====== Joint Analysis: Data analysis sandbox, with links to analysis products ======


====== Nuclear organization ======


===== Analysis of 3D genome structure population (Alber) =====

Using our population-based genome structure modeling protocol described [[https://www.nature.com/articles/nprot.2018.008|here]], we generated populations of 3D genome structures for H1 and HFF (10,000 models each) at 200-kb resolution. We used the Hi-C data available on the 4DN data portal (H1: [[https://data.4dnucleome.org/experiment-set-replicates/4DNES2M5JIGV/|4DNES2M5JIGV]], HFF: [[https://data.4dnucleome.org/experiment-set-replicates/4DNES2R6PUEK/|4DNES2R6PUEK]]).

We then calculated the average radial positions of each 200-kb genomic region across the population (see below). The radial positions range between 0 and 1; 0 means the region is at the center of the nucleus whereas 1 means the region is at the nuclear envelope.

Average radial positions (H1): [[https://wiki.4dnucleome.org/_media/4dn:nofic_steering_committee:analysis_products:h1.avgradialpositions.txt|h1.avgradialpositions.txt]]

Average radial positions (HFF): [[https://wiki.4dnucleome.org/_media/4dn:nofic_steering_committee:analysis_products:hff.avgradialpositions.txt|hff.avgradialpositions.txt]]

*** May 20 2020 ***

----

======   ======