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Series GSE99346 Query DataSets for GSE99346
Status Public on Dec 01, 2017
Title TET1 (HUES8 WT hESCs) and DNMT3B (HUES8 WT and HUES8 TET TKO hESCs) ChIP-Seq
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The TET enzymes oxidize 5-methylcytosine to 5-hydroxymethylcytosine, which can lead to DNA demethylation. However, direct connections between TET-mediated DNA demethylation and transcriptional output are difficult to establish due to challenges of distinguishing global versus locus-specific effects. Here we show that TET1/2/3 triple knockout (TKO) human embryonic stem cells (hESCs) exhibit preferential hypermethylation at bivalent promoters without corresponding gene expression changes in undifferentiated hESCs. In the absence of the TET proteins, abnormal accumulation of DNMT3B at bivalent promoters results in hypermethylation and impaired gene activation upon differentiation. Broadly, the competitive balance between the TET proteins and de novo methyltransferases at bivalent promoters could facilitate rapid changes of their methylation state to either activate or silence transcription in a cell-lineage and gene dependent manner.
 
Overall design ChIP-Seq was performed for TET1 (WT hESCs) and DNMT3B (WT and TKO hESCs). WT and TKO hESCs were cultured in standard hESC media, as described above. ~5 × 107 cells were fixed, washed and snap-frozen according to the Cell Fixation protocol from Active Motif (http://www.activemotif.com/documents/1848.pdf). Immunoprecipitation and DNA sequencing was done by Active Motif.
 
Contributor(s) Louis D, Heng P, Nipun V
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date May 26, 2017
Last update date May 15, 2019
Contact name Nipun Verma
E-mail(s) nipunver@gmail.com
Phone 646-358-2160
Organization name Memorial Sloan Kettering Cancer Center
Department Developmental Biology
Lab Danwei Huangfu lab
Street address 430 East 67th St
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (5)
GSM2642522 HUES8 WT TET1 ChIP-Seq
GSM2642523 HUES8 WT DNMT3B ChIP-Seq
GSM2642524 HUES8 TET TKO DNMT3B ChIP-Seq
This SubSeries is part of SuperSeries:
GSE89728 TET1/2/3
Relations
BioProject PRJNA388168
SRA SRP108116

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
GSE99346_TKO_DNMT3B-Input_peaks.bed.gz 714.0 Kb (ftp)(http) BED
GSE99346_WT_DNMT3B-Input_peaks.bed.gz 554.0 Kb (ftp)(http) BED
GSE99346_WT_TET1-Input_peaks.bed.gz 282.3 Kb (ftp)(http) BED
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Raw data are available in SRA
Processed data are available on Series record

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