GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE123365 Query DataSets for GSE123365
Status Public on Sep 24, 2019
Title Evolution of a Reverse Transcriptase to Map N1-Methyladenosine in Human mRNA
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Chemical modifications on mRNA are increasingly recognized as a critical regulatory layer of the flow of genetic information, but quantitative tools to monitor RNA modifications in a whole-transcriptome and site-specific manner are lacking. Here we describe a versatile directed evolution platform that rapidly selects for reverse transcriptases that install mutations during reverse transcription at sites of a given type of RNA modification, allowing for site-specific identification of the modification. To develop and validate the platform, we evolved the HIV-1 reverse transcriptase against N1-methyladenosine (m1A). Iterative rounds of selection yielded reverse transcriptases with both robust read-through and high mutation rates at m1A sites. We apply the evolved reverse transcriptase to identify thousands of statistically confident m1A sites in human mRNA, some of which can be detected in antibody-free RNA-seq libraries. Together, this work develops and validates the reverse transcriptase evolution platform and provides new tools, analysis methods, and datasets to study m1A biology.
Overall design m1A-IP-seq and m1A-quant-seq experiments were performed on mRNA extracted from HEK-293T cells with three biological replicates.
Contributor(s) Zhou H, Dickinson BC, He C
Citation(s) 31548705
Submission date Dec 05, 2018
Last update date Sep 25, 2019
Contact name Huiqing Zhou
Phone 7343899318
Organization name University of chicago
Street address LOADING DOCK BEHIND 5741 S DREXEL AVE 929 E 57TH ST
City Chicago
State/province Illinois
ZIP/Postal code 60637
Country USA
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (12)
GSM3896225 m1A-quant-seq, "-AlkB", replicate1
GSM3896226 m1A-quant-seq, "-AlkB", replicate2
GSM3896227 m1A-quant-seq, "-AlkB", replicate3
BioProject PRJNA508500
SRA SRP172548

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

Supplementary file Size Download File type/resource
GSE123365_RAW.tar 124.4 Mb (http)(custom) TAR (of CSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap