NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE131098 Query DataSets for GSE131098
Status Public on Jun 26, 2020
Title Hammer-seq to measure kinetics of DNA methylation maintenance in HeLa cells
Organisms Homo sapiens; Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Simultaneous measurement of the methylation status of parent and daughter strands of newly replicated DNA at the single molecule level has not been experimentally achieved, which is essential for measurements the kinetics of DNA methylation maintenance at base level genome wide. To achieve this, we developed a new method termed Hammer-seq (Hairpin assisted mapping of methylation of replicated DNA), which combines EdU labeling, biotin conjugation, immunopurification and hairpin bisulfite sequencing technologies. We were able to pulse label HeLa cells with EdU for as short as 4 min to capture newly synthesized DNA, and the paired-end hairpin bisulfite sequencing allowed us to simultaneously measure the methylation status of parent and daughter strands at the single molecular level with base resolution. Hammer-seq displayed strong enrichment of newly replicated regions and successfully captured maintenance intermediates, and also had robustness of measurements.
 
Overall design In this study, we arrested HeLa cells at the G1/S boundary with thymidine-aphidicolin double block, pulse labeled with EdU for 4 min immediately after cell cycle release, chased for various time points up to 24 h and performed Hammer-seq to measure the maintenance kinetics during and after S phase.
 
Contributor(s) Ming X, Zhang Z, Zou Z, Lv C, He Q, Li Y, Wang H, Zhu B
Citation(s) 32581343
Submission date May 13, 2019
Last update date Jun 09, 2023
Contact name Zhuqiang Zhang
E-mail(s) zhangzhuqiang@ibp.ac.cn
Organization name Institute of Biophysics, CAS
Street address 15 Datun Road, Chaoyang District.
City Beijing
State/province ---
ZIP/Postal code 100101
Country China
 
Platforms (4)
GPL20795 HiSeq X Ten (Homo sapiens)
GPL21273 HiSeq X Ten (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (126)
GSM3763438 WT-chase-0
GSM3763439 WT-chase-5m
GSM3763440 WT-chase-10m
Relations
BioProject PRJNA542687
SRA SRP198282

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
GSE131098_RAW.tar 9.3 Gb (http)(custom) TAR (of BIGWIG, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap