TOP TEN perturbations for Q5XF07 (Arabidopsis thaliana)

Organism: Arabidopsis thaliana
Gene: Q5XF07
Selected probe(set): 252358_at
Platform: Affymetrix Arabidopsis ATH1 Genome Array

Expression of Q5XF07 (252358_at) across 3240 perturbations tested by GENEVESTIGATOR:

shift NPA to NAA (6h) / NPA study 3

Relative Expression (log2-ratio):2.3801317
Number of Samples:3 / 3
Experimental shift NPA to NAA (6h)
Primary root samples of Col-0 grown for 3 days on vertically oriented plates containing solid Murashige-Skoog medium supplemented with 10µM NPA (1-N-naphthylphthalamic acid, an inhibitor of auxin transport), then transferred to 10µM NAA (1-naphthalene acetic acid, synthetic auxin) for 6h.
Control NPA study 3
Primary root samples of Col-0 grown for 3 days on vertically oriented plates containing solid Murashige-Skoog medium supplemented with 10µM NPA (1-N-naphthylphthalamic acid, an inhibitor of auxin transport).

shift low to high light study 4 (rap2.4a) / low light study 5 (rap2.4a)

Relative Expression (log2-ratio):2.066536
Number of Samples:3 / 3
Experimental shift low to high light study 4 (rap2.4a)
Rosette samples of rap2.4a plants grown on soil for 21 day under short day standard intensity light conditions (10h light (100µmol m-2 s-1) at 23°C / 14h dark at 18°C cycles), then shifted to low light (10h (8µmol m-2 s-1) at 23°C / 14h dark at 18°C) for 10 days, and then shifted to high light (800µmol m-2 s-1) for 6h. Other conditions: 55% relative humidity; soil mixture: Fruhsdorfer Erde Klocke P, perlite, and vermiculite (1:1:1).
Control low light study 5 (rap2.4a)
Rosette samples of rap2.4a plants grown on soil for 21 day under short day standard intensity light conditions (10h light (100µmol m-2 s-1) at 23°C / 14h dark at 18°C cycles), then shifted to low light (10h (8µmol m-2 s-1) at 23°C / 14h dark at 18°C) for 10 days and 6h. For the last 6h the plants were kept in light. Other conditions: 55% relative humidity; soil mixture: Fruhsdorfer Erde Klocke P, perlite, and vermiculite (1:1:1).

callus formation study 3 (35d + 1d) / untreated hypocotyl samples (35d)

Relative Expression (log2-ratio):2.022213
Number of Samples:3 / 3
Experimental callus formation study 3 (35d + 1d)
Hypocotyl segments (0.5cm just above the root-hypocotyl junction) were cut out from 35-days-old Col-0 plants, incubated for 1 day on solid callus inducing medium (Murashige and Skoog salts, 2.0% (w/v) glucose, 0.5 p.p.m. (w/v) 2,4-D (2,4-dichlorophenoxyacetic acid), 0.05% (w/v) MES, 0.25% (w/v) gellan gum; pH 5.7) in darkness, and harvested. Plant growth conditions prior the treatment: vertically oriented plates with solid germination medium (Murashige and Skoog salts, 1.0% (w/v) sucrose, 0.05% (w/v) MES, 1.5% (w/v) agar; pH 5,7); 16h light (4–6µmol photons m-2 s-1) / 8h dark cycles; 25°C.
Control untreated hypocotyl samples (35d)
Hypocotyl samples (0.5cm-long segments just above the root-hypocotyl junction) of 35-days-old Col-0 plants grown on vertically oriented plates with solid germination medium (Murashige and Skoog salts, 1.0% (w/v) sucrose, 0.05% (w/v) MES, 1.5% (w/v) agar; pH 5,7) under 16h light (4–6µmol photons m-2 s-1) / 8h dark cycles at 25°C.

germination (24h) / seed desiccation

Relative Expression (log2-ratio):1.9985952
Number of Samples:3 / 3
Experimental germination (24h)
Col-0 seeds were harvested, allowed to dessicate for 15 days in darkness, sterilized, plated on Murashige and Skoog medium (containing 3% sucrose), stratified at 4°C in darkness for 48h, and then transferred to continuous light (100µmol photons m-2 s-1) at 22°C for 24h.
Control seed desiccation
Col-0 seeds were harvested and allowed to dessicate for 15 days in darkness.

