Spec-seq sequencing data for CTCF [2018 series]

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. Overall design: We used two recombinant proteins, mouse CTCF(F1-F11) and CTCF(F1-F9) to ran Spec-seq analysis on degereate libraries R1,R2,R2L, R3. As expected, only the F1-F11 verson of CTCF exhibited the upstream motif recognition, therefore we confirmed the recognition its relationship. Additionally, we showed that this upstream motif can only show up conditionally in the presence of strong core motif binding. The experiment was redesigned and redone to include more variants and mutant in the updated series GSE188164