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Series GSE62631 Query DataSets for GSE62631
Status Public on Nov 02, 2014
Title Single-base resolution analysis of active DNA demethylation using methylase-assisted bisulfite sequencing
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary Active DNA demethylation in mammals involves TET-mediated iterative oxidation of 5-methylcytosine (5mC)/5-hydroxymethylcytosine (5hmC) and subsequent excision repair of highly oxidized cytosine bases 5-formylcytosine (5fC)/5-carboxylcytosine (5caC) by Thymine DNA glycosylase (TDG). However, quantitative and high-resolution analysis of active DNA demethylation activity remains challenging. Here we describe M.SssI methylase-assisted bisulfite sequencing (MAB-seq), a method that directly maps 5fC/5caC at single-base resolution. Genome-wide MAB-seq allows systematic identification of 5fC/5caC in Tdg-depleted embryonic stem cells, thereby generating a base-resolution map of active DNA demethylome. A comparison of 5fC/5caC and 5hmC distribution maps indicates that catalytic processivity of TET enzymes correlates with local chromatin accessibility. MAB-seq also reveals strong strand asymmetry of active demethylation within palindromic CpGs. Integrating MAB-seq with other base-resolution mapping methods enables quantitative measurement of cytosine modification states at key transitioning steps of active demethylation pathway, and reveals a regulatory role of 5fC/5caC excision repair in active DNA demethylation cascade.
Overall design Analysis of 5fC/5caC excision repair-dependent active DNA demethylome by MAB-seq in mouse embryonic stem cells.
Contributor(s) Wu H, Wu X, Zhang Y
Citation(s) 25362244
Submission date Oct 22, 2014
Last update date May 15, 2019
Contact name Hao Wu
Phone 617-713-8660
Organization name Harvard Medical School/HHMI
Department Genetics
Lab Yi Zhang
Street address 149G Warren Alpert Building, 200 Longwood Avenue
City Boston
State/province Massachusetts
ZIP/Postal code 02115
Country USA
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (16)
GSM1530518 WT_shCtrl_noVc_v65_H3K4me1.MABseq
GSM1530519 WT_shCtrl_Vc_v65_H3K4me1.MABseq
GSM1530520 WT_shTdg_noVc_v65_H3K4me1.MABseq
BioProject PRJNA264577
SRA SRP049191

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

Supplementary file Size Download File type/resource
GSE62631_NegCtrl_merged_H3K4me1.MABseq.txt.gz 139.9 Mb (ftp)(http) TXT
GSE62631_RAW.tar 435.2 Mb (http)(custom) TAR (of TXT)
GSE62631_README.txt 3.2 Kb (ftp)(http) TXT
GSE62631_mESC.5fC5caC.sites.mm9_pval0.00025_cov10.BEDGRAPH.gz 5.2 Mb (ftp)(http) BEDGRAPH
GSE62631_mESC.5fC5caC.sites.mm9_pval0.00025_cov5.BEDGRAPH.gz 6.5 Mb (ftp)(http) BEDGRAPH
GSE62631_mESC.MABseqRawSignal.mm9_cov5.BEDGRAPH.gz 199.3 Mb (ftp)(http) BEDGRAPH
GSE62631_mESC.coverage.mm9_cov5.BEDGRAPH.gz 193.8 Mb (ftp)(http) BEDGRAPH
GSE62631_shCtrl_noVc_Vc_merged_H3K4me1.MABseq.txt.gz 147.6 Mb (ftp)(http) TXT
GSE62631_shTdg_Vc_merged_H3K27me3.MABseq.txt.gz 31.6 Mb (ftp)(http) TXT
GSE62631_shTdg_Vc_merged_H3K4me1.MABseq.txt.gz 134.6 Mb (ftp)(http) TXT
GSE62631_shTdg_Vc_merged_WG.MABseq.txt.gz 247.9 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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