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4dn:working_groups:jawg_sandbox [2020/05/20 19:50]
asli_yildiri
4dn:working_groups:jawg_sandbox [2020/05/20 20:04] (current)
asli_yildiri
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 ===== Analysis of 3D genome structure population (Alber) ===== ===== 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]] Average radial positions (H1): [[https://​wiki.4dnucleome.org/​_media/​4dn:​nofic_steering_committee:​analysis_products:​h1.avgradialpositions.txt|h1.avgradialpositions.txt]]
  • 4dn/working_groups/jawg_sandbox.txt
  • Last modified: 2020/05/20 20:04
  • by asli_yildiri