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Series GSE90691 Query DataSets for GSE90691
Status Public on Aug 11, 2017
Title Targeted DNA methylation in vivo using an engineered dCas9-MQ1 fusion protein (ChIP-Seq)
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Comprehensive studies have shown that DNA methylation plays vital roles in both loss of pluripotency and governance of the transcriptome during embryogenesis and subsequent developmental processes. Aberrant DNA methylation patterns have been widely observed in tumorigenesis, aging, and neurodegenerative diseases, highlighting the importance of a systematic understanding of DNA methylation and the dynamic changes of methylomes during disease onset and progression. Here we describe a facile and convenient approach for efficient targeted DNA methylation by fusing inactive Cas9 (dCas9) with an engineered prokaryotic DNA methyltransferase MQ1. Our study presents a lentivirus-free strategy to achieve locus-specific cytosine modifications in the genome within 24 hours. Finally, we demonstrated our tool can induce targeted CpG methylation in mice by zygote microinjection, thereby facilitating the dissection of the functional relevance of specific CpG methylation marks at endogenous loci.
 
Overall design I) ChIP-seq of plasmid electroporated K562 cells using Illumina Nextseq 500 sequencing system. II) Reduced representation bisulfited sequencing (RRBS) of plasmid transfected HEK 293T cells using Illumina Hiseq2000 sequencing system. III) PCR amplicon deep sequencing of HEK 293T cells, K562 cells or mice tissue using Illumina Nextseq sequencing system.
 
Contributor(s) Su J, Lei Y
Citation(s) 28695892
Submission date Nov 30, 2016
Last update date May 15, 2019
Contact name Jianzhong Su
E-mail(s) jianzhongsu82@gmail.com
Phone 8322902241
Organization name Baylor college of Medicine
Street address 1 Baylor Plaza
City HOUSTON
State/province TEXAS
ZIP/Postal code 77030
Country USA
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (6)
GSM2410500 HOXA11_dMQ1 CTCF
GSM2410501 HOXA11_MQ1Q147L CTCF
GSM2410502 HOXA13_dMQ1 CTCF
This SubSeries is part of SuperSeries:
GSE90692 Targeted DNA methylation in vivo using an engineered dCas9-MQ1 fusion protein
Relations
BioProject PRJNA355620
SRA SRP094392

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
GSE90691_RAW.tar 272.8 Mb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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