Table 1.

Potential validation strategies for genomic data sets using spectraFISH.

Genomic Dataset	Probe Selection Strategy	Potential Target Validation	Refs.
Hi-C	High interaction frequency with shared gene loci	3D topology of TADs or whole chromosomes and relation to nuclear structures	18,39
4C-seq	High interaction frequency	Frequency of long-range gene interaction between >2 genes/structures
	Loss of interaction upon NB disassembly		15,21
hiFISH	Known direct interaction with NBs or genes	Frequency of long-range gene interaction between >2 genes/structures	21,29,40
NB-centric deep sequencing assays (e.g. Immuno-TRAP)	Specific co-localization with structure	Higher-order gene interaction with target nuclear structure	19,20
ChIP-seq / DamID	Shared NB/compartment marker protein or transcription factor binding sites	Gene position within CTs or relative to NBs/transcription factories	33,41