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E-GEOD-76478 - Cell-of-origin specific 3D genome structure acquired during somatic cell reprogramming [ChIP-Seq]

Status
Released on 1 March 2016, last updated on 5 March 2016
Organism
Mus musculus
Samples (26)
Protocols (3)
Description
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. ChIPseq for CTCF and H3K27ac was performed on early and late iPS cells derived from different founders
Experiment type
ChIP-seq 
Contacts
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-76478.idf.txt
Sample and data relationshipE-GEOD-76478.sdrf.txt
Processed data (1)E-GEOD-76478.processed.1.zip
Links