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E-GEOD-76480 - Cell-of-origin specific 3D genome structure acquired during somatic cell reprogramming [Expression]

Status
Released on 1 March 2016, last updated on 5 March 2016
Organism
Mus musculus
Samples (26)
Array (1)
Protocols (7)
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. Transcriptome analysis was performed in somatic cells (NSC, macrophages, MEFs and pre-B cells) and their corresponding early and late induced pluripotent stem cells. In addition, expression analysis was performed in E14 embryonic stem cells
Experiment type
transcription profiling by array 
Contacts
Elzo de Wit, Wouter de Laat
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-76480.idf.txt
Sample and data relationshipE-GEOD-76480.sdrf.txt
Raw data (2)E-GEOD-76480.raw.1.zip, E-GEOD-76480.raw.2.zip
Processed data (1)E-GEOD-76480.processed.1.zip
Array designA-GEOD-10787.adf.txt
Links