Supplementary Figure 1: In situ Hi-C-library quality-control measures.
From: Smchd1 regulates long-range chromatin interactions on the inactive X chromosome and at Hox clusters
In situ Hi-C was performed in n=3 Smchd1fl/fl and Smchd1del/del female NSC lines, one week post Cre-mediated deletion of Smchd1. a. Tapestation trace showing read-length distribution of pooled in situ HiC libraries run on a high-sensitivity D5000 Tape. Libraries were produced in the correct size range. b. These libraries were of good quality, as determined by HiCup. Pie graph from HiCup processing report representing the relative distribution of in situ HiC reads, following optimisation of restriction digest and conditions to prevent aggregation of nuclei. Valid pairs, or chimeric HiC reads, are represented in navy blue. All other colours represent a common experimental artefact. Notably the valid reads now make up 86% of the total reads. c. Multidimensional scaling (MDS) plot showing the relationship between the 3 Smchd1fl/fl and 3 Smchd1del/del in situ Hi-C samples. Samples separate by genotype on the first MDS component: Leading logFC dim1 (X axis); Leading logFC dim1: second MDS component (Y axis). d. High correlation between biological replicates indicated by a Spearman rank correlation between bins in two matrices at increasing genomic distances. e. The log interaction count (Y axis) compared to log genomic distance (X axis) shown for the 100 kb, 500 kb and 1 Mb resolution analyses. The trend line is shown for 3 different log genomic distances. These plots show the distance-dependent decay of HiC interaction frequency.