atwrky40 / Col-0

Relative Expression (log2-ratio):1.9802399
Number of Samples:3 / 3
Experimental atwrky40
Loss-of-function mutant carrying T-DNA insertion (CSHL_ET5883) in the 2nd exon of AtWRKY40 (At1g80840). AtWRKY40 is a transcription factor that binds to the W-boxes (TTGAC(C/T) in the promoters of AtWRKY40-regulated genes (e.g. genes encoding mitochondrial proteins AOX1a (Alternative oxidase 1a), NDB2 (NADH dehydrogenaseB2), and BCS1 (AAA ATPase Ubiquinol-cytochrome c reductase synthesis1); genes encoding plastid proteins HEMA1 (glutamyl-tRNA reductase) and LHCB2.4) (Van Aken et al., 2013, Plant Physiol. 162: 254-271).
Control Col-0
Arabidopsis accession Columbia-0. Origin: Poland; latitude of origin: 52°73'N, longitude of origin: 15°15'E. Col-0 is resistant to the isolate AG8 and susceptible to the isolate AG2-1 of soil-borne necrotrophic fungus Rhizoctonia solani. Freezing tolerance of non-acclimated Col-0 leaves: LT50 (temperature of 50% electrolyte leakage) = −5.34°C; freezing tolerance of Col-0 leaves after acclimation at 4°C under 16h photoperiod (90µmol photons m-2 s-1) for 14 days: LT50 = −9.68°C. Acclimated Col-0 leaves accumulate approx. 20µmol g FW-1 glucose, 10µmol g FW-1 fructose, 20µmol g FW-1 sucrose, 4µmol g FW-1 raffinose, 5.5µmol g FW-1 proline (Zuther et al., 2012, Plant Cell Environ. 35: 1860-1878). Col-0 is comparatively tolerant to ozone: ozone treated (400nl L-1 O3 for 6h) Col-0 shows less cell death than ozone treated Te-0 accession (Xu et al., 2015, Plant Cell Environ. 38: 1418-1433). Col-0 is susceptible to bacterial pathogen Pseudomonas syringae pv tomato (Pst) strain DC3000. As Col-0 carries the resistance gene RPS4 (At5g45250), it is resistant to Pst DC3000 expressing the bacterial effector avrRps4 (Howard et al., 2013, PLoS One 8: e74183). When 4-day-old Col-0 seedlings are exposed to mild drought stress (soil water content (SWC) of 1.2g H2O g-1 dry soil) for 6 days, area of their 3rd rosette leaf is reduced by approx. 30% compared to that of control Col-0 seedlings grown for 4+6 days at SWC of 2.2g H2O g-1 dry soil. When 4-day-old Col-0 seedlings are exposed to mild drought stress for 18 days (SWC is kept at 1.2g H2O g-1 dry soil for the first 6 days, then slowly decreases and is kept at 0.7g H2O g-1 dry soil till the end of the treatment), area of their 3rd rosette leaf is reduced by approx. 59% compared to that of control Col-0 plants grown for 4+18 days at SWC of 2.2g H2O g-1 dry soil (Clauw et al., 2015, Plant Physiol. 167: 800-816). In the study by (Nakano et al., 2020, Front Plant Sci. 11: 405), aluminum tolerance of Col-0 was 53.3; calculated as: (root length of 5-day-old seedlings grown in the presence of 5µM AlCl3 at pH 5.0 / root length of 5-day-old seedlings grown without Al at pH 5.0) x 100. Col-0 is moderately tolerant to submergence. For example, when rosette-stage Col-0 plants were completely submerged in water for 2 days under short-day conditions, the photosynthetic rate in their leaves decreased by approx. 36.4% compared to untreated Col-0 (Meng et al., 2020, Plant J. 103: 227-247).

germination (12h) / seed desiccation

Relative Expression (log2-ratio):1.8457985
Number of Samples:3 / 3
Experimental germination (12h)
Col-0 seeds were harvested, allowed to dessicate for 15 days in darkness, sterilized, plated on Murashige and Skoog medium (containing 3% sucrose), stratified at 4°C in darkness for 48h, and then transferred to continuous light (100µmol photons m-2 s-1) at 22°C for 12h.
Control seed desiccation
Col-0 seeds were harvested and allowed to dessicate for 15 days in darkness.

