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Series GSE62530 Query DataSets for GSE62530
Status Public on Sep 08, 2015
Title Genome-wide identification of N6-methyladenosine by microarray
Organism Mus musculus
Experiment type Expression profiling by genome tiling array
Summary Although internal PolyA RNA modification N6-methyladenosine (m6A) plays essential roles in diverse biological processes, technology to detect precise m6A sites at transcriptome-wide scale is lacking. Here, we discovered that m6A interferes A (Adenine) – U (Uracil) or A-T (Thymidine) pairing. Based on differential hybridization between methylated vs. unmethylated RNAs to a DNA probe, we developed tiling microarray to pinpoint m6A sites in mouse transcriptome. We validated some of the identified sites and provided evidence to suggest that one functional mechanism of m6A is to block small RNA targeting to methylated mRNA.
Overall design We designed a custom tiling array with to examine the precise location of m6A within meRIP-seq peaks from mouse embryonic stem cells determined in our previous publication (Wang et al., 2014). Each custom two-channel Agilent tiling array harbors 947,952 probes. Each probe is 25 nucleotides (nt), and any two adjacent probes in the genomic coordinate overlap each other by 19 nt. The Cy5 or red channel corresponds to Mettl14 knockout (M14) or DZA mutant mESC cell line, and Cy3 or green channel is associated with wild type cell line treated with scramble hairpin (SCR). Thus, in principle a higher Cy5/Cy3 signal for each probe reflects an increased hybridization to the oligonucleotide due to de-methylation of a particular RNA molecule in M14 or DZA condition relative to the SCR control. Moreover, we employed additional arrays with both channels dedicated for M14 as an external control for technical difference between the Cy5 and Cy3 dye (details below). For each comparison, we have three biological replicates, and therefore there are 9 tiling arrays in total (i.e., 3 arrays for M14 vs SCR, 3 arrays for DZA vs SCR, and 3 arrays for M14 vs M14).
Contributor(s) Wang Y, Li Y, Zhang Z, Montes de Oca AV, Zhao JC
Citation(s) 26092943
Submission date Oct 20, 2014
Last update date Sep 10, 2015
Contact name Yue Li
Organization name Massachusetts Institute of Technology
Street address 32 Vassar Street, 32-D528
City Cambridge
State/province Massachusetts
ZIP/Postal code 02139
Country USA
Platforms (1)
GPL19318 Agilent-064152 Sanford_Burnum_m6A_Full
Samples (9)
GSM1528423 MettL4 KO_vs_SCR Ctl 1
GSM1528424 MettL4 KO_vs_SCR Ctl 2
GSM1528425 MettL4 KO_vs_SCR Ctl 3
BioProject PRJNA264382

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
GSE62530_RAW.tar 2.2 Gb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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