Source was embryonic nuclear extract of wild-type fly line; bait produced from endogenous gene; prey produced from endogenous gene.

Embryonic nuclear extract was fractionated to separate p185 and p125 isoforms of XNP before immunoaffinity purification.

Source was embryonic nuclear extract of wild-type fly line; bait produced from endogenous gene; prey produced from endogenous gene.

Embryonic nuclear extract was fractionated to separate p185 and p125 isoforms of XNP before immunoaffinity purification.

Su(var)205 and XNP form a stable ~200 kDa complex.

Source was cell extract of baculovirus-infected Sf9 cell line; bait produced from transfected construct; prey produced from transfected construct.

Su(var)205 and XNP form a stable ~200 kDa complex.

Source was cell extract of baculovirus-infected Sf9 cell line; bait produced from transfected construct; prey produced from transfected construct.

Source was cross-linked nuclear extract of S2 cell line; bait produced from transfected construct; prey produced from endogenous gene.

Crude nuclear extracts were cross-linked using formaldehyde, sonicated, and subjected to ProteinA affinity purification with rabbit IgG agarose beads eluted under denaturing conditions, and subsequently using streptavidin agarose beads for Bio affinity purification. Purified peptides were eluted by on-bead trypsin digestion and mass spectrometric analysis.

Enrichment of prey protein was compared to input, mock and unrelated BioTAP affinity purifications using a statistical method (Bamse) developed by the authors to control for multiple sources of bias.