Single-Nucleus RNA-Seq: Open the Era of Great Navigation for FFPE Tissue

Single-cell sequencing (scRNA-seq) has revolutionized our ability to explore heterogeneity and genetic variations at the single-cell level, opening up new avenues for understanding disease mechanisms and cell-cell interactions. Single-nucleus RNA-sequencing (snRNA-seq) is emerging as a promising sol...

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Bibliographic Details
Published in:International journal of molecular sciences 2023-09, Vol.24 (18), p.13744
Main Authors: Guo, Yunxia, Wang, Wenjia, Ye, Kaiqiang, He, Liyong, Ge, Qinyu, Huang, Yan, Zhao, Xiangwei
Format: Article
Language:English
Subjects:
Animals
Breast cancer
Cell Nucleus - genetics
Cell Nucleus - metabolism
Enzymes
Ethylenediaminetetraacetic acid
FFPE
Flow cytometry
Formaldehyde
Formaldehyde - chemistry
Gene expression
Gene Expression Profiling - methods
Genes
Genomes
Humans
Hybridization
Liver cancer
Medical prognosis
Methods
nuclear preparation strategies
Paraffin Embedding - methods
Review
RNA
RNA sequencing
RNA, Small Nuclear - genetics
RNA-Seq - methods
Sequence Analysis, RNA - methods
Single-Cell Analysis - methods
snRNA-seq
Tissue Fixation - methods
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Summary:Single-cell sequencing (scRNA-seq) has revolutionized our ability to explore heterogeneity and genetic variations at the single-cell level, opening up new avenues for understanding disease mechanisms and cell-cell interactions. Single-nucleus RNA-sequencing (snRNA-seq) is emerging as a promising solution to scRNA-seq due to its reduced ionized transcription bias and compatibility with richer samples. This approach will provide an exciting opportunity for in-depth exploration of billions of formalin-fixed paraffin-embedded (FFPE) tissues. Recent advancements in single-cell/nucleus gene expression workflows tailored for FFPE tissues have demonstrated their feasibility and provided crucial guidance for future studies utilizing FFPE specimens. In this review, we provide a broad overview of the nuclear preparation strategies, the latest technologies of snRNA-seq applicable to FFPE samples. Finally, the limitations and potential technical developments of snRNA-seq in FFPE samples are summarized. The development of snRNA-seq technologies for FFPE samples will lay a foundation for transcriptomic studies of valuable samples in clinical medicine and human sample banks.
ISSN:1422-0067
1661-6596
1422-0067
DOI:10.3390/ijms241813744