Table 1. Read mapping and base coverage for RNA-Seq data.

Sequences from NAc libraries were aligned to the Mus musculus reference genome (2007, mm9; NCBI Build 37) using Bowtie (Langmead et al., 2009) and allowing up to 2-mismatches. (A) Aligning read numbers and percent coverage of the genome. (B) Reads were characterized as aligning to exonic, intronic, or intergenic regions based on the existing annotation.

A. High-throughput sequencing alignment information
Sample	Treatment	Number aligning reads	Total genome coverage
NAc lysate	Saline	26,563,428	5.8%
	Cocaine	24,696,981	5.8%
	Withdrawal	19,767,382	5.1%

B. Read mapping
Sample	Treatment	Exonic	Intronic	Intergenic
NAc lysate	Saline	79.4%	15.5%	5.1%
	Cocaine	79.0%	16.1%	4.9%
	Withdrawal	79.0%	16.2%	4.8%