Spreadsheet: 013a79cc-3212-47b7-a9de-f2e82917a147
Sheet: Sheet1

Additional File 3. Secondary qRT-PCR screen of selected transcription-factor genes. | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6 | Unnamed: 7 | Unnamed: 8 | Unnamed: 9 | Unnamed: 10 | Unnamed: 11 | Unnamed: 12 | Unnamed: 13 | Unnamed: 14 | Unnamed: 15 | Unnamed: 16
 |  |  |  |  | RNA source: e |  |  | RNA source: f |  |  | RNA source: g
AGI | Forward primer (5'-3') | [NAME] (5'-3') | Amplicon size (bp) |  | Normalized CT, ms1 | Normalized CT, [NAME] |  | Normalized CT, ms1 | Normalized CT, [NAME] |  | Normalized CT, ms1 | Normalized CT, [NAME] |  | Average CT, ms1 | Average DDCT | P (t-test)
AT1G01530 | ACACAACAACACAAACTTTGC | GAGAGTTCCTCCACCACTTC | 170 |  | 32.5676746929761 | 36 |  | 32.7813510096218 | 35.92834337803509 |  | 32.0764160091623 | 34.0052246221133 |  | 32.4751472372534 | 2.836042096129399 | 0.01271157787373221
AT1G04370 |  |  |  |  | 33.80879717564351 | 36 |  | 34.1107492662736 | 34.3497111562521 |  | 33.275358855333 | 34.1744226186562 |  | 33.73163509908337 | 1.109742825886068 | 0.09627607631749695
AT1G06160 |  |  |  |  | 32.6619365419235 | 32.8061956435686 |  | 31.7873611682285 | 36 |  | 31.185178377034 | 32.5993223945901 |  | 31.87815869572866 | 1.923680650324236 | 0.1252912041339741
AT1G21970 |  |  |  |  | 29.4155002790862 | 34.1506737145691 |  | 30.2277753684834 | 33.8567217917098 |  | 30.1793075607686 | 30.9178299584933 |  | 29.94086106944607 | 3.034214085477996 | 0.0628770601023083
[NAME] | CCATCCTTGATTGCGTTATCG | GCACCAGCTTCAGTAAACAG | 106 |  | 35.7700997110613 | 35.80858815107661 |  | 36 | 36 |  | 35.2592351487925 | 36 |  | 35.6764449532846 | 0.2597510970742671
AT1G28160 |  |  |  |  | 29.9027466916547 | 35.0486096181537 |  | 36 | 36 |  | 36 | 36 |  | 33.96758223055156 | 1.715287642166335 | 0.2113248654306008
AT1G30670 |  |  |  |  | 34.9865535801096 | 35.5366384483105 |  | 34.7416564958673 | 34.74866173792461 |  | 36 | 36 |  | 35.2427366919923 | 0.1856967034194028
AT1G34410 | ACTCTGGACACTCCTCCG | ACTGCTTGCTTTGGATCTCTA | 133 |  | 36 | 36 |  | 36 | 36 |  | 36 | 36 |  | 36 | 0
AT1G35240 | GGAGTCTCTCTAGCCATTCCTCTA | CCACAGCTCTTCCTATTGTTAC | 202 |  | 36 | 36 |  | 36 | 36 |  | 36 | 36 |  | 36 | 0
AT1G35520 | CTCCCCGATGAATATTTCTCTTCT | GTTTGGGCATTGGTTGGACA | 101 |  | 33.6920868710966 | 36 |  | 32.6598730175879 | 36 |  | 33.0901518516157 | 35.1039617202018 |  | 33.14737058010007 | 2.553949993300535 | 0.0119544735952771
AT1G35540 |  |  |  |  | 35.5522455964911 | 36 |  | 34.9070006780269 | 36 |  | 36 | 36 |  | 35.48641542483934 | 0.5135845751606638
AT1G43160 |  |  |  |  | 36 | 29.4520838957197 |  | 35.9258360685795 | 32.5479740398129 |  | 36 | 33.5473416939869 |  | 35.9752786895265 | -4.126145479686666
AT1G49120 |  |  |  |  | 32.5657137346208 | 35.0473418652472 |  | 33.010011304014 | 33.35226561417321 |  | 33.8479719310202 | 33.30504879644489 |  | 33.14123232321833 | 0.7603197687367688
[NAME] |  |  |  |  | 35.63375851755779 | 36 |  | 33.5901469737882 | 36 |  | 33.9553461424917 | 36 |  | 34.39308387794589 | 1.606916122054102 | 0.06259091182885923
AT1G49900 |  |  |  |  | 36 | 36 |  | 36 | 36 |  | 36 | 36 |  | 36 | 0
AT1G55600 | GTATCAAACATGATTGGAGCCAC | TTTGACGACTTTCTGACCGTATT | 126 |  | 32.6726557746193 | 35.9584126947551 |  | 31.0627017112707 | 35.6017566930396 |  | 32.3701501675929 | 35.7904630824888 |  | 32.03516921782764 | 3.74837493893353 | 0.005522753024316281
