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Series GSE108556 Query DataSets for GSE108556
Status Public on Dec 13, 2018
Title Genome-wide stability of DNA replication program in single mammalian cells
Organisms Homo sapiens; Mus musculus
Experiment type Other
Expression profiling by high throughput sequencing
Summary We report the establishment of a single-cell DNA replication sequencing method, scRepli-seq, which is a simple genome-wide methodology that measures copy number differences between replicated and unreplicated DNA. Using scRepli-seq, we demonstrate that replication domain organization is conserved among individual mouse embryonic stem cells (mESCs). Differentiated mESCs exhibited distinct replication profiles, which were conserved from cell to cell. Haplotype-resolved scRepli-seq revealed similar replication timing profiles of homologous autosomes, while the inactive X chromosome was clearly replicated later than its active counterpart. However, a small degree of cell-to-cell replication timing heterogeneity was present, and we discovered that developmentally regulated domains are a source of such variability, suggesting a link between cell-to-cell heterogeneity and developmental plasticity. Together, our results form a foundation for single-cell-level understanding of DNA replication regulation and provide insights into 3D genome organization.
 
Overall design BrdUIP Repli-seq, Population Repli-seq, 100-cells Repli-seq and single-cell Repli-seq experiments in hTERT-RPE1, female mouse embryonic stem cells (CBMS1 mESCs) and 7-day differentiated mESCs. We only deposited single-cell data sets which passed our filtering steps.
RNA-Seq: CBMS1 mESCs sample with 3 individual replicates
 
Contributor(s) Miura H, Takahashi S, Takebayashi S, Hiratani I
Citation(s) 30804559
Submission date Dec 27, 2017
Last update date Jun 20, 2020
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 (3)
GPL17303 Ion Torrent Proton (Homo sapiens)
GPL18460 Illumina HiSeq 1500 (Homo sapiens)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
Samples (266)
GSM2904945 RPE1_BrdUIP_EarlyS
GSM2904946 RPE1_BrdUIP_LateS
GSM2904947 RPE1_100cells_G1_rep1
Relations
BioProject PRJNA427668
SRA SRP130912

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
GSE108556_CBMS1_allele_specific_genetable.txt.gz 560.1 Kb (ftp)(http) TXT
GSE108556_P239_01_02_rpm_cba_400k_BrdUIP_Percent_q0.05.bedGraph.gz 63.5 Kb (ftp)(http) BEDGRAPH
GSE108556_P239_01_02_rpm_msm_400k_BrdUIP_Percent_q0.05.bedGraph.gz 63.5 Kb (ftp)(http) BEDGRAPH
GSE108556_P239_01_02_rpm_w200ks80k_BrdUIP_Percent_q0.05.bedGraph.gz 410.3 Kb (ftp)(http) BEDGRAPH
GSE108556_P259_23_24_rpm_cba_400k_BrdUIP_Percent_q0.05.bedGraph.gz 61.4 Kb (ftp)(http) BEDGRAPH
GSE108556_P259_23_24_rpm_msm_400k_BrdUIP_Percent_q0.05.bedGraph.gz 60.4 Kb (ftp)(http) BEDGRAPH
GSE108556_P259_23_24_rpm_w200ks80k_BrdUIP_Percent_q0.05.bedGraph.gz 395.8 Kb (ftp)(http) BEDGRAPH
GSE108556_P263_27_28_rpm_cba_400k_BrdUIP_Percent_q0.05.bedGraph.gz 59.9 Kb (ftp)(http) BEDGRAPH
GSE108556_P263_27_28_rpm_msm_400k_BrdUIP_Percent_q0.05.bedGraph.gz 59.8 Kb (ftp)(http) BEDGRAPH
GSE108556_P263_27_28_rpm_w200ks80k_BrdUIP_Percent_q0.05.bedGraph.gz 390.3 Kb (ftp)(http) BEDGRAPH
GSE108556_P276_21_22_rpm_cba_400k_BrdUIP_Percent_q0.05.bedGraph.gz 60.1 Kb (ftp)(http) BEDGRAPH
GSE108556_P276_21_22_rpm_msm_400k_BrdUIP_Percent_q0.05.bedGraph.gz 60.4 Kb (ftp)(http) BEDGRAPH
GSE108556_P276_21_22_rpm_w200ks80k_BrdUIP_Percent_q0.05.bedGraph.gz 395.1 Kb (ftp)(http) BEDGRAPH
GSE108556_RAW.tar 75.5 Mb (http)(custom) TAR (of BEDGRAPH, BIGWIG)
GSE108556_RPE1_rpm_w200ks40k_BrdUIP_Percent_q0.05.bedGraph.gz 957.0 Kb (ftp)(http) BEDGRAPH
GSE108556_RT_MC12plus6TG_3rep_mean_IP_Aneu_rmdup_w200ks80k_P374_83-88_Percent_q0.05.bedGraph.gz 401.3 Kb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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