This repository contains the scripts and pipelines used in the manuscript "Effects of CTCF on the regulatory landscape of the mouse Sox2 locus" by Eder et al.
In this study we investigated the location dependent effect of ectopic CTCF binding sites (CBS) with and without a Sox2 promotore reporter on the expression of the mouse Sox2 locus. We created high resolution functional maps of the locus by relocating either CBS-only or CBS-Sox2P reporter constructs to thousdands of alternative positions.
This repository contains information about
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Tagmentation: Tn5_tagmentation mapping (pipeline)
- including all config files used for the data in the paper
- including txt files with all mapped integrations from this study
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Info_files
- file containing FACS sorting statistics for each experiment (needed for expression score calculation)
- file containing FI from sorted experiments and population (needed for expression score calculation)
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General functions: includes the calculation of expression score
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Figures: R markdown files to create paper figures
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Pipline for genotyping 1xCBS_Fw_Sox2P clones