Accessory Publication Table S1. Mean signal intensity for the complete set of microarray elements. Each element (i.e. probe) is identified by a unique identifier (UID). Clones that have a unique probe set identifier are singletons within our data set. Probes that have been assigned to a particular contig will be identified by a probe set identifier that is shared with other clones in the list. The number of clones within each probe set is listed in the column “count cDNAs in probe set”. The mean signal, standard error (se), and log 2 ratio for each of the 3 vertical stem segments (TOP, MID, BOT), are as shown, and “SAM FDR” is the local false discovery rate (%) in a multiclass test for differences in mean signal intensity between stem segments. Although up to 7053 cDNAs were deposited as microarray elements, only selected cDNAs were sequenced, thus microarray elements for which no sequence information is available are indicated by a dash: “- -”. All DNA sequences have been deposited in Genbank, as shown by the corresponding accession numbers UID annotation functional category probe set contig count GB accession DNA sequence mean signal TOP mean signal MID mean signal BOT se signal TOP se signal MID se signal BOT log log log SAM cDNAs ratio ratio ratio FDR in probe TOP/ TOP/ MID/ set BOT MID BOT 2932 26S proteasome amino acid & protein metabolism 5 singleton 1 EG974479 CTCAGATACTCAAAAGCTTTCTCTTTTCGTTCTCTCTTTGTTCCCCTCAGATTAACAAAAATGGG TCAAGGAACTCCCGGTGGTCTCAACCGTCAGGGTTTACCCGGAGATCGGAAACCTGACGGCGGCG ACGAGGGGGAGAAGAAGTTTGAGCCCGCGGCGCCGCCGGCTAGAGTTGGTCGCAAGCAACGGAAG CAAAAGGGTCCCGAAGCTGCGGCTAGGCTTCCGACTGTAACCCCTTTAACTAAGTGCAAGTTGAG GCTTTTAAAGCTTGAGCGAATCAAGGATTATCTGCTTATGGAGGAAGAGTTTGTTACTAATCAGG AGCGACTCAAGCCTCAGGAAGAGGAAGCTGAAGAGGATAGATCCAAGGTTGACGATCTTAGAGGT TCGCCTATGAGCGTTGGTAATCTTGAGGAGCTTATCGATGAGAGCCATGCCATCGTTTCTTCCTC TGTTGGGCCTGAGTATTATGTGGGGATTTTGTCTTTTG 23237.5 49896.04167 37769.41667 2797.645379 7271.02035 4380.048523 −0.7 −1.1 −0.4 0 2896 4-coumarate:coA ligase secondary metabolism 235 singleton 1 EG974522 TGAAGGTGCTCAAGAGTGGTGCCGCACCATTGGGGAAGGAGCTTGAAGACACGGTCAGAGCTAAG TTTCCCAACGTCACGTTAGGCCAGGGATATGGAATGACAGAGGCAGGGCGGGGGCTAACGATGTC GTTGGCATTTGCAAAGGAAGCTTTTGATGTAAAAGCTGGGGCTTGTGGAACTGTGGTAAGGAATG CAGAGATGAAAATTGTTGACCCTGAAACTGGTTCCTCTTTGCCACGTAATCAGCCTGGAGAGATT TGCATTAGGGGTGACCAAATCATGAAAGGTTATTTGAACGATCCAGAATCAACAAAGAATACAAT AGACAAAGAAGGATGGCTACACACAGGAGATATAGGGTTTGTGGATGATGATGATGAATTATTCA TTGTTGATCGATTAAAGGAGCTTATCAAGTACAAAGGCTTTCAAGTTGCCCCTGCTGA GCTCGAAGCTTTGC 22761.45833 112872.1667 72421.95833 3496.739079 16169.81587 7998.789118 −1.7 −2.3 −0.6 0.1 5167 50S ribosomal protein L24, chloroplast precursor [Arabidopsis thaliana] amino acid & protein metabolism 17 singleton 1 EG974474 GGGGAAGTGGAAGAAGAGATAACAAGGCGAACTCTGAGAATCCGAACCAAAGAAACAACGACGAT GGCAGCCATGGCTGCACTGCAAAGCTCCATGACCTCTTTTTCCCTAACCTCCAATTCCTTCTTGG GACAACGTCTCTCCCCAGCCACTCTCTGTATTGTGCCAATTAAGTCAACAGAGAAGCCATGTCTC ATTTCCGCAAAGCTTAAGCGATGGGAGCGGAAGGAGTGTAAGCCAAACAGTCTTCCTGTCTTACA AAAAATGCATGTTAAGGTTGGTGATACAGTGAAAGTAATATCTGGACGTGACAAGGGAAAAATTG GAGAGATAACCAAGATCTTCAAGCATAATAGTACAGTGGTAATATCAGAGATTAACTTAAAGACG AAACATGTGAAGAGCAGAGAAGAGGGTGAACCAGGACAAATAATCAAGATTGAAGCAC CCATCCATAGCTCCAATG 25670.125 14834.875 9153.541667 4029.317973 2634.208543 1124.807555 1.5 0.8 −0.7 0 5515 60S acidic ribosomal protein P0 amino acid & protein metabolism 12 singleton 1 EG974475 GTAAAGGTCTCTCTAGGGTTTCTTCCTTAAACCTTCTTTACTTTCCACATTATAGAGAGGTTAAA GGTCGGCGCTGCTCTTGCCGTCCGCCTTGATTAAGCTATAGCTGCTTCGTCTTGGCCCTCGATTT TGCTTTAACTCTAATATCCATTATCTTCCATTTTCAAACCCCAAATTTTCATAATGGGCAAGCTC TCAAAGGCCGAGAAGAAGATCAACTACGACTCCAAGCTATGCCAGCTTTTGGACGATTTCACCCA GGTTCTTATTGTGGCTGCTGACAATGTTGGATCTACCCAGCTCCAGAACATTCGTAAGGGTCTTC GTGGAGATTCAGTGGTGCTTATGGGTAAGAACACTATGATGAAGCGTTCAATCAGGATCCACTCT GAGAAGACAGGCAACCAGGCCTATCTCAATCTCATTCCCCTTCTTGTGGGTAATGTTGGTCTGAT TTTCACCAAGG 60725 60809.04167 30530.70833 10998.45954 10120.82706 2636.600507 1 0 −1 4.3 5407 ABC transporter 1 transport 259 contig 2 EG974566 GCGTGCTCGAGCAGGCAAAACTCTTGCACTTGTTGGGTCGTAGAACCGTTGTACCAATGCAATAA CCGAGCTCTTTCCACATCCACTAGGACCAACAAGTGCAAGAGTTTTGCCTGCTCGAGCACGAAGA CTTAAGTCACGGAAGACAGGGATATCAGGGCGAGAAGGGTAAGAGAAGTCTACATGCTTTAATTC AACTTCACCACGCAGCCGATCAGGAGCTGGTGTGGCATCTGGATCATCAGGTTCTATTGGATGTG GAAAGAGCTCGGTTATTGCATTGGTACAACGGTTCTACGACCCAACATCAGGCCGGGTTATGATT GATGGCAAAGACATTAGAAAATACAATCTCAAGTCCCTCAGAAAGCACATAGCTGTAGTGCCGCA GGAGCCATGCCTTTTCGCTACAACTATATATGAGAACATAGCTTATGGTCATGAGTCAGCAACTG AGGCTGAGATC 10704.625 23845.33333 14325.33333 1629.665614 4218.537568 2018.021705 −0.4 −1.2 −0.7 0 5609 ABC transporter 1 transport 259 contig 2 EG974568 GGCTCGAGCAGGCAAAACTCTTGCACTTGTTGGTCCTAGTGGATGTGGAAAGAGCTCGGTTATTG CATTGGTACAACGGTTCTACGACCCAACATCAGGCCGGGTTATGATTGATGGCAAAGACATTAGA AAATACAATCTCAAGTCCCTCAGAAAGCACATAGCTGTAGTGCCGCAGGAGCCATGCCTTTTCGC TACAACTATATATGAGAACATAGCTTATGGTCATGAGTCAGCAACTGAGGCTGAAATCATAGAAG CTGCAACTATGGCCAATGCTCACAAATTTGTATCTTCATTGCCTGATGGATACAAAACATTTGTT GGGGAAAGAGGAGTCCAGTTATCCGGGGGTCAAAAACAAAGAATCGCAATCGCTCGAGCATTATT GAGGAAGGCAGAGCTTATGCTGCTTGACGAGGCAACTAGTGCACTAGATGCTGAGTCTGAAAGAT CTGTTCAAGAGG 60976.20833 135760.0833 103112.4583 6890.786533 18070.8427 14004.97758 −0.8 −1.2 −0.4 0 6682 ABC transporter 2 transport 260 singleton 1 EG974567 CCGGTCCGGAATTCCCGGGTTCTTTAGGCGTCCGCACTCATGTTAGTTGCCTGCACAGCCGTATT TGTTCTGCACTGGCGTCTTGCCCTTGTCCTGGTAGCCGTCTTCCCTGTCGTTGTTGCTGCCACTG TCTTACAGAAAATGTTCATGACTGGTTTCTCTGGAGACCTTGAAGCTGCACATTCCAAGGCCACC CAACTAGCTGGGGAGGCCATAGCCAATGTAAGAACTGTAGCTGCCTTCAATTCAGAGGGAAAAAT AGTTGGTCTATTCACAACCAACCTCGAGGCTCCATTACGACGCTGCTTTTGGAAGGGTCAGATTG CTGGAAGTGGATTTGGGATAGCTCAGTTTGCACTTTATGCCTCTTATGCCCTTGGTCTTTGGTAT GCTTCGTGGCTTGTTAAACATGAGATCTCTGATTTCTCGAAAACTATCAGAGTTTTCATGGTCCT TATGGTGTCTGCCAATGGAGCAGCTGAAACATTGACCTTAGCTCCTG 37688.125 88601 57888.08333 4085.257055 10736.48542 8723.591286 −0.6 −1.2 −0.6 0 3039 acetoacyl-CoA-thiolase miscellaneous 163 singleton 1 EG974323 GAAAAGATAATTGATGGCATGCTTAAAGATGGCTTGTGGGATGTCTATAATGATTTTGGAATGGG AGTTTGTGCGGAGATATGTGCTGAAAAATATACTATCTCGAGAGAAGAACAGGATTCTTATGCAA TACAGAGCTTTAACCGAGGAATGGCTGCACAAAAAAATGGTTTATTTGCATGGGAAATAGCTCCC GTTGAAGTGCCTGGGGGGCGAGGGAAGCCATCCATAATTGTTGACAAGGATGAAGGTCTGGAAAA GTTCGATGCTGCAAAATTGAGAAAACTCAGACCGAGTTTCAAGCAGAACGGGGGCTCTGTTACGG CTGGCAATGCTTCTATCATAAGTGATGGTGCGGCTGCATTAGTCCTAGTGAGTGGAGAGAAAGCG CTTCAACTTGGATTGCACGTAATCGCAAAGATTAAGGGATATGCTGATGCAGCTCAGGCACCTGA ATTCTTCACAA 40023.25 11442.41667 9550.875 6471.978987 1979.436404 1535.502979 2.1 1.8 −0.3 0.1 4654 acetyl-CoA synthetase miscellaneous 117 singleton 1 EG974406 GCTAAATGGCAAGACGGAAGAGATGTATGGTGGCAGGATGTCATTCCTAAATATCCAACTGAGTG TGCAGTGGAGTGGGTTGATGCTGAGGATCCACTATTTCTGTTATACACTAGTGGTAGTACTGGAA AACCTAAGGGTGGTCTGCATACAACTGGAGGATATATGGTGTATACCGCAACAACATTCAAATAT GCATTTGATTATAAACCATCTGATGTATACTGGTGTACAGCTGACTGTGGTTGGATTACTGGGCA CAGCTATGTCTCTTATGGACCACTGCTCAATGGAGCATCTTGCATAGTTTTTGAAGGGGCTCCTA ATTATCCAGATTCAGGACGCTGTTGGGACATTGTAGATAAATACAAAGTAACAATATTTTACACT GCCCCTACATTAGTGCGATCCCTCATGCGCGATGGTGATGAGTATGTAACTCGCTACTCAAGAAA ATCCTTA 21938.08333 55625.875 33490.04167 3407.991501 8556.284934 3470.291186 −0.6 −1.3 −0.7 0 6855 actin-depolymerizing factor 1 miscellaneous 133 contig 4 EG974400 GCACTCATTTATCCATCTTTATCGTCCCCTTTCTTTCTCTCTCTCTCTCTCTCCCTCCCTGTCCT GAAGCCCTAGATTTTCTCTTCCCGATATTCTCTCGTCCAAAATGGCAAACGCTGCATCAGGAATG GCTGTCGATGATGACTGCAAGCTCAAGTTTCTAGAGCTTAAGACAAAAAGAAGTTATCGTTTCAT TGTCTATAAGATTGAGGAAAAGCAAAAGCAAGTTATGGTGGAAAAGCTCGGTGAACCAGCTCAGA GCTATGAGGAGTTTTCTGCTCTCCTTCCGGCCGATGAATGCCGATACGCTGTTTATGACTTTGAT TTTCTCACTGAGGAGAACGTACCAAAAAGCAGGATTTTTTTCATTGCATGGTCCCCTGACACAGC AAAGGTGAGAAGCAAGATGATTTATGCTAGCTCCAAGGACAGGTTCAAGAGAGAGTTGGATGGAA TTCAGATTGAG 213599.0417 413493.9583 278350.5417 26776.96931 54709.21354 27178.37555 −0.4 −1 −0.6 0
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