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Table 2 Experimental data used for parameter inference

From: Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations

Dataset Observable Experimental technique Data points (n) Reference
O1 Median 3D distance between pairs of subtelomeric loci Imaging, live cells 62 [50]
O2 Median angle between locus, nuclear and nucleolar centroids Imaging, live cells 37 [31, 50]
O3 Median distance between chromosome 12 locus and nucleolus Imaging, live cells 15 [64]
O4 Median 2D distance between pairs of loci on chromosome 4 Imaging, live cells 12 this study
O5 Mean 3D distances between intrachromosomal pairs of loci on several chromosomes Imaging, fixed cells (FISH) 13 [51]
O6 Mode of 3D distances between intrachromosomal pairs of loci on chromosome 14 Imaging, fixed cells (FISH) 8 [80]
O7 Mode of 3D distances between SPB and telomeres Imaging, fixed cell (Immunofluorescence) 7 [80]
O8 Mean contact frequencies within chromosomes (16) and of each chromosome with the other chromosomes (16) + Intrachromosomal contact frequencies for genomic distances 25–85 Kb at 5 Kb intervals, averaged over the genome (12) + relative to the centromere (12) Hi-C 56 [29]
O9 Same Hi-C 56 [30]
  Total   266  
  1. This table summarizes the nine experimental datasets used for parameter inference in this study. Additional data used for model validation only are: Hi-C data from [62], Micro-C XL data from [63], and chromatin dynamics data from [6466]. For more details, see Additional file 3 and Additional file 1: Supplementary Methods