Accession | PRJCA014083 | ||||||||||||
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Title | High-throughput single nucleus total RNA sequencing of formalin-fixed paraffin-embedded (FFPE) tissues by snRandom-seq | ||||||||||||
Relevance | Medical | ||||||||||||
Data types |
Transcriptome or Gene expression
Raw sequence reads Single cell sequencing |
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Organisms |
Mus musculus
Homo sapiens |
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Description | Formalin-fixed paraffin-embedded (FFPE) tissues constitute a vast and valuable patient material bank. It is still challenging to achieve single cell/nucleus RNA (sc/snRNA) profile in FFPE tissues. Here, we developed a droplet-based snRNA sequencing technology (snRandom-seq) for FFPE tissues by capturing full-length total RNAs with random primers. snRandom-seq showed a minor doublet rate (0.3%), a much higher RNA coverage, and detected more non-coding RNAs and nascent RNAs, compared with state-of-art high-throughput scRNA-seq technologies. We used snRandom-seq to profile ~20,000 single nuclei from multiple FFPE mouse tissues. A median of >3,000 genes per nucleus was detected and 25 typical cell types were identified. Moreover, we applied snRandom-seq on a clinical FFPE human liver cancer specimen and revealed an interesting subpopulation of nuclei with high proliferative activity. Our method provides a powerful snRNA-seq platform for clinical FFPE specimens and promises enormous applications in biomedical research. | ||||||||||||
Sample scope | Single cell | ||||||||||||
Release date | 2023-04-25 | ||||||||||||
Publication |
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Grants |
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Submitter | Yongcheng Wang (yongcheng@zju.edu.cn) | ||||||||||||
Organization | First Affiliated Hospital, Zhejiang University | ||||||||||||
Submission date | 2022-12-27 |