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Series GSE113981 Query DataSets for GSE113981
Status Public on Jun 26, 2019
Title Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization [HiC-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary In mammals, chromosomes are partitioned into megabase-sized topologically associating domains (TADs). TADs can be in either A (active) or B (inactive) subnuclear compartments, which correspond to early (E) and late (L) replicating timing (RT) domains, respectively. Here, we show that RT changes are tightly correlated with A/B compartment changes during mouse embryonic stem cell (mESC) differentiation. A/B compartments changed mostly by a “boundary shift,” frequently causing compartment switching of single TADs, which coincided with or preceded RT changes. Upon differentiation, mESCs acquired an A/B compartment organization that closely resembled EpiSCs (epiblast-derived stem cells), suggesting that accumulation of compartment boundary repositioning eventually led to naïve-to-primed pluripotency transition in A/B compartment organization. We propose that large-scale reorganization of A/B compartments, which is reflected in RT domain reorganization, represents major cell fate changes. Collectively, our data provides valuable insights into the regulatory principles of 3-dimensional (3D) genome organization during early embryonic stages.
 
Overall design Hi-C: 10 cell types, with a total of 22 individual replicates (in duplicates or triplicates).
 
Contributor(s) Miura H, Takahashi S, Poonperm R, Tanigawa A, Takebayashi S, Hiratani I
Citation(s) 31406346
Submission date May 02, 2018
Last update date Sep 25, 2019
Contact name Ichiro Hiratani
E-mail(s) ichiro.hiratani@riken.jp
Phone +81-78-306-3179
Organization name RIKEN
Department Center for Developmental Biology
Lab Laboratory for Developmental Epigenetics
Street address 2-2-3 Minatojima-minamimachi, Chuo-ku
City Kobe
State/province Hyogo
ZIP/Postal code 650-0047
Country Japan
 
Platforms (1)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
Samples (22)
GSM3127755 CBMS1_rep1_d0_Undiff
GSM3127756 CBMS1_rep1_d2_EpiLC
GSM3127757 CBMS1_rep1_d3_EpiLC_EB_d1
This SubSeries is part of SuperSeries:
GSE113985 Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization
Relations
BioProject PRJNA454725
SRA SRP144391

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
GSE113981_RAW.tar 19.7 Mb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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