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Series GSE143422 Query DataSets for GSE143422
Status Public on Jul 29, 2020
Title Transposase assisted tagmentation of RNA/DNA hybrid duplexes
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Tn5-mediated transposition of double-strand DNA has been widely utilized in various high-throughput sequencing applications. Here, we report that the Tn5 transposase is also capable of direct tagmentation of RNA/DNA hybrids in vitro. As a proof-of-concept application, we utilized this activity to replace the traditional library construction procedure of RNA sequencing, which contains many laborious and time-consuming processes. Results of Transposase assisted RNA/DNA hybrids Co-tagmEntation (termed “TRACE-seq”) are comparable to traditional RNA-seq methods in terms of detected gene number, gene body coverage, gene expression measurement, library complexity, and differential expression analysis; at the meantime, TRACE-seq enables a one-tube library construction protocol and hence is more rapid (within 6h) and convenient. We expect this tagmentation activity on RNA/DNA hybrids to have broad potentials on RNA biology and chromatin research.
 
Overall design mRNA profiles of HEK293T cells were generated by TRACE-seq with different RT primers (random primer, in duplicates; oligodT primer, in duplicates) and by NEBNext Ultra II RNA kit in duplicates with 10ng mRNA as input. In addition, mRNA profiles of HEK293T cells were generated by TRACE-seq with different amounts of total RNA as input (200ng total RNA, in triplicates; 20ng total RNA, in duplicates; 2ng total RNA, in duplicates) and by Smart-seq2 with 20ng and 2ng total RNA as input in duplicates respectively. What's more, differential gene expression analysis between differential and undifferential mESC cells was performed by TRACE-seq and NEBNext Ultra II RNA kit in triplicates respectively.
 
Contributor(s) Lu B, Dong L, Yi D, Zhang M, Yi C
Citation(s) 32701057
Submission date Jan 10, 2020
Last update date Aug 02, 2020
Contact name Chengqi Yi
E-mail(s) chengqi.yi@pku.edu.cn
Organization name Peking University
Street address No.5 YiHeYuan Road
City Beijing
ZIP/Postal code 100871
Country China
 
Platforms (2)
GPL20795 HiSeq X Ten (Homo sapiens)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (29)
GSM4633421 TRACE_seq_200ng_replicate_1
GSM4633422 TRACE_seq_200ng_replicate_2
GSM4633423 TRACE_seq_200ng_replicate_3
Relations
BioProject PRJNA600433
SRA SRP241175

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE143422_RAW.tar 3.5 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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