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Series GSE125240 Query DataSets for GSE125240
Status Public on Jul 03, 2019
Title Single base mapping of m6A by an antibody-independent method
Organisms Homo sapiens; Mus musculus; Rattus norvegicus
Experiment type Methylation profiling by high throughput sequencing
Summary N6-methyladenosine (m6A) is one of the most abundant mRNA modifications in eukaryotes, related to pivotal RNA metabolism processes. The most popular high-throughput m6A identification method relies on the commercial m6A antibody but suffers from poor reproducibility and limited resolution. Exact location of m6A site is of great vital for understanding the dynamics, functions and machinery of RNA methylation. Here, we developed a precise and high-throughput antibody-independent m6A identification method based on the m6A-sensitive RNA endoribonuclease recognizing ACA motif (m6A-sensitive RNA-Endoribonuclease–Facilitated sequencing or m6A-REF-seq). Whole-transcriptomic single base m6A map generated by m6A-REF-seq displayed a typical distribution pattern with enrichment adjacent to stop codon. Ligase-based and qPCR validation methods were used to confirm the individual m6A sites and quantify the methylation level, reinforcing the high accuracy of m6A-REF-seq. We applied m6A-REF-seq on five tissues from three mammals, showing that m6A sites were conserved and tend to gather together among species. (m6A-REF-seq had been named as Aim-seq.)
Overall design For human HEK293T cell line, three pairs of replicates with MazF treatment and negative control were provided. For the samples of human tissues (brain, liver and kidney), mouse tissues (brain, liver, heart, testis and kidney) and rat tissues (brain, liver and kidney), MazF treatment and negative control were provided.
Contributor(s) Zhang Z, Chen L, Luo G
Citation(s) 31281898
Submission date Jan 17, 2019
Last update date Jul 16, 2019
Contact name Zhang Zhang
Organization name Sun Yat-sen University
Street address Xingangxi Roda 135#
City Guangzhou
State/province Guangdong
ZIP/Postal code 510275
Country China
Platforms (3)
GPL20795 HiSeq X Ten (Homo sapiens)
GPL21273 HiSeq X Ten (Mus musculus)
GPL24688 HiSeq X Ten (Rattus norvegicus)
Samples (28)
GSM3566973 HEK293_MazF_rep1
GSM3566974 HEK293_FTO_rep1
GSM3566975 HEK293_MazF_rep2
BioProject PRJNA515628
SRA SRP179955

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Supplementary file Size Download File type/resource
GSE125240_HEK293_Aimseq_m6A.txt.gz 83.3 Kb (ftp)(http) TXT
GSE125240_Human_brain_Aimseq_m6A.txt.gz 86.3 Kb (ftp)(http) TXT
GSE125240_Human_kidney_Aimseq_m6A.txt.gz 97.1 Kb (ftp)(http) TXT
GSE125240_Human_liver_Aimseq_m6A.txt.gz 56.6 Kb (ftp)(http) TXT
GSE125240_Mouse_brain_Aimseq_m6A.txt.gz 152.6 Kb (ftp)(http) TXT
GSE125240_Mouse_heart_Aimseq_m6A.txt.gz 48.1 Kb (ftp)(http) TXT
GSE125240_Mouse_kidney_Aimseq_m6A.txt.gz 85.9 Kb (ftp)(http) TXT
GSE125240_Mouse_liver_Aimseq_m6A.txt.gz 90.4 Kb (ftp)(http) TXT
GSE125240_Mouse_testis_Aimseq_m6A.txt.gz 102.9 Kb (ftp)(http) TXT
GSE125240_Rat_brain_Aimseq_m6A.txt.gz 44.4 Kb (ftp)(http) TXT
GSE125240_Rat_kidney_Aimseq_m6A.txt.gz 72.3 Kb (ftp)(http) TXT
GSE125240_Rat_liver_Aimseq_m6A.txt.gz 38.6 Kb (ftp)(http) TXT
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