Single-nucleus total RNA sequencing of formalin-fixed paraffin-embedded samples using snRandom-seq

Gnanapragasam, V. J. Unlocking the molecular archive: the emerging use of formalin-fixed paraffin-embedded tissue for biomarker research in urological cancer. BJU Int. 105, 274–278 (2010).

Article  PubMed  Google Scholar 

Wang, K. et al. Archival single-cell genomics reveals persistent subclones during DCIS progression. Cell 186, 3968–3982.e15 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Evers, D. L., He, J., Kim, Y. H., Mason, J. T. & O’Leary, T. J. Paraffin embedding contributes to RNA aggregation, reduced RNA yield, and low RNA quality. J. Mol. Diagn. 13, 687–694 (2011).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zheng, G. X. Y. et al. Massively parallel digital transcriptional profiling of single cells. Nat. Commun. 8, 14049 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Llora-Batlle, O. et al. 10x Genomics Gene Expression Flex is a powerful tool for single-cell transcriptomics of xenograft models. Preprint at https://www.biorxiv.org/content/10.1101/2024.01.25.577066v2 (2024).

Wang, T. et al. snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archives. Commun. Biol. 7, 1340 (2024).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hattie, C. et al. SnFFPE-Seq: towards scalable single nucleus RNA-Seq of formalin-fixed paraffin-embedded (FFPE) tissue. Preprint at https://www.biorxiv.org/content/10.1101/2022.08.25.505257v1 (2022).

Isakova, A., Neff, N. & Quake, S. R. Single-cell quantification of a broad RNA spectrum reveals unique noncoding patterns associated with cell types and states. Proc. Natl Acad. Sci. USA 118, e2113568118 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Salmen, F. et al. High-throughput total RNA sequencing in single cells using VASA-seq. Nat. Biotechnol. 40, 1780–1793 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rosenberg, A. B. et al. Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding. Science 360, 176–182 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Xu, Z. et al. High-throughput single nucleus total RNA sequencing of formalin-fixed paraffin-embedded tissues by snRandom-seq. Nat. Commun. 14, 2734 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sun, X. et al. A pathologically friendly strategy for determining the organ-specific spatial tumor microenvironment topology in lung adenocarcinoma through the integration of snRandom-seq and imaging mass cytometry. Adv. Sci. (Weinh.) 11, e2308892 (2024).

PubMed  Google Scholar 

Xu, Z. et al. Single nucleus total RNA sequencing of formalin-fixed paraffin-embedded gliomas. Small Methods 8, e2301801 (2024).

Article  PubMed  Google Scholar 

Chen, H. et al. Pan-cancer single-nucleus total RNA sequencing using snHH-Seq. Adv. Sci. (Weinh.) 11, e2304755 (2024).

PubMed  Google Scholar 

Niu, M. et al. Droplet-based transcriptome profiling of individual synapses. Nat. Biotechnol. 41, 1332–1344 (2023).

Article  CAS  PubMed  Google Scholar 

Amini, P. et al. An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing. BMC Mol. Biol. 18, 22 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Bai, Z. et al. Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues. Cell 187, 6760–6779.e24 (2024).

Article  CAS  PubMed  Google Scholar 

Okubo, Y. et al. Effective preparation of FFPE tissue samples for preserving appropriate nucleic acid quality for genomic analysis in thyroid carcinoma. Endocr. Pathol. 35, 372–384 (2024).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zong, C., Lu, S., Chapman, A. R. & Xie, X. S. Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science 338, 1622–1626 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zilionis, R. et al. Single-cell barcoding and sequencing using droplet microfluidics. Nat. Protoc. 12, 44–73 (2017).

Article  CAS  PubMed  Google Scholar 

Xu, Z., Lyu, Y., Chen, H., Chen, Y. & Wang, Y. Single-nucleus total RNA sequencing of formalin-fixed paraffin-embedded samples using snRandom-seq. Zenodo https://doi.org/10.5281/zenodo.15063307 (2024).

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