StaticSection

Comparison Across Cell Types

While insulation and compartment score tracks show cell-to-cell variability, interphase cells of various cell types share a significant portion of their chromosome conformations, due to the presence of constitutive heterochromatin, housekeeping genes, and other constitutive features. Therefore, genome-wide correlation for these tracks between cell types can constitute a quality control on the score calculations.

After the pipelines were run on the released data in the data portal (insulation scores were only run on mcool files with over 100M reads, see above), Spearman correlations were calculated relative to reference tracks. The deep Micro-C datasets for H1-ESC (4DNES21D8SP8) and HFFc6 (4DNESWST3UBH) were used as reference for insulation scores and compartments respectively. Below is the distribution of those correlations.

The datasets were divided into six categories: **Low Cis/Trans Ratio:** Datasets that have either a cis/trans ratio less than 50 or less than 40 for H1 cell lines. **CTCF & Cohesion Depletion:** Datasets where CTCF or Cohesin were depleted. **Cohesion Release Reduction:** Datasets where Cohesin release factors (WALP & PDS5A/B) were depleted. **Protocol Variations:** Datasets produced by major variations to the standard Hi-C protocol, such as skipping the ligation step. ** Cell Cycle Studies:** Datasets where different phases of the cell cycle were studied. **Regular:** Datasets that do not fall in any of the categories above. The table used to generate the plot above can be downloaded here.