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Series GSE80006 Query DataSets for GSE80006
Status Public on Mar 23, 2017
Title Single-cell Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition
Organisms Homo sapiens; Mus musculus
Experiment type Other
Summary Chromatin is reorganized and reprogrammed after fertilization to produce a totipotent zygote with the potential to generate a new organism. In mammals, the maternal genome inherited through the oocyte and the paternal genome provided by sperm coexist as separate haploid nuclei in interphase of the first cell cycle. How these two epigenetically distinct genomes are spatially organized remains poorly understood. Existing chromosome conformation capture-based methods are inapplicable to oocytes and zygotes due to paucity of material. To study the three-dimensional organization of chromatin in rare cell types, we developed a simplified single-cell Hi-C (sscHi-C) protocol that provides 100-fold more contacts per cell than a previous method. Using sscHi-C, we show that chromatin architecture is uniquely reorganized during the oocyte-to-zygote transition. We found that major features of chromosome organization, compartments, domains and loops are all present in individual cells, with noticeable cell-to-cell variation and differences between male and female nuclei in zygotes. Compartments detected in male nuclei are notably absent from female nuclei, indicating these are the first mammalian interphase nuclei lacking this higher-order structure. While compartments in single cells closely resemble compartments from the cell population, TADs manifest themselves as contact domains (CDs) that differ from cell to cell, nevertheless averaging into TADs in pooled data. Finally, scaling of contact probability with genomic separations suggests that chromosome conformations in oocyte and zygote nuclei are fundamentally different and each are distinct from the global organization of chromosomes in other interphase cells. We conclude that chromatin organization of zygote nuclei is unique and can serve as the chromatin "ground state" of a totipotent cell.
Overall design We generated 98 HiC libraries from single oocytes (includes comparison of NSN and SN oocytes + two different experimental conditions), 82 libraries from nuclei of zygotes (comparison of maternal vs paternal nuclei + 2 experimental conditions), 2 libraries of bulk K562 cells compared to 34 libraries of single K562 cells and 2 libraries of bulk MEL cells (with 2 different fixation conditions).
Contributor(s) Flyamer IM, Gassler J, Imakaev M, Brandao HB, Ulianov SV, Abdennur N, Razin SV, Mirny L, Tachibana-Konwalski K
Citation(s) 28355183
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 GM114190 Polymer models of mitotic and interphase chromosomes MASSACHUSETTS INSTITUTE OF TECHNOLOGY Leonid A Mirny
U54 DK107980 Center for 3D Structure and Physics of the Genome UNIV OF MASSACHUSETTS MED SCHOOL Leonid A Mirny
Submission date Apr 07, 2016
Last update date May 15, 2019
Contact name Ilya M. Flyamer
Organization name University of Edinburgh
Department IGMM, HGU
Lab Bickmore
Street address Crewe Road, Western General Hospital
City Edinburgh
ZIP/Postal code EH4 2GH
Country United Kingdom
Platforms (3)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (246)
GSM2109886 K562_bulkB
GSM2109887 K562_bulkA
GSM2109888 1_oocyte_NSN
BioProject PRJNA317616
SRA SRP072973

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
GSE80006_Intermediate-200kb.csv.gz 1.4 Mb (ftp)(http) CSV
GSE80006_Intermediate-40kb.csv.gz 3.1 Mb (ftp)(http) CSV
GSE80006_Intermediate-Hoechst-200kb.csv.gz 1.3 Mb (ftp)(http) CSV
