Accession PRJCA014083
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
Organisms Mus musculus
Homo sapiens
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
PubMed ID Article title Journal name DOI Year
37173341 High-throughput single nucleus total RNA sequencing of formalin-fixed paraffin-embedded tissues by snRandom-seq Nature Communications 10.1038/s41467-023-38409-5 2023
Grants
Agency program Grant ID Grant title
National Natural Science Foundation of China (NSFC) 82200977
National Natural Science Foundation of China (NSFC) 32200073
Submitter Yongcheng Wang (yongcheng@zju.edu.cn)
Organization First Affiliated Hospital, Zhejiang University
Submission date 2022-12-27

Project Data

Resource name Description
BioSample (30)  show -
GSA (1) -
CRA010745 High-throughput single nucleus total RNA sequencing of formalin-fixed paraffin-embedded (FFPE) tissues by snRandom-seq_4