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Series GSE82185 Query DataSets for GSE82185
Status Public on Jul 12, 2017
Title Allelic reprogramming of 3D chromatin architecture during early mammalian development
Organism Mus musculus
Experiment type Other
Expression profiling by high throughput sequencing
Summary In mammals, chromatin organization undergoes drastic reprogramming after fertilization. However, the three-dimensional structure of chromatin and its reprogramming in preimplantation development remain poorly understood. Here, by developing a low-input Hi-C (genomewide chromosome conformation capture) approach, we examined the reprogramming of chromatin organization during early development in mice. We found that oocytes in metaphase II show homogeneous chromatin folding that lacks detectable topologically associating domains (TADs) and chromatin compartments. Strikingly, chromatin shows greatly diminished higher-order structure after fertilization. Unexpectedly, the subsequent establishment of chromatin organization is a prolonged process that extends through preimplantation development, as characterized by slow consolidation of TADs and segregation of chromatin compartments. The two sets of parental chromosomes are spatially separated from each other and display distinct compartmentalization in zygotes. Such allele separation and allelic compartmentalization can be found as late as the 8-cell stage. Finally, we show that chromatin compaction in preimplantation embryos can partially proceed in the absence of zygotic transcription and is a multi-level hierarchical process. Taken together, our data suggest that chromatin may exist in a markedly relaxed state after fertilization, followed by progressive maturation of higher-order chromatin architecture during early development.
Overall design Mouse preimplantation embryos were obtained from crosses of C57BL/6N and PWK/PhJ. Hi-C were performed on these embryos at various stages in preimplantation development.
Contributor(s) Du Z, Xie W
Citation(s) 28703188
Submission date Jun 02, 2016
Last update date Jul 25, 2021
Contact name Zhenhai Du
Organization name Tsinghua University
Street address Qinghua Yuan, Haidian District
City Beijing
ZIP/Postal code 100084
Country China
Platforms (3)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (44)
GSM2203829 Hi-C MII oocytes rep1
GSM2203830 Hi-C MII oocytes rep2
GSM2203831 Hi-C PN5 zygote rep1
BioProject PRJNA326112
SRA SRP076723

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
GSE82185_8cell_rep123_allValidPairs.txt.gz 5.4 Gb (ftp)(http) TXT
GSE82185_8cell_rep123_maternal_allValidPairs.txt.gz 2.1 Gb (ftp)(http) TXT
GSE82185_8cell_rep123_paternal_allValidPairs.txt.gz 1.6 Gb (ftp)(http) TXT
GSE82185_ICM_rep123_allValidPairs.txt.gz 4.2 Gb (ftp)(http) TXT
GSE82185_ICM_rep123_maternal_allValidPairs.txt.gz 1.6 Gb (ftp)(http) TXT
GSE82185_ICM_rep123_paternal_allValidPairs.txt.gz 1.3 Gb (ftp)(http) TXT
GSE82185_MII_rep12_allValidPairs.txt.gz 1.6 Gb (ftp)(http) TXT
GSE82185_PN3_rep12_allValidPairs.txt.gz 2.4 Gb (ftp)(http) TXT
GSE82185_PN3_rep12_maternal_allValidPairs.txt.gz 1008.5 Mb (ftp)(http) TXT
GSE82185_PN3_rep12_paternal_allValidPairs.txt.gz 727.3 Mb (ftp)(http) TXT
GSE82185_PN5_rep1234_allValidPairs.txt.gz 4.7 Gb (ftp)(http) TXT
GSE82185_PN5_rep1234_maternal_allValidPairs.txt.gz 1.9 Gb (ftp)(http) TXT
GSE82185_PN5_rep1234_paternal_allValidPairs.txt.gz 1.4 Gb (ftp)(http) TXT
GSE82185_RAW.tar 59.7 Gb (http)(custom) TAR (of TXT)
GSE82185_alpha_amanitin_20h_rep12_allValidPairs.txt.gz 1.4 Gb (ftp)(http) TXT
GSE82185_alpha_amanitin_45h_rep12_allValidPairs.txt.gz 2.6 Gb (ftp)(http) TXT
GSE82185_alpha_amanitin_experiments_RNAseq_FPKM.txt.gz 478.2 Kb (ftp)(http) TXT
GSE82185_cortex_rep12_maternal_allValidPairs.txt.gz 366.1 Mb (ftp)(http) TXT
GSE82185_cortex_rep12_paternal_allValidPairs.txt.gz 321.8 Mb (ftp)(http) TXT
GSE82185_early_2cell_rep123_allValidPairs.txt.gz 4.5 Gb (ftp)(http) TXT
GSE82185_early_2cell_rep123_maternal_allValidPairs.txt.gz 1.8 Gb (ftp)(http) TXT
GSE82185_early_2cell_rep123_paternal_allValidPairs.txt.gz 1.2 Gb (ftp)(http) TXT
GSE82185_invitro_8cell_rep12_allValidPairs.txt.gz 3.0 Gb (ftp)(http) TXT
GSE82185_invitro_late_2cell_rep12_allValidPairs.txt.gz 2.3 Gb (ftp)(http) TXT
GSE82185_late_2cell_rep1234_allValidPairs.txt.gz 5.9 Gb (ftp)(http) TXT
GSE82185_late_2cell_rep1234_maternal_allValidPairs.txt.gz 2.3 Gb (ftp)(http) TXT
GSE82185_late_2cell_rep1234_paternal_allValidPairs.txt.gz 1.8 Gb (ftp)(http) TXT
GSE82185_mESC_500_rep12_allValidPairs.txt.gz 3.0 Gb (ftp)(http) TXT
GSE82185_sperm_rep123_allValidPairs.txt.gz 1.2 Gb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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