GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE144903 Query DataSets for GSE144903
Status Public on Nov 10, 2020
Title Genome-wide investigation of the dynamic changes of epigenome modifications after DNA methylation editing [RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary 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.
Contributor(s) Broche J, Kungulovski G, Bashtrykov P, Rathert P, Jeltsch A
Citation(s) 33300025
Submission date Feb 06, 2020
Last update date Jan 19, 2021
Contact name Albert Jeltsch
Phone +49 685 64390
Organization name University Stuttgart
Department Institute of Biochemistry and Technical Biochemistry
Street address Allmandring 31
City Stuttgart
ZIP/Postal code 70569
Country Germany
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (6)
GSM4300556 no_dox_Rep1_RNA-seq
GSM4300557 no_dox_Rep2_RNA-seq
GSM4300558 3d_dox_Rep1_RNA-seq
This SubSeries is part of SuperSeries:
GSE144904 Genome-wide investigation of the dynamic changes of epigenome modifications after DNA methylation editing
BioProject PRJNA605248
SRA SRP247613

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE144903_3d_dox_Rep1+2_merged_RNA-seq_CPM.bigwig 25.7 Mb (ftp)(http) BIGWIG
GSE144903_5d_off_Rep1+2_merged_RNA-seq_CPM.bigwig 28.6 Mb (ftp)(http) BIGWIG
GSE144903_Gene_FPKM_tracking.txt.gz 794.9 Kb (ftp)(http) TXT
GSE144903_no_dox_Rep1+2_merged_RNA-seq_CPM.bigwig 24.6 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap