RNA m6A methylome from zebrafish zygotes, mouse liver polyA-selected RNAs, mouse embryonic stem cells, spike-in RNA controls, and single mouse oocytes and embryos

N6-methyladenosine (m6A) is a prevalent RNA modification that has key roles in distinct biological processes, including meiosis and early embryo development. Despite advances in methodology for m6A mapping, the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing (picoMeRIP-seq) method, also suitable for single-cell (scMeRIP-seq). We validate the down-scaling of the method by profiling m6A from picogram amounts of mouse liver polyA-selected RNA, mouse embryonic stem cells, and zebrafish zygotes. We provide proof-of-principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome-wide manner. Overall design: Transcriptome-wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes, 3 biological replicates for 5 zygotes, and 5 biological replicates for single zygote. 6 mouse liver polyA-selected RNA samples: 10 ng, 1 ng, and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell (R1 cell line, from ATCC, SCRC-1011) samples: 1000 cells, 100 cells, and 10 cells; 3 biological replicates for each amount. 3 spike-in RNA control (add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without m6A modification into the 12 ng polyA-selected RNAs) related samples: 12 ng polyA-selected RNA from mouse liver; 6 ng polyA-selected RNA from mouse liver and 6 ng polyA-selected RNA from wild-type/WT mouse embryonic stem cells (from Geula, S., et al. Science 2015); and 6 ng polyA-selected RNA from mouse liver and 6 ng polyA-selected RNA from Mettl3 knock-out/KO mouse embryonic stem cells (from Geula, S., et al. Science 2015). 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle (GV) and metaphase II (MII) stages, and embryos at zygote, 2-cell, 8-cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte (GSM5746922), zygote (GSM5746930), 2-cell (GSM5746911) and 8-cell (GSM5746914) stages can be found in GSE192440.