. 2015 Dec 28;113(2):350–355. doi: 10.1073/pnas.1518648113

Table S1.

Efficiencies of primers used for all assays

Primer set	Primer sequences, forward and reverse, 5′ to 3′	R²	Efficiency	Slope 95% confidence interval
Drosophila
Intact	CGACAGCATTCCTGCGTAGTAAGA	0.995	106.6%	−3.34 < s < −3.01
Intact	ACAATGCAAATTGCCCCTTA	0.995	106.6%	−3.34 < s < −3.01
Depurinated	CGACAGCATTCCTGCGTAGTAAGT	0.997	101.4%	−3.44 < s < −3.13
Depurinated	ACAATGCAAATTGCCCCTTA	0.997	101.4%	−3.44 < s < −3.13
Normalizer	CAAGGACATTGCCAGGTAGG	0.997	102.7%	−3.40 < s < −3.12
Normalizer	AGCTTTTGCTGTCCCTGTGT	0.997	102.7%	−3.40 < s < −3.12
Howardula
Intact	TGATAGTAATCCTGCTTAGTAAGA	0.997	98.0%	−3.52 < s < −3.22
Intact	CACCGGAGAGCAACGATATT	0.997	98.0%	−3.52 < s < −3.22
Depurinated	TGATAGTAATCCTGCTTAGTAAGT	0.998	105.4%	−3.32 < s < −3.08
Depurinated	CACCGGAGAGCAACGATATT	0.998	105.4%	−3.32 < s < −3.08
Normalizer	CAAATGCCTCGTCGGATG	0.991	92.1%	−3.81 < s < −3.24
Normalizer	GCCAAAGCCTCCCACTTATAC	0.991	92.1%	−3.81 < s < −3.24
Rabbit
Intact	GGGTTTAGACCGTCGTGAGA	0.998	79.6%	−4.03 < s < −3.83
Intact	AGTGGAACCGCAGGTTCAGA	0.998	79.6%	−4.03 < s < −3.83
Depurinated	GGGTTTAGACCGTCGTGAGA	0.997	78.9%	−4.13 < s < −3.80
Depurinated	TGTGGAACCGCAGGTTCAGA	0.997	78.9%	−4.13 < s < −3.80
Normalizer	CGTTGGATTGTTCACCCACT	0.999	96.4%	−3.48 < s < −3.33
Normalizer	CATACACCAAATGTCTGAACCTG	0.999	96.4%	−3.48 < s < −3.33

Efficiency and specificity were validated on standard curves of 5 × 10-fold serial dilutions of synthetic DNA (IDT gBlocks) for all primer sets, except for the primer pair for the Howardula normalizing primer set, which was tested using a dilution series of cDNA reverse-transcribed from Howardula-infected flies. Bases specific to sites of depurination are in bold, and deliberate mismatches are underlined.