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Series GSE65510 Query DataSets for GSE65510
Status Public on Feb 03, 2015
Title Transient Pairing of Homologous Oct4 Alleles Accompanies the Onset of Embryonic Stem Cell Differentiation
Organism Mus musculus
Experiment type Other
Summary The relationship between chromatin organization and transcriptional regulation is an area of intense investigation. We have characterized the spatial relationships between alleles of the Oct4, Sox2, and Nanog genes in single cells during the earliest stages of mouse embryonic stem cell (ESC) differentiation and during embryonic development. We describe homologous pairing of the Oct4 alleles during ESC differentiation and embryogenesis, and present evidence that pairing is correlated with the kinetics of ESC differentiation. Importantly, we identify critical DNA elements within the Oct4 promoter/enhancer region that mediate pairing of Oct4 alleles. Finally, we show that mutation of OCT4/SOX2 binding sites within this region abolishes inter-chromosomal interactions and affects accumulation of the repressive H3K9me2 modification at the Oct4 enhancer. Our findings demonstrate that chromatin organization and transcriptional programs are intimately connected in ESCs, and that the dynamic positioning of the Oct4 alleles is associated with the transition from pluripotency to lineage specification.
Overall design Examination of chromatin contacts between Oct4 alleles using PE-4Cseq
Contributor(s) Hogan MS, Zepeda Mendoza CJ, Spector DL
Citation(s) 25748933
Submission date Feb 02, 2015
Last update date Jul 31, 2019
Contact name Cinthya J Zepeda-Mendoza
Phone 5163678478
Organization name Cold Spring Harbor Laboratory
Lab David L. spector
Street address 1 Bungtown Road
City Cold Spring Harbor
State/province NY
ZIP/Postal code 11724
Country USA
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (24)
GSM1599068 OctSox_d0_154.9_1strep
GSM1599069 OctSox_d0_154.9_2ndrep
GSM1599070 OctSox_d0_Ocf_Mut_OctSox_chr11_1strep
BioProject PRJNA274253
SRA SRP053044

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Supplementary file Size Download File type/resource
GSE65510_OctSox154.9_FourCSeqResults.txt.gz 76.0 Kb (ftp)(http) TXT
GSE65510_OctSoxOcfWTOct4_FourCSeqResults.txt.gz 6.8 Kb (ftp)(http) TXT
GSE65510_OctSox_d0_d3_154.9_countmatrix.txt.gz 62.1 Kb (ftp)(http) TXT
GSE65510_OctSox_d0_d3_Ocf_Mut_OctSox_chr11_countmatrix.txt.gz 19.7 Kb (ftp)(http) TXT
GSE65510_OctSox_d0_d3_Ocf_WT_Oct4_countmatrix.txt.gz 26.8 Kb (ftp)(http) TXT
GSE65510_RAW.tar 708.1 Mb (http)(custom) TAR (of FA)
GSE65510_YY1154.9_FourCSeqResults.txt.gz 116.2 Kb (ftp)(http) TXT
GSE65510_YY1OcfWTOct4_FourCSeqResults.txt.gz 7.0 Kb (ftp)(http) TXT
GSE65510_YY1_d0_d3_154.9_countmatrix.txt.gz 69.3 Kb (ftp)(http) TXT
GSE65510_YY1_d0_d3_Ocf_Mut_YY1_chr11_countmatrix.txt.gz 32.0 Kb (ftp)(http) TXT
GSE65510_YY1_d0_d3_Ocf_WT_Oct4_countmatrix.txt.gz 34.7 Kb (ftp)(http) TXT
GSE65510_chr11_hindiii_fragments.txt.gz 212.9 Kb (ftp)(http) TXT
GSE65510_chr17_hindiii_fragments.txt.gz 166.7 Kb (ftp)(http) TXT
GSE65510_chr4_hindiii_fragments.txt.gz 283.8 Kb (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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