Hi-C analysis of genomic contacts revealed karyotype abnormalities in chicken HD3 cell line

The chicken LSCC-HD3 cell line (HD3) generated from erythroid precursors is an established avian model for erythroid differentiation and lineage-specific gene expression. We obtained Hi-C maps of genomic interactions for HD3 cell line and revealed A/B compartments and topologically-associating domains. By analysis of contact patterns in the Hi-C maps of HD3 cells we identified more than 25 interchromosomal translocations of regions =200 Kb on both micro- and macrochromosomes. Intrachromosomal inversions, deletions and duplications were also detected in HD3 cells. Hi-C data obtained for HD3 chicken cell line demonstrate that it has a highly rearranged karyotype, with most of the chromosomes involved in unbalanced translocations. Overall design: Hi-C of chicken HD3 cell line (LSCC-HD3) (2 replicates)