GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE114470 Query DataSets for GSE114470
Status Public on Jun 26, 2019
Title Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization [scRepli-seq]
Organism Mus musculus
Experiment type Other
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 scRepli-seq: Single-cell Repli-seq experiments in G1 and S-phase cells (total 884 cells) of 7-day differentiation (d0~d7) of female mouse embryonic stem cells (CBMS1 mESCs) and epiblast stem cells (EpiSCs) incorporating our previous scRepli-seq data (under GSE108556). We also selected the sample sets from our previous scRepli-seq data (under GSE108556) to obtain additional sequence reads for analyzing the resolution at 40kb (28 Mid-S single cells for mESCs, and 15 Mid-S single cells for 7-day differentiated mESCs).

Please note that, as most (49 out of 51 [GSM3142337 to GSM3142387]) of the re-analyzed GSE108556 samples/data include additional raw data, duplicated sample records (e.g. GSM3142338 for GSM2904979 in GSE108556) were created to link all associated raw data and re-analyzed processed data, as described in the corresponding sample description field.
Contributor(s) Miura H, Takahashi S, Poonperm R, Tanigawa A, Takebayashi S, Hiratani I
Citation(s) 31406346
Submission date May 15, 2018
Last update date Jun 23, 2020
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 (2)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (884)
GSM3142337 CBMS1_ESC_single_G1_01 [scRepli-seq]
GSM3142338 CBMS1_ESC_single_G1_02 [scRepli-seq]
GSM3142339 CBMS1_ESC_single_G1_03 [scRepli-seq]
This SubSeries is part of SuperSeries:
GSE113985 Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization
BioProject PRJNA471506
SRA SRP146065

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
GSE114470_RAW.tar 50.1 Mb (http)(custom) TAR (of BEDGRAPH, BIGWIG)
GSE114470_README.txt 1.5 Kb (ftp)(http) TXT
GSE114470_scRepliseq_d0_33_CBA_XX_chrX_only_400kb.txt.gz 4.1 Kb (ftp)(http) TXT
GSE114470_scRepliseq_d0_33_MsM_XX_chrX_only_400kb.txt.gz 4.2 Kb (ftp)(http) TXT
GSE114470_scRepliseq_d2_27_CBA_XX_chrX_only_400kb.txt.gz 4.0 Kb (ftp)(http) TXT
GSE114470_scRepliseq_d2_27_MsM_XX_chrX_only_400kb.txt.gz 4.0 Kb (ftp)(http) TXT
GSE114470_scRepliseq_d7_36_XX_Xa_chrX_only_400kb.txt.gz 4.3 Kb (ftp)(http) TXT
GSE114470_scRepliseq_d7_36_XX_Xi_chrX_only_400kb.txt.gz 3.3 Kb (ftp)(http) TXT
GSE114470_scRepliseq_data_884cells_G1_Sphase_binary_data_80kb.txt.gz 3.9 Mb (ftp)(http) TXT
GSE114470_scRepliseq_data_sample_Info.txt.gz 10.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap