Supplemental Table A. The 50 most prevalent nuclear transcripts Identification Tag sequence Whole brain Lateral striatum Tag count Medial striatum Nucleus accumbens 148 102 116 99 56 84 57 69 46 77 12 58 36 48 14 55 18 53 39 Somatosensory cortex 81 99 54 64 102 70 50 35 22 37 103 39 35 32 32 32 17 26 27
Multiple matches (repeated motif) Ubiquitin B (X51703) Multiple matches (repeated motif) Cystatin C (AK002438) Calmodulin 1 (X61432) Multiple matches (repeated motif) Neurochondrin (BC017126) Ribosomal protein S29 (L31609) Myelin basic protein (M15060) Ribosomal protein S19 (AK013524) No reliable match Heat shock 70 kD protein 8 (M19141) Ribosomal protein L41 (AI851260) Ribosomal protein, large, P1 (U29402) Creatine kinase, brain (BC015271) Apolipoprotein E (M12414) Purkinje cell protein 4 (X17320) Ribosomal protein L3 (BC009655) Ribosomal protein S24 (X60289)
TGACTCCCTC TTTGCCGGCA TGACGCCCTC ATGCAGACTG AGAGAAGCAG TGATGCCCTC GCCAAGTTCA ATGCTAGTCT AGACAGTCTT GCTGGACAGG GGCCGGAGCA AATGATGAGG GCCTGGAGAA AATGCCCTCA GAAACTCTCT TTCCAGGCCC ACAGTCCTAG GCATTGCCAA TGCGGTGACT
119 89 84 74 81 75 44 89 77 30 39 49 43 37 56 27 19 29 56
96 85 56 82 78 72 72 38 55 25 27 24 28 33 25 24 77 19 12
132 95 79 59 55 52 102 57 76 54 36 32 47 31 46 33 36 40 29
Calcineurin catalytic subunit, alpha isoform (BQ176158) Ribosomal protein L11 (AK002998) ATPase, Na /K transporting, beta 1 polypeptide (X61433) Cytochrome c oxidase, subunit VIIc (X52940) Glyceraldehyde-3-phosphate dehydrogenase (M32599) Ribosomal protein S28 (U11248) Small nuclear ribonucleoprotein N (X62648) Proteolipid protein (myelin) (X07221) Carboxypeptidase E (X61232) Actin, gamma, cytoplasmic (M21495) Calmodulin 2 (BC021347) Cytochrome c oxidase, subunit VIa, polypeptide 1 (L06465) Multiple matches Multiple matches Ribosomal protein S23 (BC002145) Thymosin, beta 4, X chromosome (BC018286) Cytochrome c oxidase, subunit VIIIa (U37721) Ribosomal protein L26 (X80699) Neuron-specific 19 kD Golgi apparatus protein (U17259) Ferritin heavy chain (J03941) N-myc downstream regulated 4 (BC006595) Tubulin, alpha 1 or 2 (AI035721, W81977) Triosephosphate isomerase (X53333)
+ +
AAAGCATGCA CAAAAAGCTA TTGTGTCAGT TGAAAATTGG TGACGTGCCG TGCAACTGTT AAGCCAAAGA AAGGAAGGTG CTGGTAATGC TGTGCAGGGT AGGGAAGCAG TTCCATCCCT AAAAAAAAAA AAATAAAGTT ATAAAATTTG AAGTTTAAAT ATGTTATTCA GAGAAGATGC AACAAATCTT CCCACTTATG TGGCAGATGT AGTTAATTTG ATTTATGGAG
19 40 35 34 22 41 33 43 38 35 44 27 24 38 28 47 35 40 13 56 21 32 23
47 20 21 27 15 14 23 26 23 23 36 30 34 20 21 21 31 17 16 16 28 16 19
53 32 19 29 25 19 16 33 18 26 15 15 33 26 22 18 13 20 35 23 41 11 19
7 30 27 16 38 32 23 18 31 25 6 28 13 18 37 16 22 24 41 13 9 30 25
30 25 44 39 40 31 40 13 22 22 28 27 22 22 16 21 21 20 15 11 20 28 30
ATP synthase, H+ transporting mitochondrial F1 complex, beta subunit (AK011035) Neurogranin (AK002933) Ribosomal protein S12 (X15962) ESTs (AI267078) Synaptosomal-associated protein, 25 kD (BC018249)
2+
TCTCCATATC CCGGAGCCAA GAGAGGGCAA GTTCTCACCC TTCTACGTCT GAATTAAAGA TGCCGCAAGT
28 22 25 18 23 5 24 26
18 29 16 22 16 58 12 20
17 16 19 20 9 35 28 19
30 1 31 19 16 8 22 22
21 45 22 34 49 4 23 18
Phosphodiesterase 1B, Ca -calmodulin-dependent, 63 kD (L01695) AATAAAGAAG Reticulon 1 (BQ030824) Ubiquitin A-52 residue ribosomal protein fusion product 1 (AF118402)
Transcripts are displayed in decreasing order of the corresponding tag count in all five libraries, from n = 576 to n = 105.