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UV light for 24 hrs

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					                                                                                                                        Lilly, et al. Supplemental Data




                                      DNA microarray analysis of UV light for 24 hours treatment


  Complete medium = Cy3 (Green); UV treatment for 24 hours = Cy5 (Red)           Complete medium = Cy5 (Red); UV treatment = Cy3 (Green)




Averaged microarray data from TIGR multiple experiment viewer where green represents abundance lower in the UV treatment and red represents
abundance higher UV treatment, spot positions are noted next to image
row/column        1            2            3          4       row/column          1               2             3              4
      1                                                                  1     Blank           Blank          Blank         Blank
      2                                                                  2     b-ca-1          Lhcb5      SF assemblin     PNPase
      3                                                                  3     VSP1         Ferredoxin        lcha2      gametelysin
      4                                                                  4     mdh2             oee3           gdch         Lhca1
      5                                                                  5     SAC1        gamma tublin        GTR           VFL1
      6                                                                  6     PSAJ          25s rDNA        NAC2           SOD1
      7                                                                  7      psbZ            nad6          rbcS1          atpH
      8                                                                  8     psaC             rps7          rps12          atpE
      9                                                                  9      psbK            nad1           Actin         atpD
     10                                                                 10    ORF-50           rrn23           ccsA      ORF 2971B
     11                                                                 11     Blank           Blank          Blank         Blank
     12                                                                 12 cp peroxidase starch synthease    a-tub-1       Lhca-1
     13                                                                 13      rps2           AOX1            rps3         AOX2
     14                                                                 14    ORF140         Ubiquitin      ORF112          MBB1
     15                                                                 15      trnR             psbi     psbA-exon-4        psbT
     16                                                                 16      ADP           ORF271            rpl5          trnT
     17                                                                 17     rps18           Sigma          psbN           Nrt2
     18                                                                 18      psbJ             rrn5          rps9          petC
     19                                                                 19      oee1           rbcS2           petE           cob
     20                                                                 20     ycf10           psbC            cox1        ORF-50
     21                                                                 21     Blank           Blank          Blank         Blank
     22                                                                 22      raa3            mut6         ac115           cox3
     23                                                                 23      atpF            psbL           psbF        trnfMet
     24                                                                 24      rpoA             ycf4          trnE          petB
     25                                                                 25     aaDA        RPOB1 cDNA          GFP           psaD
     26                                                                 26      psaB         ORF1995      RPOB2 cDNA         nad2
     27                                                                 27     rrn16            tscA           psaF          ycf12
     28                                                                 28      clpP            trnW          rrnL7          petD
     29                                                                 29      rpl2             Cao           petA           atpI
     30                                                                 30      atpB          rpoC1b       ORF 2971A         Ars1
     31                                                                 31     Blank           Blank          Blank         Blank
     32                                                                 32 Calmodulin            Lci5          Eye2          Mat3
     33                                                                 33      rpl14            ycf3          petL          petG
     34                                                                 34      rpl16           psbE           oee2          PSR
     35                                                                 35      atpA            atpC           Nar1          cab2
     36                                                                 36      rbcL            nad4           chlB          psbD
     37                                                                 37      psaA           psaG           psbM           psbH
     38                                                                 38       trnS         rpoC1a          rrnS4          rpl20
     39                                                                 39   psbA-ex2           chlN           chlL            rt1
     40                                                                 40       tufA           psbB           nad5         rpoC2
                                                                                                            Lilly, et al. Supplemental Data



