This is an analysis record to accompany the paper:
YY1 binding is a gene-intrinsic barrier to Xist-mediated gene silencing
Joseph S Bowness, Mafalda Almeida, Tatyana B Nesterova, Neil Brockdorff
EMBO Rep. 2024 Apr 23. doi: https://doi.org/10.1038/s44319-024-00136-3
First, we run scripts for allelic analysis of ATAC-seq from the time-course of mESC-to-NPC differentiation in iXist-ChrX-Dom cells: AllelicATAC_iXistChrXDom and then AllelicATAC_EDM. Plots which form the panels of Figure 2A can also be found within these records.
Following the first two scripts, the records of the analysis performed to generate all other R plots in the paper can be found below:
Most files which are loaded by these scripts have been uploaded to the “files” folder of this Github repository. Some larger raw data files (eg genome-wide “counts tables” outputs from featureCounts) are not attached but can be downloaded from GEO. The specific GEO accessions are provided in the analysis records.