Fig. S2.

Hybridization efficiency of FISH experiments. (A) Probes reached saturating conditions for RNA FISH at the puncta level. The number of Xist puncta with different probe sets were counted in MEF cells after RNA FISH. Four different probe sets were tested in RNA FISH: Set 1 with a single probe containing five labels; Set 2 with three probes of five labels each; Set 3 with three probes of one label each (used in Fig. 1C); or Set 4 containing a pool of eight probes targeting Repeats C and E and the three-probe set (Set 2). The detected signals did not differ statistically, indicating that RNA FISH has reached saturating conditions. Please note that higher number of puncta here compared with Fig. 1C probably due to experimental variation. (B) DNA FISH of the Xist using probe Set 4 and an Ftx-containing BAC probe as a control shows efficient detection of single-copy Xist targets. Arrows indicate loci detected by both Xist oligoprobe and control Ftx BAC probe.