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Series GSE123109 Query DataSets for GSE123109
Status Public on May 26, 2019
Title Single-cell three dimensional genome structures of rice egg, sperm, and unicellular zygote
Organism Oryza sativa Japonica Group
Experiment type Other
Summary Chromatin conformation capture assays, such as 3C and Hi-C, allow for studies of three-dimensional (3D) genome structures in bulk samples through proximity ligation of DNA. However, the difference between cells can only be observed by single-cell measurements that avoid ensemble averaging3, 4,5. To study 3D chromatin organization and dynamics before and after fertilization in flowering plants, we analyzed the 3D genomes of rice egg, sperm, and unicellular zygote as well as shoot cells. We show that chromatin architectures of rice egg and sperm are comparable to that of somatic cells and are reorganized after fertilization in unicellular zygote. The rice single cell 3D genomes display specific features of chromosome compartments and configuration of telomeres/centromeres compared to those shown in mammalian single cells. Active and silent chromatin domains gather to form multiple foci in the nuclear space. Notably, the 3D genomes of egg, unicellular zygote, and shoot cells contain a compact silent center (CSC), which is absent in sperm. CSC is dynamically reorganized after fertilization and is likely to be involved in gene regulation related to zygotic genome activation (ZGA). Our results reveal specific 3D genome features of plant gametes and unicellular zygote and provide a spatial chromatin basis for ZGA and gene expression in plant.
 
Overall design Single-cell Hi-C sequencing data of four eggs, four sperms, three unicellular zygotes, and two shoot cells
 
Contributor(s) Zhou S, Zhou DX
Citation(s) 31332313
Submission date Nov 29, 2018
Last update date Oct 13, 2020
Contact name shaoli zhou
E-mail(s) zhoushaoli@webmail.hzau.edu.cn
Organization name Huazhong Agricultural University
Department National Key Laboratory of Crop Genetic Improvement
Street address shizishan street
City Wuhan
State/province Hubei
ZIP/Postal code 430070
Country China
 
Platforms (1)
GPL23876 HiSeq X Ten (Oryza sativa Japonica Group)
Samples (15)
GSM3495873 Single-cell Hi-C data of egg 1
GSM3495874 Single-cell Hi-C data of egg 2
GSM3495875 Single-cell Hi-C data of egg 3
Relations
BioProject PRJNA507566
SRA SRP171133

Download family Format
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE123109_RAW.tar 25.8 Mb (http)(custom) TAR (of PDB, TXT)
GSE123109_chromosome_chain_annotation.txt.gz 141 b (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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