U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SRX1513740: GSM2026242: CTCF_ChIP_NSC_p20_1; Mus musculus; ChIP-Seq
1 ILLUMINA (NextSeq 500) run: 48.7M spots, 2.4G bases, 1.5Gb downloads

Submitted by: NCBI (GEO)
Study: Cell-of-origin specific 3D genome structure acquired during somatic cell reprogramming [ChIP-Seq]
show Abstracthide Abstract
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
Sample: CTCF_ChIP_NSC_p20_1
SAMN04382646 • SRS1232674 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: NextSeq 500
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: SINGLE
Construction protocol: ChIP experiments were performed as described previously (van Oevelen et al., 2008) using an antibody against H3K27ac (ab4729, Abcam) and CTCF (Millipore, 07-729). DNA libraries were prepared using Illumina's reagents and instructions.
Experiment attributes:
GEO Accession: GSM2026242
Links:
Runs: 1 run, 48.7M spots, 2.4G bases, 1.5Gb
Run# of Spots# of BasesSizePublished
SRR308175648,717,0442.4G1.5Gb2016-03-01

ID:
2141838

Supplemental Content

Search details

See more...

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...