Ensuring RNA Quality from FFPE Samples for Single-Cell Transcriptomics

High-throughput single-cell transcriptome sequencing has significantly advanced the field of biomedicine, primarily utilizing fresh or frozen samples. However, FFPE (Formalin-Fixed Paraffin-Embedded) sample preparation poses some challenges. The processes involved—such as high-temperature incubation, oxidative exposure, and cross-linking between nucleic acids and proteins—can severely compromise RNA quality, especially given RNA's inherent vulnerability to degradation. Moreover, the prolonged room-temperature storage of paraffin samples exacerbates RNA degradation.

To ensure the preservation of RNA quality and quantity for single-cell transcriptomics research, proper sample preparation and efficient RNA extraction are crucial.

At SeekGene, our innovative SeekOne? DD FFPE Single Cell Transcriptome-seq Solution is designed specifically to address the “cross-linking & degradation” characteristics of FFPE samples.

Employing a strategic “2*2” approach—two steps for de-crosslinking and two steps for reverse transcription—we maximize RNA yield and capture.

For more information about our products and how we can assist in your research, please reach out to your account manager or contact us at [email protected].

Paraffin-embedding protocol retrieved from Zhanmu, O., Yang, X., Gong, H. et al. Paraffin-embedding for large volume bio-tissue. Sci Rep 10, 12639 (2020). https://doi.org/10.1038/s41598-020-68876-5