GSE80006_Intermediate-Hoechst-40kb.csv.gz 2.9 Mb (ftp)(http) CSV
GSE80006_Intermediate-Hoechst-reads.csv.gz 9.1 Mb (ftp)(http) CSV
GSE80006_Intermediate-reads.csv.gz 11.8 Mb (ftp)(http) CSV
GSE80006_K562-200kb.csv.gz 2.6 Mb (ftp)(http) CSV
GSE80006_K562-40kb.csv.gz 5.3 Mb (ftp)(http) CSV
GSE80006_K562-A-200kb.csv.gz 276.2 Kb (ftp)(http) CSV
GSE80006_K562-A-40kb.csv.gz 436.3 Kb (ftp)(http) CSV
GSE80006_K562-A-reads.csv.gz 721.5 Kb (ftp)(http) CSV
GSE80006_K562-B-200kb.csv.gz 2.5 Mb (ftp)(http) CSV
GSE80006_K562-B-40kb.csv.gz 5.1 Mb (ftp)(http) CSV
GSE80006_K562-B-reads.csv.gz 15.4 Mb (ftp)(http) CSV
GSE80006_K562-bulk-200kb.csv.gz 6.5 Mb (ftp)(http) CSV
GSE80006_K562-bulk-40kb.csv.gz 13.7 Mb (ftp)(http) CSV
GSE80006_K562-bulk-reads.csv.gz 36.9 Mb (ftp)(http) CSV
GSE80006_K562-reads.csv.gz 16.1 Mb (ftp)(http) CSV
GSE80006_NSN-200kb.csv.gz 8.3 Mb (ftp)(http) CSV
GSE80006_NSN-40kb.csv.gz 20.3 Mb (ftp)(http) CSV
GSE80006_NSN-Hoechst-200kb.csv.gz 1.8 Mb (ftp)(http) CSV
GSE80006_NSN-Hoechst-40kb.csv.gz 3.8 Mb (ftp)(http) CSV
GSE80006_NSN-Hoechst-reads.csv.gz 13.2 Mb (ftp)(http) CSV
GSE80006_NSN-reads.csv.gz 100.4 Mb (ftp)(http) CSV
GSE80006_RAW.tar 820.2 Mb (http)(custom) TAR (of CSV)
GSE80006_SN-200kb.csv.gz 6.2 Mb (ftp)(http) CSV
GSE80006_SN-40kb.csv.gz 15.2 Mb (ftp)(http) CSV
GSE80006_SN-Hoechst-200kb.csv.gz 9.8 Mb (ftp)(http) CSV
GSE80006_SN-Hoechst-40kb.csv.gz 24.1 Mb (ftp)(http) CSV
GSE80006_SN-Hoechst-reads.csv.gz 103.2 Mb (ftp)(http) CSV
GSE80006_SN-reads.csv.gz 81.0 Mb (ftp)(http) CSV
GSE80006_oocyte-200kb.csv.gz 21.5 Mb (ftp)(http) CSV
GSE80006_oocyte-40kb.csv.gz 51.7 Mb (ftp)(http) CSV
GSE80006_oocyte-reads.csv.gz 305.3 Mb (ftp)(http) CSV
GSE80006_pronuc-female-200kb.csv.gz 2.8 Mb (ftp)(http) CSV
GSE80006_pronuc-female-40kb.csv.gz 6.5 Mb (ftp)(http) CSV
GSE80006_pronuc-female-reads.csv.gz 35.2 Mb (ftp)(http) CSV
GSE80006_pronuc-male-200kb.csv.gz 1.9 Mb (ftp)(http) CSV
GSE80006_pronuc-male-40kb.csv.gz 4.5 Mb (ftp)(http) CSV
GSE80006_pronuc-male-reads.csv.gz 24.3 Mb (ftp)(http) CSV
GSE80006_pronuc-w-o-inh-both-200kb.csv.gz 901.0 Kb (ftp)(http) CSV
GSE80006_pronuc-w-o-inh-both-40kb.csv.gz 2.1 Mb (ftp)(http) CSV
GSE80006_pronuc-w-o-inh-both-reads.csv.gz 8.6 Mb (ftp)(http) CSV
GSE80006_pronuc-w-o-inh-female-200kb.csv.gz 715.0 Kb (ftp)(http) CSV
GSE80006_pronuc-w-o-inh-female-40kb.csv.gz 1.7 Mb (ftp)(http) CSV
GSE80006_pronuc-w-o-inh-female-reads.csv.gz 6.2 Mb (ftp)(http) CSV
GSE80006_pronuc-w-o-inh-male-200kb.csv.gz 1.2 Mb (ftp)(http) CSV
GSE80006_pronuc-w-o-inh-male-40kb.csv.gz 2.8 Mb (ftp)(http) CSV
GSE80006_pronuc-w-o-inh-male-reads.csv.gz 13.1 Mb (ftp)(http) CSV
GSE80006_pronuc-w-o-inh-undef_sex-200kb.csv.gz 2.0 Mb (ftp)(http) CSV
GSE80006_pronuc-w-o-inh-undef_sex-40kb.csv.gz 4.4 Mb (ftp)(http) CSV
GSE80006_pronuc-w-o-inh-undef_sex-reads.csv.gz 17.6 Mb (ftp)(http) CSV
GSE80006_pronucleus-200kb.csv.gz 7.1 Mb (ftp)(http) CSV
GSE80006_pronucleus-40kb.csv.gz 15.5 Mb (ftp)(http) CSV
GSE80006_pronucleus-female-200kb.csv.gz 3.2 Mb (ftp)(http) CSV
GSE80006_pronucleus-female-40kb.csv.gz 7.4 Mb (ftp)(http) CSV
GSE80006_pronucleus-female-reads.csv.gz 41.0 Mb (ftp)(http) CSV
GSE80006_pronucleus-male-200kb.csv.gz 2.8 Mb (ftp)(http) CSV
GSE80006_pronucleus-male-40kb.csv.gz 6.3 Mb (ftp)(http) CSV
GSE80006_pronucleus-male-reads.csv.gz 36.8 Mb (ftp)(http) CSV
GSE80006_pronucleus-reads.csv.gz 100.5 Mb (ftp)(http) CSV
GSE80006_readme.txt 1.9 Kb (ftp)(http) TXT
GSE80006_statistics.csv.gz 21.4 Kb (ftp)(http) CSV
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data is available on Series record

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