1 Cell Stem Cell, Volume 4 Supplemental Data A Genome-Scale RNAi Screen for Oct4 Modulators Defines a Role of the Paf1 Complex for Embryonic Stem Cell Identity

Analysis of high throughput screening data To avoid false positives caused by insufficient statistical power due to low cell counts, we filtered out all genes with strong cell viability phenotypes (Z-score> 2) as measured by overall counts in each well during the FACS analyses. EsiRNAs that did not cause a strong cell viability effect were analyzed for an increase or decrease in GFP negative versus GFP positive cells greater than 2 times the s.d. (Z-score>2) on average, using the negative controls as the standard. For the 30 top hits (Z-score>4), we synthesized 29 independent Deqor-optimized esiRNAs (Henschel et al., 2004). One of the 30 candidate genes did not amplify during the PCR reaction and was not analyzed further. The primer sequences of the Deqor-optimized esiRNAs are presented in supplemental table S2. Expression array analyses Four independent total RNA preparations, each 1 µg from Ctr9 esiRNA and Luc (control) esiRNA transfected ESCs, were labeled with the One-cycle