P12-CA experiment
The PCR products were amplified with the following forward and reverse primers in separate reactions, and then pooled.  Forward . Reverse . sample(comment) ACTGAGACGCACTCGGACACTGACATGGACTGAAGGAGTA .  TCAGGCTCATAGTCTTGGTAGCCTTC . 2983-68C7 transgenic mouse mesencephalon (SNCA 5' RACE (oligo-dT and random primers))  ACTGTCTCTATGCGGAATCGGAGTTCTTCAGAAGCCT .     CGCTACGTAACGGCATGACAGTG . 2983-68C7 transgenic mouse mesencephalon (SNCA proximal exon 3' RACE (oligo dT))  ACTGACGAGTGCGTggAAgAAgAgTCTgTTCgCTggAg .      CGCTACGTAACGGCATGACAGTG . 2983-68C7 transgenic mouse mesencephalon (SNCA distal exon 3' RACE (oligo dT))  ACTGTACTGAGCTAGGGGTTGGGGATTTAGCTCAGTGGT .  CGCTACGTAACGGCATGACAGTG . 2982-68B7 transgenic mouse brain ( BC1 3' RACE ( random primers ), total brain)  ACTGTGATACGTCTGGGGTTGGGGATTTAGCTCAGTGGT .  CGCTACGTAACGGCATGACAGTG . transgenic mouse brain (BC1 3' RACE (oligo dT) total brain)  ACTGCGTGTCTCTAGGGGTTGGGGATTTAGCTCAGTGGT . CGCTACGTAACGGCATGACAGTG .  2983-68C7 transgenic mouse mesencephalon(BC1 3' RACE (random primers), midbrain )  ACTGCTCGCGTGTCGGGGTTGGGGATTTAGCTCAGTGGT .  GCGCGAAATTAACCCTCACTAAAGGGAG . 2980-68I6 transgenic mouse cerebellum ( BC1 3' RACE (oligo dT),cerebellum )  ACTGTAGTATCAGCGGGGTTGGGGATTTAGCTCAGTGGT . GCGCGAAATTAACCCTCACTAAAGGGAG .  2980-68I6 transgenic mouse cerebellum ( BC1 3' RACE (random primers), cerebellum)  ACTGACGCTCGACAGGGGTTGGGGATTTAGCTCAGTGGT . GCGCGAAATTAACCCTCACTAAAGGGAG . 2981-68A7 transgenic mouse mesencephalon (BC1 3' RACE (oligo dT), midbrain)  The 454 adapters were ligated to PCR products, therefore the sequencing is not directional and the 454 reads can start with either PCR primer sequence.  When the reads are long enough, they may end with the reverse complement of either primer sequence.  454 sequencers generate mismatches and indels, and therefore not all reads will match perfectly.