery of new cell types. However, performing scRNA-seq experiments can be challenging, particularly when dealing with scalability and cost.

Cyrille Delley, PhD, a postdoctoral scholar of Bioengineering at UCSF, has been using the PIPseq 3’ Single Cell RNA kit to analyze single-nuclei from schwannomas and melanoma metastases. Dr. Delley discusses the common challenges faced in the UCSF lab and how PIPseq has revolutionized their workflow by simplifying the process, increasing cell recovery rates, and reducing clogging.

Fluent BioSciences: What common challenges do you face in your lab when performing single cell RNA-seq experiments? 

UCSF: As I work with cryosections, the input material is typically limited and the nuclei suspension is not as clean as when working with larger samples. This combination makes it challenging for many single-cell workflows, as I cannot use FACS and other common methods to improve the sample quality because of the low input. Directly using microfluidic based approaches is also problematic because the tissue debris can cause clogging, leading to poor data quality.

Fluent BioSciences: What are the greatest advantages of the PIPseq workflow ?

UCSF: PIPseq allows for ease of use and speed to get the cells or nuclei into suspension. This is incredibly helpful when processing multiple samples in parallel, while not worrying about RNA degradation. In addition, PIPseq has a great cell recovery rate and since no microfluidics are involved, the clogging problems are eliminated. We are also quite pleased with the data quality .

Fluent BioSciences: What sets PIPseq apart compared to some of the previous technologies you have used in the past?

UCSF: I have previously used other microfluidic platforms and custom built microfluidic workflows (a main expertise of our lab). PIPseq streamlines scRNA-seq experiments even more so than the competition, yet only costs a fraction of the price. Some applications may require  custom microfluidics for specialized experiments, but for RNA work, PIPseq makes this completely obsolete.  In addition, the capability and flexibility to run one to multiple samples in parallel is a true asset.

The PIPseq 3’ Single Cell RNA kit has been shown to simplify and improve the process of scRNA-seq experiments, especially in cases where input material is limited or difficult to obtain. With its ease of use, lack of capital investment, and cost efficiency, PIPseq is becoming a solution for researchers across various fields and applications.  

If you are interested in learning more about how PIPseq can help revolutionize your single-cell workflow and address your specific experimental needs, we encourage you to contact our sales team at