GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE76479 Query DataSets for GSE76479
Status Public on Mar 01, 2016
Title Cell-of-origin specific 3D genome structure acquired during somatic cell reprogramming [HiC-Seq]
Organism Mus musculus
Experiment type Other
Summary We studied genome topology dynamics during reprogramming of different somatic cell types with highly distinct genome conformations. We find large-scale TAD repositioning and alterations of tissue-restricted genomic neighborhoods and chromatin loops, effectively erasing the somatic cell specific genome structures while establishing an embryonic stem cell-like 3D genome. Yet, early passage iPSCs carry topological hallmarks that enable discerning their cell-of-origin. These hallmarks are not remnants of somatic chromosome topologies. Instead, the distinguishing topological features are acquired during reprogramming, as we also find for cell-of-origin dependent gene expression patterns.
Overall design Hi-C was performed in somatic cells (NSC, macrophages, MEFs and pre-B cells) and their corresponding early and late induced pluripotent stem cells. In addition Hi-C was performed in E14 embryonic stem cells
Contributor(s) de Wit E, de Laat W
Citation(s) 26971819
Submission date Jan 04, 2016
Last update date May 15, 2019
Contact name Elzo de Wit
Phone +31 30 2121 800
Organization name Hubrecht Institute
Street address Uppsalalaan 8
City Utrecht
ZIP/Postal code 3584 CT
Country Netherlands
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (33)
GSM2026260 E14_ESC_1 Hi-C
GSM2026261 macrophages_1 Hi-C
GSM2026262 macrophages_2 Hi-C
This SubSeries is part of SuperSeries:
GSE76481 Cell-of-origin specific 3D genome structure acquired during somatic cell reprogramming
BioProject PRJNA307548
SRA SRP068009

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
GSE76479_RAW.tar 7.5 Gb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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