Additional file 1.

Differentially regulated probes in response to DNA damage. This is a combined table of all probes that were significantly differentially regulated in response to 1 Gy IR (p ≤ 0.05, FC ≥ ±1.5) in WT pre-B cells lines and in response to RAG induced DSBs (p ≤ 0.05, FC ≥ ±1.5). Three independent WT lines were used to determine the response to genotoxic IR-induced DNA damage. These cells were exposed to STI-571 for 48 hours, treated with 0 or 1 Gy IR and mRNA expression was measured at 2 hours post IR. The intensity values were averaged from the 3 treated or untreated samples and used to determine fold change of 1 Gy/0 Gy. Significantly differentially regulated IR-induced probe fold change values are shown in column D. To determine differentially regulated probes in response to RAG-induced breaks, three independent Rag2-/- (no DSBs) lines and three independent Artemis-/- (unrepaired RAG-induced DSBs) lines were exposed to STI-571 for 48 hours and mRNA expression was measured. The intensity values were averaged for each genotype. Values are fold change of Artemis-/-/Rag2-/- and significantly differentially regulated fold change values are shown in column E. Differentially regulated probes common to IR- and RAG-induced break responses are indicated in column F with a # for a commonly expressed specific probe ID and ## for a commonly expressed gene. For the latter, multiple probes representing the same gene were differentially regulated in the same direction (up or down-regulated) following both IR- and RAG-induced breaks. Differentially regulated probes unique to IR-induced DNA damage response are indicated in column G with an *. This column includes all probes that were differentially regulated in the WT response to IR (p ≤ 0.05, FC ≥ ±1.5) but not in the physiological response to RAG-induced breaks. Annotation of all genes listed is based on build 32 from Affymetrix.

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Innes et al. BMC Genomics 2013 14:163   doi:10.1186/1471-2164-14-163