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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
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
BioProject PRJNA454725
SRA SRP144391

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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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