Raw values from two dye-swapping replicates of control cells versus UV treatment (254nm) for 24 hr
               Rep 1 Cy3 Rep 1 Cy5                                           Rep 2 Cy3     Rep 2 Cy5
Gene           Complete UV treatment                           Gene          UV treatment Complete
b-ca-1            543814      1567250                          b-ca-1              2930009        2963812
Lhcb5            9573410      8271101                          Lhcb5                249954        1028786
SF assemblin     1321645       768878                          SF assemblin         905011         869317
PNPase            642665       447055                          PNPase               430865         839529
VSP1             3306342       861951                          VSP1                 734662        2151521
Ferredoxin       2201680      1752037                          Ferredoxin           989307        3182926
Lhca2            1416315       681156                          Lhca2                754687        1172395
gametelysin            0            0                          gametelysin               0              0
mdh2             1709999       935483                          mdh2                 351480        1174711
oee3             2532433       706933                          oee3                 769289        4369028
gdch              189934       178239                          gdch                 337576         618355
Lhca1            3082392      6459517                          Lhca1                262375        1100344
SAC1             3565079      1459625                          SAC1                1222477        2111342
TBG1                   0            0                          TBG1                      0              0
GTR              5349611      3078447                          GTR                 2696830        2775100
VFL1              507905       841696                          VFL1                 891568        1405324
PSAJ            14057407      3757648                          PSAJ                2011946        2678778
25s rDNA         1042142       937289                          25s rDNA             370507        1034195
NAC2             3773528      1001103                          NAC2                1443146        1996539
SOD1              797749       879870                          SOD1                 677814        1321659
ycf9             6403927      3605300                          ycf9                1329368        1545481
nad6             7142778      8333816                          nad6                1327210        1593945
rbcS1             520322       961167                          rbcS1               1044474        1314866
atpH             1527470      1336898                          atpH                2753238        2418028
psaC             1347262       795585                          psaC                 770611        1003253
rps7                   0            0                          rps7                      0              0
rps12            1070111      1245846                          rps12               1580668        2003568
atpE             1055611      2428623                          atpE                4822032        5636880
psbK             1035577       813979                          psbK                 488075         887048
nad1             5248485      7823033                          nad1                1260241        1435617
Actin            3531302      1856257                          Actin               1978242        3298376
atpD             1003678      3229621                          atpD                5193660        5733574
ORF-50           2456611      2476972                          ORF-50              2830469        3425035
rrn23             692922       912705                          rrn23                389532         761873
ccsA             1516483      2701000                          ccsA                6300323        1637648
ORF 2971B        4488584      1006927                          ORF 2971B           2590880        2122777
cp peroxidase    5349611      3078447                          cp peroxidase       2696830        2775100
starch synthease 4684563       969845                          starch synthease    2462237        1963928
a-tub-1          2718390      4108366                          a-tub-1              388198        1463438
lcha-1           2889486      1396760                          lcha-1              1071053        6824783
rps2             1397058      1114279                          rps2                 445034         815454
AOX1             2794400      1666527                          AOX1                2079155        2207074
rps3             8619908      4818651                          rps3                6734496        8913669
AOX2             1371763       589109                          AOX2                 861421        1242536
ORF140           7631466      2668221                          ORF140              5712086        6614439
Ubiquitin        1374893      1307133                          Ubiquitin           1695883        2081832
ORF112            906435      1069444                          ORF112               905669        1217818
MBB1                   0            0                          MBB1                      0              0
trnR             3197823      2057924                          trnR                2268496        2816716
psbI             5778290      3588004                          psbI                2424976        4449683
psbA-ex-4         525846       602083                          psbA-ex-4            709394         652527
psbT                   0            0                          psbT                      0              0
ADP                    0       359898                          ADP                  388798         363172
ORF271          10327978      9118744                          ORF271              1601056        3034419
rpl5                   0            0                          rpl5                      0              0
trnT                   0            0                          trnT                      0              0
rps18            1513457      1156028                          rps18                962553        1066515
Sigma-1          4433339      2414974                          Sigma-1             2071498        6542977
psbN             5358503      6340969                          psbN                8137905        5929053
Nrt2              921421       662960                          Nrt2                1029627        1184122
psbJ             5587465      1085658                          psbJ                1440838        1667041
rrn5             8133784      4278004                          rrn5                7157363        7726144
rps9                   0       333392                          rps9                 353656         480827
petC             2219639      6002889                          petC                3683637        4986767
oee1             8537320      3521934                          oee1                 491150        1393741
rbcS2             951675       722925                          rbcS2                558077         936879
petE              884415      1523818                          petE                 532134        1458255
cob               737893      1072752                          cob                 1680484        1589842
ycf10            5852415      6670429                          ycf10                946792        1230864
psbC              977964      1649404                          psbC                 665123         844395
cox1             3226079      3436133                          cox1                1300586        1451557
ORF-50           2593657      2777255                          ORF-50              6254460        7756452
raa3             3519671      2561648                          raa3                3111597        4793069
mut6             6647522      5816440                          mut6                4489715        9920705
ac115            3592965      1838007                          ac115               1088616        1917048
cox3             2199120       858138                          cox3                 885860        2703472
atpF             3045879       434673                          atpF                 933749         943699
psbL                   0            0                          psbL                 105365         259171
                                                                     Lilly, et al. Supplemental Data




