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Series GSE35721 Query DataSets for GSE35721
Status Public on Apr 11, 2012
Title Spatial organisation of the X inactivation center
Organism Mus musculus
Experiment type Other
Summary We report the application of Chromosome Conformation Capture Carbon-copy (5C) to a 4.5 Mb stretch of the mouse X chromosome encompassing the X inactivation center locus. We uncover a series of discrete 200kb-1Mb topologically associating domains (TADs). These align with several domain-wide epigenomic features as well as co-regulated gene clusters. 5C analysis in EED and G9A mutants reveal that this segmental organisation in TADs does not relie on the underlying H3K27me3 or H3K9me2 blocks. Deletion of a boundary between two TADs leads to ectopic chromosomal contacts between them. Analysis of mESCs, mNPCs and MEFs suggest that the positioning of TADs on the chromosome is stable during cell differentiation though their internal organisation changes. Comparison of male (XY) and female (XX) differentiated cells highlights that the long-range chromosomal contacts within TADs are dampened on the inactive X compared to the active X.
Overall design 5C oligonucleotides were designed around HindIII restriction site following an alternative scheme
Contributor(s) Nora EP, Lajoie BR, Dekker J, Heard E
Citation(s) 22495304
Submission date Feb 10, 2012
Last update date May 15, 2019
Contact name Elphege Pierre Nora
Organization name Institut Curie
Department Mammalian developmental epigenetics
Lab Edith Heard
Street address 11-13 rue Pierre et Marie Curie
City Paris
ZIP/Postal code 75005
Country France
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (20)
GSM873924 female-MEFs-replicate-1
GSM873925 female-MEFs-replicate-2
GSM873926 female-mESCs-day-2-PGK12.1-replicate-1
SRA SRP010881
BioProject PRJNA152121

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
GSE35721_PRIMERPOOL_769_XIC3.fa.gz 28.0 Kb (ftp)(http) FA
GSE35721_RAW.tar 8.6 Mb (http)(custom) TAR (of TXT)
GSE35721_sample_matrix_data_Readme.txt 479 b (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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