Genomics

Dataset Information

159

Methyl-Spec-seq control data sets


ABSTRACT: We developed a novel in-vitro experimental method to characterize the protein-DNA interaction specificity and methylation sensitivity, we called Methyl-Spec-seq. In this data set, mouse ZFP57 (F1-F3) was used as a positive control example to show that Methyl-Spec-seq can determine the relative binding energy for variants with different methylation property, i.e., unmethylated, top hemimethylated, bottom hemimethylated, duplex methylated by either chemical synthesis or enzymatic treatment. Overall design: Except different methylation types of DNA, the overall design is the same as conventional Spec-seq, which we have published work before.

INSTRUMENT(S): Illumina MiSeq (Mus musculus)

SUBMITTER: Basab Roy  

PROVIDER: GSE98686 | GEO | 2017-08-31

SECONDARY ACCESSION(S): PRJNA385913

REPOSITORIES: GEO

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Publications

Measuring quantitative effects of methylation on transcription factor-DNA binding affinity.

Zuo Zheng Z   Roy Basab B   Chang Yiming Kenny YK   Granas David D   Stormo Gary D GD  

Science advances 20171117 11


Methylation of CpG (cytosine-phosphate-guanine) dinucleotides is a common epigenetic mark that influences gene expression. The effects of methylation on transcription factor (TF) binding are unknown for most TFs and, even when known, such knowledge is often only qualitative. In reality, methylation sensitivity is a quantitative effect, just as changes to the DNA sequence have quantitative effects on TF binding affinity. We describe Methyl-Spec-seq, an easy-to-use method that measures the effects  ...[more]

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