Monday, April 13, 2009

Breaking Reports: RNAi Screens in Mammalian ES Cells


What's on my desk today?  Reports of genome-scale RNAi screens in mammalian embryonic stem cells:

Ding et al. (2009) A genome-scale RNAi screen for Oct4 modulators defines a role of the Paf1 complex for embryonic stem cell identity. Cell Stem Cell.

Hu et al. (2009) A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal. Genes & Development (free full text).

Why these two papers? They are among the best-controlled large-scale mammalian RNAi screens I've seen.  In Ding et al. they use esiRNAs to screen and follow up with verification of gene expression by RT-PCR; test with independent esiRNAs against primary hits; tests in another cell line; additional cell-based assays; cross-species rescue; and integration of ChIP & mass spec data. Similarly, in Hu et al. they use pooled siRNAs to screen and follow up with test of individual siRNAs; expression analysis via Affymetrix chips; qPCR to verify knockdown; additional cell-based assays; and integration of ChIP-chip data.

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