Holo-Seq: single-cell sequencing of holo-transcriptome

Current single-cell RNA-seq approaches are hindered by preamplification bias, loss of strand of origin information, and the inability to observe small-RNA and mRNA dual transcriptomes. Here, we introduce a single-cell holo-transcriptome sequencing (Holo-Seq) that overcomes all three hurdles. Holo-Se...

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Published inGenome Biology Vol. 19; no. 1; p. 163
Main Authors Xiao, Zhengyun, Cheng, Guo, Jiao, Yang, Pan, Chen, Li, Ran, Jia, Danmei, Zhu, Jing, Wu, Chao, Zheng, Min, Jia, Junling
Format Journal Article
LanguageEnglish
Published England BioMed Central 17.10.2018
BMC
Subjects
Accuracy
Animals
Anti-sense transcript
Archives & records
Cell growth
Gene expression
Genomes
HEK293 Cells
Hepatocellular carcinoma
Hepatology
Humans
Introns - genetics
Kinases
Liver cancer
Male
MCF-7 Cells
Metastasis
Method
Mice, Inbred C57BL
MicroRNAs
Middle Aged
mRNA-Seq
RNA, Antisense - metabolism
RNA, Messenger - genetics
RNA, Messenger - metabolism
Sequence Analysis, RNA - methods
Single cell
Single-Cell Analysis
Small-RNA-Seq
Stem cells
Super-enhancer
Total RNA-Seq
Transcriptome - genetics
Tumorigenesis
Tumors
Liver cancer
Single cell
mRNA-Seq
Small-RNA-Seq
Super-enhancer
Anti-sense transcript
Total RNA-Seq
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Summary:Current single-cell RNA-seq approaches are hindered by preamplification bias, loss of strand of origin information, and the inability to observe small-RNA and mRNA dual transcriptomes. Here, we introduce a single-cell holo-transcriptome sequencing (Holo-Seq) that overcomes all three hurdles. Holo-Seq has the same quantitative accuracy and uniform coverage with a complete strand of origin information as bulk RNA-seq. Most importantly, Holo-Seq can simultaneously observe small RNAs and mRNAs in a single cell. Furthermore, we acquire small RNA and mRNA dual transcriptomes of 32 human hepatocellular carcinoma single cells, which display the genome-wide super-enhancer activity and hepatic neoplasm kinetics of these cells.
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ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-018-1553-7