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Series GSE156933 Query DataSets for GSE156933
Status Public on Aug 01, 2021
Title A Quantitative Sequencing Method for 5-Formylcytosine in RNA
Organisms Homo sapiens; Mus musculus; synthetic construct
Experiment type Other
Summary 5-Formylcytosine (f5C) modification is present in human mitochondrial methionine tRNA (mt-tRNAMet) and cytosolic leucine tRNA (ct-tRNALeu), with their formation mediated by NSUN3 and ALKBH1. f5C has also been detected in mRNA of yeast and human cells, but its transcriptome-wide distribution has not been studied. Here we report f5C-seq, a quantitative sequencing method to map f5C transcriptome-wide in HeLa and mouse embryonic stem cells (mESCs). We show that f5C in RNA can be reduced to dihydrouracil (DHU) by pico-brane, and DHU can be exclusively read as U during reverse transcription (RT) reaction, allowing the detection and quantification of f5C sites by a unique C-to-U mutation signature. We validated f5C-seq by identifying and quantifying the two known f5C sites in tRNA, in which the f5C modification fractions dropped significantly in ALKBH1-depleted cells. By applying f5C-seq to small RNA, we identified 13 and 11 new f5C sites in HeLa and mESC tRNA, respectively.
 
Overall design We developped a quantitative sequencing method to map f5C transcriptome-wide in HeLa and mouse embryonic stem cells (mESCs).
 
Contributor(s) Lyu R, Dai Q, He C
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Submission date Aug 26, 2020
Last update date Aug 02, 2021
Contact name Ruitu Lyu
E-mail(s) lvruitu@uchicago.edu
Organization name The University of Chicago
Department Chemistry
Lab Chuan He
Street address 929 E 57th Street
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
 
Platforms (3)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
GPL26526 Illumina NovaSeq 6000 (synthetic construct)
Samples (52)
GSM4748610 f5C_spikein_65C_ACN
GSM4748611 f5C_spikein_65C_DMSO
GSM4748612 f5C_spikein_70C_ACN
Relations
BioProject PRJNA659533
SRA SRP278892

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
GSE156933_RAW.tar 364.1 Mb (http)(custom) TAR (of TXT)
GSE156933_f5C_SpikeIn_context.xlsx 90.7 Kb (ftp)(http) XLSX
GSE156933_f5C_calibration_curve.xlsx 15.4 Kb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record
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