AT1G55650 |  |  |  |  | 36 | 36 |  | 36 | 34.3088850992733 |  | 35.1487489288096 | 36 |  | 35.71624964293653 | -0.2799546098454281
AT1G56650 | AGAGACATTACGCCCATTCCTA | TTGAGATGGTTGCAGTCGTT | 101 |  | 25.5182902888149 | 29.0992526757749 |  | 25.5097321182316 | 25.7155598782716 |  | 24.3236795381583 | 27.3055567439706 |  | 25.11723398173494 | 2.256222450937432 | 0.08109980399655276
AT1G59940 |  |  |  |  | 30.9166005219581 | 30.8062218738556 |  | 32.0402971945801 | 31.6279315089318 |  | 31.3359972882095 | 31.6031673468178 |  | 31.43096500158256 | -0.08519142504750003
AT1G60280 |  |  |  |  | 30.7454215360151 | 35.5645494996904 |  | 31.6416394519315 | 36 |  | 31.3772480755819 | 35.0741997351641 |  | 31.25476968784283 | 4.291480057108665 | 0.00285475143677068
AT1G66390 |  |  |  |  | 32.4304293114437 | 36 |  | 29.8837038783641 | 30.9088947600248 |  | 28.3979951594912 | 34.8325741836505 |  | 30.237376116433 | 3.676446864792098 | 0.07144898118155292
AT1G67030 |  |  |  |  | 31.806574478265 | 33.0217102334529 |  | 31.1327058228984 | 34.21875417090629 |  | 31.7846278688536 | 34.7589464366176 |  | 31.57463605667233 | 2.425167556986596 | 0.0285594733314143
AT1G68880 |  |  |  |  | 30.6257083823777 | 31.0141040583266 |  | 30.7103426243081 | 30.2181864878517 |  | 31.5073039128227 | 30.1322561344686 |  | 30.9477849731695 | -0.4929360796205356
AT1G69490 |  |  |  |  | 29.1514749211702 | 25.5777770882071 |  | 29.0213815366263 | 28.3079218109681 |  | 30.6293090855292 | 27.1691408283789 |  | 29.60072184777523 | -2.582441938590533
AT1G71692 |  |  |  |  | 33.3860272409793 | 32.4424220950085 |  | 32.6895498314873 | 31.5849415019815 |  | 32.949387201064 | 31.8848970185043 |  | 33.0083214245102 | -1.037567886012098
AT1G75250 | CAAGAAGTTCAATCTCACCATGGA | GAGAATGTCATAGTGGCGCT | 158 |  | 33.9524666702176 | 36 |  | 34.1188746900392 | 36 |  | 34.80702426184421 | 36 |  | 34.29278854070034 | 1.707211459299664 | 0.01133935442312689
AT1G75490 |  |  |  |  | 27.5520872705125 | 26.3521893180714 |  | 28.0932978597523 | 28.0991813937783 |  | 28.1542761749516 | 28.0425672117109 |  | 27.93322043507213 | -0.4352411272185973
AT1G79700 |  |  |  |  | 25.1295104701216 | 22.8839945292127 |  | 25.4214019097807 | 25.8437516385636 |  | 26.3120878297217 | 24.9041664936834 |  | 25.62100006987467 | -1.077029182721435
AT2G22750 |  |  |  |  | 34.9841000961041 | 34.9168635604924 |  | 34.1153098956668 | 35.4665626803576 |  | 34.88891639335259 | 36 |  | 34.66277546170783 | 0.7983666185755022
AT2G24840 |  |  |  |  | 31.3883294389007 | 35.4342339993033 |  | 31.7208330249552 | 36 |  | 32.626032653978 | 36 |  | 31.91173170594464 | 3.899679627156468 | 0.002403327201401212
AT2G26880 | TCTAGACGTTGAGAGAGCTAGGA | TGAAGTTTCATACCCAATTTGCTG | 160 |  | 36 | 36 |  | 36 | 36 |  | 36 | 36 |  | 36 | 0
AT2G31180 |  |  |  |  | 36 | 34.1792951419302 |  | 34.9317865703827 | 33.46718790582089 |  | 36 | 36 |  | 35.64392885679423 | -1.095101174210536
AT2G33710 |  |  |  |  | 34.5428860222805 | 35.9711200520461 |  | 34.257269760471 | 36 |  | 33.5978691607303 | 35.2540688863667 |  | 34.1326749811606 | 1.609054664977002 | 0.001690459864699795
AT2G37260 |  |  |  |  | 26.4463609721669 | 26.1749168424749 |  | 26.2147083165066 | 26.1228434027244 |  | 27.935767283379 | 26.5115675818119 |  | 26.86561219068416 | -0.595836248347099
