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Series GSE76478 Query DataSets for GSE76478
Status Public on Mar 01, 2016
Title Cell-of-origin specific 3D genome structure acquired during somatic cell reprogramming [ChIP-Seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
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 ChIPseq for CTCF and H3K27ac was performed on early and late iPS cells derived from different founders
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 (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (26)
GSM2026234 CTCF_ChIP_macrophage_p20_1
GSM2026235 CTCF_ChIP_macrophage_p20_2
GSM2026236 CTCF_ChIP_macrophage_p3_1
This SubSeries is part of SuperSeries:
GSE76481 Cell-of-origin specific 3D genome structure acquired during somatic cell reprogramming
BioProject PRJNA307549
SRA SRP068008

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Supplementary file Size Download File type/resource
GSE76478_RAW.tar 37.8 Mb (http)(custom) TAR (of NARROWPEAK)
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Raw data are available in SRA
Processed data provided as supplementary file

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