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| Status |
Public on May 05, 2023 |
| Title |
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 |
| Organisms |
Danio rerio; Mus musculus |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
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.
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| 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.
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| Contributor(s) |
Li Y, Wang Y, Klungland A, Au K, Dahl JA |
| Citation(s) |
37349523 |
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| Submission date |
Sep 28, 2021 |
| Last update date |
Aug 04, 2023 |
| Contact name |
Kin Fai Au |
| E-mail(s) |
kinfai@med.umich.edu
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| Phone |
734-615-5510
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| Organization name |
University of Michigan
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| Department |
Department of Computational Medicine and Bioinformatics
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| Lab |
Room 2035, Palmer Commons
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| Street address |
100 Washtenaw Avenue
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| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
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| Platforms (2) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL24995 |
Illumina NovaSeq 6000 (Danio rerio) |
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| Samples (52)
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| GSM5599716 |
ZF zygote IP 10cell Rep2 |
| GSM5599717 |
ZF zygote IP 10cell Rep3 |
| GSM5599718 |
ZF zygote IP 5cell Rep1 |
| GSM5599719 |
ZF zygote IP 5cell Rep2 |
| GSM5599720 |
ZF zygote IP 5cell Rep3 |
| GSM5599721 |
ZF zygote IP 1cell Rep1 |
| GSM5599722 |
ZF zygote IP 1cell Rep2 |
| GSM5599723 |
ZF zygote IP 1cell Rep3 |
| GSM5599724 |
ZF zygote IP 1cell Rep4 |
| GSM5599725 |
ZF zygote IP 1cell Rep5 |
| GSM5599726 |
MS liver Input 10ng |
| GSM5599727 |
MS liver Input 100pg |
| GSM5599728 |
MS liver IP 10ng Rep1 |
| GSM5599729 |
MS liver IP 10ng Rep2 |
| GSM5599730 |
MS liver IP 1ng Rep1 |
| GSM5599731 |
MS liver IP 1ng Rep2 |
| GSM5599732 |
MS liver IP 100pg Rep1 |
| GSM5599733 |
MS liver IP 100pg Rep2 |
| GSM5599734 |
MS MII oocyte Input 100cell |
| GSM5599739 |
MS blastocyst Input 9blastocyst |
| GSM7174060 |
MS ESC Input 1000cell Rep1 |
| GSM7174061 |
MS ESC Input 1000cell Rep2 |
| GSM7174062 |
MS ESC IP 1000cell Rep1 |
| GSM7174063 |
MS ESC IP 1000cell Rep2 |
| GSM7174064 |
MS ESC IP 1000cell Rep3 |
| GSM7174065 |
MS ESC IP 100cell Rep1 |
| GSM7174066 |
MS ESC IP 100cell Rep2 |
| GSM7174067 |
MS ESC IP 100cell Rep3 |
| GSM7174068 |
MS ESC IP 10cell Rep1 |
| GSM7174069 |
MS ESC IP 10cell Rep2 |
| GSM7174070 |
MS ESC IP 10cell Rep3 |
| GSM7174071 |
MS liver 12ng, spike in, Input |
| GSM7174072 |
MS liver 12ng, spike in, IP |
| GSM7174073 |
MS liver 6ng, KO ESC 6ng, spike in, Input |
| GSM7174074 |
MS liver 6ng, KO ESC 6ng, spike in, IP |
| GSM7174075 |
MS liver 6ng, WT ESC 6ng, spike in, Input |
| GSM7174076 |
MS liver 6ng, WT ESC 6ng, spike in, IP |
| GSM7174077 |
MS GV IP Rep1 |
| GSM7174078 |
MS GV IP Rep2 |
| GSM7174079 |
MS MII IP Rep1 |
| GSM7174080 |
MS MII IP Rep2 |
| GSM7174081 |
MS zygote IP Rep1 |
| GSM7174082 |
MS zygote IP Rep2 |
| GSM7174083 |
MS 2cell IP Rep1 |
| GSM7174084 |
MS 2cell IP Rep2 |
| GSM7174085 |
MS 8cell IP Rep1 |
| GSM7174086 |
MS 8cell IP Rep2 |
| GSM7174087 |
MS blastocyst IP Rep1 |
| GSM7174088 |
MS blastocyst IP Rep2 |
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| Relations |
| BioProject |
PRJNA766854 |
| SRA |
SRP339082 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE184893_RAW.tar |
753.0 Mb |
(http)(custom) |
TAR (of BIGWIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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