Lord2008

A high-throughput RNA interference screen for DNA repair determinants of PARP inhibitor sensitivity.

• Lord CJ,et al DNA Repair (Amst). 2008 Dec 1;7(12):2010-9

This siRNA library targeted over 98% of all of the known DNA repair proteins, as defined by Wood et al. [16] and in particular encompassed siRNA targeting all the major components of BER (21 genes), MMR (11 genes), NER (28 genes), HR(19 genes) and NHE The HTS was performed using the diploid CAL51 breast cancer cell line.

We used a log 2 surviving fraction (log 2 SF) threshold of −0.1 or less to identify siRNAs that significantly sensitized to KU0058948 in the HTS (Supplementary Tables 1–3). This threshold represented the limit of three standard deviations from the median of effects in siCON transfected cells. 67 of the 460 experimental siRNA satisfied this hit criteria (Fig. 3A). Using this distinction, eight genes, plus the control (BRCA1) were identified where both siRNA in the library. significantly sensitized to KU0058948 (Fig. 3C); ATR, BRCA2, DDB1, LIG1, PCNA, RAD51, XAB2 and XRCC1. We have previously reported, using a different assay system, that silencing of ATR, BRCA2 or RAD51 expression significantly sensitizes cells to KU0058948, presumably by causing defective HR [3,6]. The following parse takes these 8 interactions to be true SL. We additionally generate a list of negative SLs using the criteria that neither of the cells attained an effect that was even half as strong

The data come as pairs of lines. We will first store the pairs and then only take those that satisfy the criteria for positive or negative (PARP sensitization). There are actually 9 SLA pairs including RPA3, which is shown in Figure 4C but not mentioned in the text. That is what we get with this parse!