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SRX7692236: GSM4301078: H3K27me3 5d off; Homo sapiens; ChIP-Seq
1 ILLUMINA (Illumina HiSeq 3000) run: 10.7M spots, 3.2G bases, 1.2Gb downloads

Submitted by: NCBI (GEO)
Study: Genome-wide investigation of the dynamic changes of epigenome modifications after DNA methylation editing [ChIP-Seq]
show Abstracthide Abstract
The aim of this study was to investigate the stability of DNA methylation, the dynamics of different histone modifications and the changes in expression after genome-wide introduction of DNA methylation in promotor CpG islands. Therefore, the catalytic domain of DNMT3A was fused to a zinc finger protein and expressed for three days to globally introduce de novo DNA methylation and subsequently, the changes in the epigenome were monitored for up to eleven days. Overall design: A stable HEK293 cell line was constructed with the catalytic domain of DNMT3A fused to a zinc finger (ZnF-3AC) which is under the control of a doxycycline (dox)-inducible promoter. GFP is co-expressed via an IRES and serves as a reporter. Cells were either harvested before dox treatment ("no dox") or grown under dox conditions for three days ("3d dox"). GFP-positive cells were enriched by FACS after 3d dox and a fraction of these cells was re-seeded on a 6-Well-plate without supplementation of dox. Five and eight days after dox removal ("5d / 8d / 11d off"), cells were harvested and a fraction of cells was re-seeded again. After eleven days of dox removal ("11d off"), cells were harvested and the experiment was stopped.
Sample: H3K27me3 5d off
SAMN14056060 • SRS6118333 • All experiments • All runs
Organism: Homo sapiens
Library:
Instrument: Illumina HiSeq 3000
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: PAIRED
Construction protocol: For ZnF(3xHA)-ChIP, chromatin was crosslinked with 1% formaldehyde, sheared using a probe sonicator (100 - 1000 bp fragment size) and preciptated with an antibody. In case of nChIP experiments, chromatin was fragmented by Mnase digest and precipitated with an antibody. Libraries for all samples (except H3K27ac) were constructed by the Max Planck-Genome-centre Cologne. In case of H3K27ac, libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer's protocol.
Experiment attributes:
GEO Accession: GSM4301078
Links:
Runs: 1 run, 10.7M spots, 3.2G bases, 1.2Gb
Run# of Spots# of BasesSizePublished
SRR1104043610,674,6493.2G1.2Gb2020-11-10

ID:
10040457

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