ABSTRACT: We used Spec-seq method to quantifiy the in-vitro binding specificity of mouse CTCF insulator protein, particularly concerning its upstream motif. Our results confirmed the previously found "upstream motif“ with 5 or 6nt space to the core motif, which is conferred by CTCF's finger 10 and 11.
Project description:This series is an updated dataset consisting of the Spec-seq and Methyl-Spec-seq samples for human CTCF with a bigger sequencing libraries and different epigenetic modifications. Each sample has replicate to gurantee the reproducibility for each measurement.
Project description: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.
Project description: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.
Project description: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 HOXB13 (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.
Project description: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 AP1 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.
Project description:This dataset consists of Spec-seq samples data for four tandem zinc finger proteins in human genome, each with two replicates. The Spec-seq is a medium throughput technique to characterize the binding specificity of a TF of interest to thousands of binding sites with resolution down to 0.2kT. Similar samples were deposited to NCBI GEO database before (GSE188166). The data analysis workflow for each ZFP can be accessed through https://github.com/zeropin/ZFPCookbook.
Project description:We used previously developed method, Spec-seq, to characterize the protein-DNA interaction specificity of human and mouse Zinc Finger Y protein.