AT2G40220 |  |  |  |  | 30.7021213896857 | 36 |  | 31.0223423716819 | 36 |  | 31.7113435716374 | 33.2119101360193 |  | 31.14526911100167 | 3.925367601004766 | 0.04201656031987547
AT3G01030 |  |  |  |  | 33.16201534502341 | 34.9969200087283 |  | 32.4432414438624 | 33.70024815296441 |  | 33.1213777449987 | 34.3087432812159 |  | 32.9088781779615 | 1.426425636341366 | 0.01003929817315364
AT3G03260 |  |  |  |  | 32.9074805372169 | 33.9016072916057 |  | 33.1411483546668 | 31.8394228031149 |  | 31.8720674692888 | 34.2244625383095 |  | 32.64023212039083 | 0.6815987572858676
AT3G13540 |  |  |  |  | 26.7430868919395 | 26.5496495606126 |  | 26.5685636769458 | 26.4551859065446 |  | 26.8714293069668 | 26.730121430107 |  | 26.7276932919507 | -0.1493743261959667
AT3G15270 |  |  |  |  | 23.574636742785 | 24.4598015286836 |  | 23.4052545779501 | 23.4716010497102 |  | 23.0927143451983 | 23.5964338427407 |  | 23.3575352219778 | 0.4850769184003643
AT3G17100 |  |  |  |  | 23.7564827682996 | 23.7807235906348 |  | 23.8356339586478 | 23.8327019074813 |  | 24.1458920689485 | 24.0827492571972 |  | 23.91266959863196 | -0.01394468019419885
AT3G25790 |  |  |  |  | 35.9949882753674 | 36 |  | 36 | 36 |  | 36 | 36 |  | 35.99832942512247 | 0.001670574877531787
AT3G26790 |  |  |  |  | 32.7180316120576 | 33.4547144601331 |  | 32.11040002565259 | 31.0517101697963 |  | 33.5270835209899 | 34.7163055346265 |  | 32.7851717195667 | 0.2890716686186015
AT3G27785 | ATTGGTCCAAGAAACATGAGAG | CATAGCCGCCAATGACG | 150 |  | 36 | 36 |  | 36 | 36 |  | 36 | 36 |  | 36 | 0
AT3G30210 |  |  |  |  | 36 | 33.77029821694489 |  | 36 | 33.8196772304605 |  | 36 | 33.648819984087 |  | 36 | -2.253734856169203
AT3G50330 |  |  |  |  | 36 | 36 |  | 36 | 36 |  | 36 | 36 |  | 36 | 0
AT4G00540 | TCAGTAGACTCAGTTTGTGCAAG | ATAATGGAGGGTGTGTCGAA | 146 |  | 32.07487248921321 | 36 |  | 33.2600857714575 | 36 |  | 33.6087151350008 | 35.5697001429459 |  | 32.98122446522384 | 2.875342249091467 | 0.01862507126208882
AT4G05170 |  |  |  |  | 36 | 36 |  | 36 | 36 |  | 36 | 36 |  | 36 | 0
AT4G28811 |  |  |  |  | 36 | 36 |  | 36 | 36 |  | 36 | 36 |  | 36 | 0
AT4G38070 |  |  |  |  | 32.6277388594766 | 35.5737111476478 |  | 33.4985846330808 | 34.8564312846387 |  | 33.6565714224181 | 36 |  | 33.2609649716585 | 2.215749172437005 | 0.02048833534687686
AT5G01380 |  |  |  |  | 28.1647637138815 | 28.9244216984 |  | 27.9099113199244 | 27.2785923483967 |  | 27.8262973604378 | 27.8915625712381 |  | 27.96699079808123 | 0.06453474126370295
AT5G01860 |  |  |  |  | 28.6137712701304 | 31.8237991188138 |  | 28.7185944727064 | 31.6430260002412 |  | 29.1511390617469 | 31.6647209762667 |  | 28.82783493486123 | 2.882680430246003 | 0.002440278582839377
AT5G11050 |  |  |  |  | 27.4933521521564 | 31.4046880008221 |  | 27.2290889919379 | 31.6989382922306 |  | 27.716175195339 | 31.8752810894286 |  | 27.4795387798111 | 4.180097014349331 | 0.0007453287756822681
AT5G15830 |  |  |  |  | 34.0976769308366 | 33.816082366524 |  | 36 | 35.03782541750969 |  | 34.8741098995028 | 34.0357722188004 |  | 34.99059561011313 | -0.6940356091684331
AT5G27880 |  |  |  |  | 28.9162687584943 | 36 |  | 29.1194692704205 | 35.4781055987589 |  | 28.8411762528703 | 35.27671825369269 |  | 28.9589714272617 | 6.625969856888834 | 0.0006011357790074573
