High throughput functional screen to detect epigenetic silencing factors. In A: Top, the siRNA library (Epigenetic family, Qiagen Corp.) was transferred to a sample plate along with sextuplicate or octuplicate control siRNAs targeting HDAC1 or GAPDH, as described previously (23). siRNA transfection of GFP-silent reporter cells is described under “Experimental Procedures.” Middle: stylized depiction of assay indicating typical responses measured with positive (green) and negative (black) controls, and test (yellow) siRNAs. Bottom: typical GFP FACS fluorescence profiles of GFP reporter cells after transfection with GAPDH and HDAC1 control siRNAs. Gating for GPF-negative cells (purple, gate 1) or GFP-positive cells (green, gate 2) is shown. B, pie chart describing the composition of the 200 gene siRNA library (Epigenetic family). Subfamilies are indicated: RITS, RNA-induced initiation of transcriptional silencing; HDACs, histone deacetylases; CHD, chromodomain/helicase/DNA-binding domain; HMG, high mobility group proteins; Swi/SNF2, switch/sucrose nonfermentable; ISWI, imitation SWI; DNMT, DNA methyltransferase; KMT, histone lysine methyltransferase; KAT, histone lysine acetyltransferase; PcG, polycomb group; KDM, histone lysine demethylase; and MBD, methyl-CpG-binding protein. A complete target list is provided in supplemental Table S1. C, representative results of initial screen. See “Experimental Procedures” for details of siRNA transfection and analysis. Results are scored as percentage of GFP-positive cells as measured by 96-well Millipore-Guava EasyCyte FACS analysis. Triplicate wells containing positive (HDAC1, black bars) and negative (GAPDH, white) controls are shown (at the far left). Results shown are duplicate samples, and error bars are indicated. Criteria for hit validation with independent siRNAs, and detailed statistical analyses, are presented in supplemental Fig. S1 and Table S1.