Table 1. Fusion gene count and its fold expression relative to nearest control locus.

The genes involved in the fusions are shown; for Klc1 and Arhgef10 the different fusion events are shown independently. Average read counts identified by RNA-seq in each of the 3 independent replicates from either saline or cocaine-treated animals is presented. The expression level of the fusion relative to the nearest control locus (same exon) for saline- and cocaine-exposed animals, respectively, was estimated by qRT-PCR using primers that amplified the repeat-exon junction or the junction between the same exon with the nearest canonical adjacent locus (exon). For more details see Methods. Average fold-change between saline- and cocaine- treated samples, and total standard error are shown; NA = not analyzed. In italic and bold are the 3 genes that are expressed at similar or higher levels than the non-fusion counterpart. Last column represents the results as the ratio of non-fusion over fusion gene expression; i.e. for every 1 transcript of non-fusion Atp2b1 there are 40 transcripts expressing the fusion isoform.

	Mean fusion gene count		Fold expression relative to nearest control locus				Wild-type/fusion ratio
Fusion gene	saline	cocaine	saline	cocaine	total mean	total se
Atp2b1	595.3	621.3	40.006	38.952	39.479	1.495	1:40
Klc1 fusion A	64.7	58.3	0.274	0.273	0.273	0.007	4:1
Klc1 fusion B	117.0	127.0	0.325	0.333	0.329	0.007	3:1
Klc1 fusion C	276.0	269.3	0.524	0.526	0.525	0.015	2:1
Elfn2	31.0	28.0	0.058	0.053	0.056	0.002	18:1
Macf	21.3	28.0	0.528	0.541	0.535	0.012	2:1
Celf2	155.3	157.0	10.527	10.408	10.467	0.340	1:10
Srrm2	44.0	50.3	0.149	0.144	0.146	0.006	7:1
Pgc1α	5.3	4.0	1.187	1.155	1.171	0.038	1:1
Arhgef10 fusion A	1.0	3.0	0.024	NA	0.024	NA	42:1
Arhgef10 fusion B	0.0	0.7	0.007	NA	0.007	NA	143:1