AT5G35550 | AAGAATCATTGGAACTCAAACCTC | CATACATTATTCTCGTTGTTCGTCG | 101 |  | 29.3552960846172 | 30.7902405717234 |  | 28.7364087698101 | 28.3836500168824 |  | 28.5846886027733 | 28.9166941641032 |  | 28.8921311524002 | 0.4713970985027984
AT5G39700 | AGAGGAGAAGAAGAAGAAACATAGG | TAATCTTCGGATCGAGCTGGTTAAA | 179 |  | 36 | 36 |  | 36 | 36 |  | 36 | 36 |  | 36 | 0
AT5G41090 |  |  |  |  | 26.5390477107475 | 30.0472632338897 |  | 26.0250998111884 | 30.3174088344657 |  | 26.4023095098471 | 30.0205474978135 |  | 26.32215234392767 | 3.806254178128635 | 0.002060387499200287
AT5G41200 |  |  |  |  | 36 | 36 |  | 36 | 36 |  | 36 | 36 |  | 36 | 0
AT5G42640 | GTGTAACGGTGTGTTTGATACTT | TATTTCTTGCACGAAATCTTTGGT | 107 |  | 36 | 36 |  | 36 | 36 |  | 36 | 36 |  | 36 | 0
AT5G45980 |  |  |  |  | 32.8137085850955 | 35.561493153046 |  | 33.72810196467761 | 35.6061350980926 |  | 33.7380171383622 | 36 |  | 33.42660922937844 | 2.295933521001103 | 0.005900650932510329
AT5G50490 |  |  |  |  | 35.7331752793411 | 34.9162882210675 |  | 36 | 36 |  | 34.7825712875516 | 34.8033362651301 |  | 35.5052488556309 | -0.265374026898364
[NAME] |  |  |  |  | 36 | 35.1752756353449 |  | 36 | 35.1733947491989 |  | 35.7045563588694 | 34.3546716680481 |  | 35.9015187862898 | -1.000404768759168
AT5G54070 | TTTGGTGAACAATCAAAGCGG | TTGCTCTACTCTATCTCTATCCTCC | 111 |  | 32.1110828684517 | 36 |  | 30.9150805837705 | 35.6775423324257 |  | 31.9092890874541 | 36 |  | 31.64515084655876 | 4.247363264249803 | 0.001921369121295128
AT5G55690 |  |  |  |  | 34.8556465095008 | 31.0541386822891 |  | 35.1888905454543 | 34.50088974107881 |  | 36 | 33.8917266158637 |  | 35.34817901831837 | -2.199260671907832
AT5G56200 | TCATCCACTTGGTAATTCATCGTC | TCCAATTCCAAATTACTGTCCCAT | 150 |  | 32.5123969435197 | 36 |  | 31.6435659058166 | 33.6125444173024 |  | 31.9396365154973 | 34.3535011921622 |  | 32.03186645494453 | 2.623482081543671 | 0.01413659464326126
AT5G58010 |  |  |  |  | 36 | 36 |  | 34.8648532700023 | 36 |  | 36 | 34.7782291100793 |  | 35.62161775666743 | -0.02887471997433029
AT5G58850 |  |  |  |  | 27.7016326995362 | 30.4010523543786 |  | 27.5799998403119 | 28.9749080205018 |  | 27.9201852306164 | 30.5035063862615 |  | 27.7339392568215 | 2.225882996892464 | 0.01666308078920354
AT5G59780 | AGAGAAGAAGCGACCTATGT | CCGTCTTCGCATTCTTGATT | 126 |  | 31.0461798370647 | 28.9931956889791 |  | 30.5998432196253 | 30.5329699690932 |  | 31.2026590883991 | 30.5307612811024 |  | 30.9495607150297 | -0.9305850686381317
AT5G61890 |  |  |  |  | 29.0458981939951 | 33.0985753733857 |  | 28.8644172536923 | 31.1367298724859 |  | 29.0625338331994 | 31.9379243395373 |  | 28.9909497602956 | 3.066793434840701 | 0.01392507439631085
The mRNA levels of 69 transcription-factor genes identified in the primary qRT-PCR screen (DDCT >1.5; Additional File 1) were analyzed using three additional pairs of ms1-dif1 RNAs (e-g; Additional File 9). The AGI numbers are listed in ascending order along with the sequence and amplicon size of the 17 primer-pairs re-designed for the secondary qRT-PCR screen (the remaining primers were as described in Additional File 1). Normalized CT values were calculated as described in Methods. A one-tailed, paired Student's t-test was performed for genes with average DDCT values above 1.0. Significant P-values (a = 0.10) are in bold. The AGI numbers of the 24 genes subsequently analyzed using promoter fusions (Additional File 5) are highlighted in yellow.