psbF          3367517   2657643   psbF          3209444    3913543
trnfMet       3748722    378118   trnfMet             0          0
rpoA          4775059   1045430   rpoA          2292373    6107526
ycf4          7559799   6279230   ycf4          5579360    6072079
trnE           719247    418799   trnE          1156795     839155
petB           874897    948145   petB           974427    1129531
aaDA           344670    343870   aaDA           190245     242906
RPOB1 cDNA     775498    850561   RPOB1 cDNA     656434     843371
GFP                 0         0   GFP                 0          0
psaD          7015531   5824300   psaD          1635360    4665158
psaB          1367229    849505   psaB          1180410    1802060
ORF1995       8972702   3031967   ORF1995        852567    1478434
RPOB2 cDNA   10195854   1705542   RPOB2 cDNA     977537    2375637
nad2          4493708   5038139   nad2          6551837    9197193
rrn16          797373    971349   rrn16          902816    1199457
tscA          1045019   1026219   tscA         11458849    9551453
psaF          2253168   1388019   psaF          2013080    5202441
ycf12          179474    642392   ycf12         1149231    3448588
clpP           274465    232513   clpP           352828     255179
trnW          5407867   1389894   trnW          4821449    2073545
rrnL7          527318   1017601   rrnL7         5301429    7569112
petD           941444    794365   petD           886967     983700
rpl2          5054269   4012062   rpl2           580728    1000470
Cao            400221    173721   Cao            609102     617352
petA          4810799   4490496   petA           526501     687506
atpI                0         0   atpI                0          0
atpB          2784054   3150384   atpB          1256207    8998214
rpoC1b        4529272    979576   rpoC1b        1090768    4728813
ORF 2971A     6883836   1136378   ORF 2971A     4897125    3270958
Ars1          1902973    786682   Ars1          2021118    2052716
Calmodulin    1647041   1099933   Calmodulin    2255501    6329603
Lci5          1213068    463289   Lci5          1398109    2048193
Eye2          1012565    850077   Eye2          1685215    2107592
Mat3          6385223   1037038   Mat3          1438998    1813610
rpl14        10119699   3481912   rpl14         7249844    7327673
ycf3          9785980   3939165   ycf3         12010478   10236441
petL         10503707   6275303   petL          7937381    8365927
petG          4420142   1934898   petG          5140402    3286387
rpl16         9579294   3394054   rpl16         8748352    8535795
psbE          4015602   1436491   psbE          5772313    3491789
oee2          9247106   5870429   oee2           882466    1291748
PSR           8323092   5891139   PSR           8741937    7223579
atpA          4498505   4141344   atpA           443527     487179
atpC           719223   1540199   atpC          1567996    1774026
Nar1           959956    414196   Nar1           851547     531618
cab2          6766088   5541237   cab2           602986    1194314
rbcL          5094862   6680180   rbcL          4885930    6256686
nad4          4954052   6771306   nad4          2309652    2740662
chlB          8524805   7477394   chlB         11660556    9690048
psbD           863821   1005205   psbD           538215     641264
psaA           817273    976603   psaA          5633392    1675419
psaG          1833655   2184480   psaG          1912810    9858123
psbM          4673763   3114581   psbM           827675    1103263
psbH          2348745   2638635   psbH          1495999    2299627
trnS          3151304   1136399   trnS          1550352    1673485
rpoC1a        8712112   1837131   rpoC1a        1361553    2233433
rrnS4          666989    801173   rrnS4         2616654    5198656
rpl20               0         0   rpl20               0          0
psbA-ex2       553811    651414   psbA-ex2       350323     391510
chlN          1126843    947851   chlN           613636     715412
chlL          1386352    740413   chlL          1500705     393964
rt1           4444109   2945846   rt1           6444840    3581632
tufA          9452908   1604692   tufA           173464     759595
psbB          1050637    861030   psbB           664369    1002466
nad5          2943954   3450872   nad5          6062564    8025971
rpoC2         1667862    307689   rpoC2          369961    1650103

				
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