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--- 4dn:working_groups:jawg_sandbox [2020/05/20 19:50]
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+++ 4dn:working_groups:jawg_sandbox [2020/05/20 20:04] (current)
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 ===== 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 region in the genome 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.
+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]]