Accession

PRJCA002113

Title

A DNA methylation state transition model reveals the programmed epigenetic heterogeneity in pre-implantation embryos

Relevance

Model organism

Data types

Transcriptome or Gene expression

Organisms

Mus musculus

Description

We found that the DNA methylation heterogeneity was largely programmed by the initial DNA methylation state in zygote by building a mathematical model. Further, to clarify the causality of transcriptional expression heterogeneity and DNA methylation heterogeneity, we disrupted DNA methylation status during mouse early embryogenesis by knocked out (KO) DNA methylation-related genes Dppa3 in gamete cells. Then we performed single cell RNA-seq on each cell of the KO embryos in 4-cell stage and 8-cell stage.

Sample scope

Single cell

Release date

2020-10-10

Publication

PubMed ID	Article title	Journal name	DOI	Year
33198783	A DNA methylation state transition model reveals the programmed epigenetic heterogeneity in human pre-implantation embryos	Genome Biology	10.1186/s13059-020-02189-8	2020

Biomaterial provider

Shaorong Gao Lab in Tongji University

Grants

Agency	program	Grant ID
Ministry of Science and Technology of the People's Republic of China (MOST)	National Key Technologies R&D Program	2017YFA0102600
Ministry of Science and Technology of the People's Republic of China (MOST)	National Key Technologies R&D Program	2016YFA0100400
National Natural Science Foundation of China (NSFC)	General Program	32030022
National Natural Science Foundation of China (NSFC)	General Program	31970642
National Natural Science Foundation of China (NSFC)	General Program	31721003
National Natural Science Foundation of China (NSFC)	Young Scientists Fund	31900491
National Natural Science Foundation of China (NSFC)	Young Scientists Fund	31601079
National Natural Science Foundation of China (NSFC)	General Program	62072277
Shanghai Science and Technology Committee (STCSM)	Program of Shanghai Academic Research Leader	17XD1403600
Postdoctoral Research Foundation of China	Postdoctoral Research Foundation of China	2018M642073
Shanghai Science and Technology Committee (STCSM)	Shanghai Municipal Science and Technology Major Project	2018SHZDZX01
Shanghai Science and Technology Committee (STCSM)	Excellent Youth Training Programs of Health Department of Shanghai Municipal Government	17QA1402700

Accessions in other database

Accession	Database name
E MTAB 9360	EBI

Submitter

Yong Zhang (yzhang@tongji.edu.cn)

Organization

Tongji University

Submission date

2020-01-06

Project Data

Resource name	Description
BioSample (28) show	-
SAMC129369	RNA-seq of Dppa3-KO 8-cell stage embryo_2-cell_8
SAMC129368	RNA-seq of Dppa3-KO 8-cell stage embryo_2-cell_7
SAMC129367	RNA-seq of Dppa3-KO 8-cell stage embryo_2-cell_6
SAMC129366	RNA-seq of Dppa3-KO 8-cell stage embryo_2-cell_5
SAMC129365	RNA-seq of Dppa3-KO 8-cell stage embryo_2-cell_4
SAMC129364	RNA-seq of Dppa3-KO 8-cell stage embryo_2-cell_3
SAMC129363	RNA-seq of Dppa3-KO 8-cell stage embryo_2-cell_2
SAMC129362	RNA-seq of Dppa3-KO 8-cell stage embryo_2-cell_1
SAMC129361	RNA-seq of Dppa3-KO 8-cell stage embryo_1-cell_8
SAMC129360	RNA-seq of Dppa3-KO 8-cell stage embryo_1-cell_7
SAMC129359	RNA-seq of Dppa3-KO 8-cell stage embryo_1-cell_6
SAMC129358	RNA-seq of Dppa3-KO 8-cell stage embryo_1-cell_5
SAMC129357	RNA-seq of Dppa3-KO 8-cell stage embryo_1-cell_4
SAMC129356	RNA-seq of Dppa3-KO 8-cell stage embryo_1-cell_3
SAMC129355	RNA-seq of Dppa3-KO 8-cell stage embryo_1-cell_2
SAMC129354	RNA-seq of Dppa3-KO 8-cell stage embryo_1-cell_1
SAMC129353	RNA-seq of Dppa3-KO 4-cell stage embryo_3-cell_4
SAMC129352	RNA-seq of Dppa3-KO 4-cell stage embryo_3-cell_3
SAMC129351	RNA-seq of Dppa3-KO 4-cell stage embryo_3-cell_2
SAMC129350	RNA-seq of Dppa3-KO 4-cell stage embryo_3-cell_1
SAMC129349	RNA-seq of Dppa3-KO 4-cell stage embryo_2-cell_4
SAMC129348	RNA-seq of Dppa3-KO 4-cell stage embryo_2-cell_3
SAMC129347	RNA-seq of Dppa3-KO 4-cell stage embryo_2-cell_2
SAMC129346	RNA-seq of Dppa3-KO 4-cell stage embryo_2-cell_1
SAMC129345	RNA-seq of Dppa3-KO 4-cell stage embryo_1-cell_4
SAMC129344	RNA-seq of Dppa3-KO 4-cell stage embryo_1-cell_3
SAMC129343	RNA-seq of Dppa3-KO 4-cell stage embryo_1-cell_2
SAMC129342	RNA-seq of Dppa3-KO 4-cell stage embryo_1-cell_1
GSA (1)	-
CRA002264	single cell RNA-seq of Dppa3-KO mouse embryos in 4/8-cell stage