Reducing costs associated with single cell sequencing.

Implementing single-cell sequencing can be costly. However, the DepleteX^® Single Cell RNA Boost Kit provides cost savings by efficiently eliminating abundant and uninformative fragments before sequencing, reallocating 50% of sequencing clusters to informative reads that would typically be filtered out during secondary analysis. 
 

Figure 1: Double the reads mapped to the transcriptome with the DepleteX^® Single Cell RNA Boost Kit.

Reduction of single cell sequencing data complexity.

Single-cell sequencing generates large and complex datasets. Analyzing these data requires robust computational methods and expertise. The sensitivity of scRNA sequencing can lead to high levels of technical noise. The DepleteX^® Single Cell RNA Boost Kit empowers you to reduce noise and optimize usable data in your single-cell RNA sequencing. Figure 2 illustrates a 1.5x improvement in detection after depletion with this kit. 
 

Figure 2: 1.5x improvement in detection with depletion

FAQs

Q: Can I use the DepleteX® Single Cell RNA Boost Kit on mouse samples?

A: Yes, but the depletion rate is lower since the guides are designed for human samples.

Q: Does the DepleteX® Single Cell RNA Boost Kit use all of the cDNA from my 10X prep?

A: No, only 1 tube of the available cDNA from a given 10X prep is used in general. The customer is free to customize this as needed to hit the 100-150 ng input recommendation.

Q: Is this kit compatible with the 5’ Chromium assay (10X Genomics), the TotalSeq™ reagents and Visium™ spatial (10X Genomics)?

A: Yes, it is compatible with all these workflows. Our depletion panel is designed to tile across the full length of transcripts.

Q: What is the sequencing depth recommendation for the depleted condition?

A: general, single cell users use between 25K – 50K reads/cell depending on their application. For the depleted condition, users can choose to sequence 12.5K – 25K reads/cell to see the same information or sequence at the same depth to see more information.

Q: Can I still use mitochondrial reads to separate “intact” cell from “compromised” cells?

A: Mitochondrial reads are targeted by the DepleteX® Single Cell RNA Boost Kit but removal is not complete. They can be used to separate intact from compromised cells. Instead of setting an arbitrary 10% threshold, alternative approaches are described in the Python and R guides provided.

1. Currenti, J., Qiao, L., Pai, R., Gupta, S., Khyriem, C., Wise, K., Sun, X., Armstrong, J., Crane, J., Pathak, S., Yang, B., George, J., Plummer, J., Martelotto, L., & Sharma, A. (2022). STOmics-GenX: CRISPR-based approach to improve cell identity-specific gene detection from spatially resolved transcriptomics. bioRxiv. Advance online publication.
2. Pandey, A. C., Bezney, J., DeAscanis, D., Kirsch, E., Ahmed, F., Crinklaw, A., Choudhary, K. S., Mandala, T., Deason, J., Hamdi, J., Siddique, A., Ranganathan, S., Ordoukhanian, P., Brown, K., Armstrong, J., Head, S., & Topol, E. J. (2022). A CRISPR/Cas9-based enhancement of high-throughput single-cell transcriptomics. bioRxiv. Advance online publication.