callus formation (96h) / untreated root samples

Relative Expression (log2-ratio):1.7515182
Number of Samples:3 / 3
Experimental callus formation (96h)
Root segments were cut out from 10-days-old Col-0 plantlets and incubated on callus inducing medium for 96h. Plant growth conditions prior the treatment: solid Murashige and Skoog medium, 22°C, 16h light / 8h dark.
Control untreated root samples
Root segments were cut out from 10-days-old Col-0 plantlets grown on solid Murashige and Skoog medium, 22°C, 16h light / 8h dark.

germination (6h) / seed desiccation

Relative Expression (log2-ratio):1.7420053
Number of Samples:3 / 3
Experimental germination (6h)
Col-0 seeds were harvested, allowed to dessicate for 15 days in darkness, sterilized, plated on Murashige and Skoog medium (containing 3% sucrose), stratified at 4°C in darkness for 48h, and then transferred to continuous light (100µmol photons m-2 s-1) at 22°C for 6h.
Control seed desiccation
Col-0 seeds were harvested and allowed to dessicate for 15 days in darkness.

shift low to high light study 4 (Col-0) / low light study 5 (Col-0)

Relative Expression (log2-ratio):1.7362947
Number of Samples:3 / 3
Experimental shift low to high light study 4 (Col-0)
Rosette samples of Col-0 plants grown on soil for 21 day under short day standard intensity light conditions (10h light (100µmol m-2 s-1) at 23°C / 14h dark at 18°C cycles), then shifted to low light (10h (8µmol m-2 s-1) at 23°C / 14h dark at 18°C) for 10 days, and then shifted to high light (800µmol m-2 s-1) for 6h. Other conditions: 55% relative humidity; soil mixture: Fruhsdorfer Erde Klocke P, perlite, and vermiculite (1:1:1).
Control low light study 5 (Col-0)
Rosette samples of Col-0 plants grown on soil for 21 day under short day standard intensity light conditions (10h light (100µmol m-2 s-1) at 23°C / 14h dark at 18°C cycles), then shifted to low light (10h (8µmol m-2 s-1) at 23°C / 14h dark at 18°C) for 10 days and 6h. For the last 6h the plants were kept in light. Other conditions: 55% relative humidity; soil mixture: Fruhsdorfer Erde Klocke P, perlite, and vermiculite (1:1:1).

elevated CO2 study 3 (mature leaf 10) / elevated CO2 study 3 (leaf 10 primordia)

Relative Expression (log2-ratio):-1.70611
Number of Samples:4 / 4
Experimental elevated CO2 study 3 (mature leaf 10)
Fully expanded rosette leaf 10 samples of Col-0 grown for 7 days under ambient CO2 (370ppm), then transferred to elevated CO2 (750ppm) for 23 days. The rosette leaf 10 started to form at least 8 days after the elevated CO2 treatment began. Other plant growth conditions: Conviron PGR14 growth chamber, 10h light (300µmol photons m-2 s-1) at 21°C / 14h dark at 18°C cycles, 70% relative humidity; plants were grown on soil (LC1 Sunshine Mix from Sun Gro Horticulture, Canada) and watered with 40% Long Ashton solution containing 6mM NH4NO3. CO2 concentration was maintained using a custom retrofitted chamber CO2 scrubbing and delivery system. Long Ashton nutrient solution as described in (Hewitt and Smith, 1975, Plant Mineral Nutrition, John Wiley and Sons, New York, NY, USA). The leaf samples were harvested 7h after the beginning of the dark period on the treatment day 23 (day 30 after germination).
Control elevated CO2 study 3 (leaf 10 primordia)
Rosette leaf 10 primordia samples of Col-0 grown for 7 days under ambient CO2 (370ppm), then transferred to elevated CO2 (750ppm) for 9 days. The rosette leaf 10 started to form at least 8 days after the elevated CO2 treatment began. Other plant growth conditions: Conviron PGR14 growth chamber, 10h light (300µmol photons m-2 s-1) at 21°C / 14h dark at 18°C cycles, 70% relative humidity; plants were grown on soil (LC1 Sunshine Mix from Sun Gro Horticulture, Canada) and watered with 40% Long Ashton solution containing 6mM NH4NO3. CO2 concentration was maintained using a custom retrofitted chamber CO2 scrubbing and delivery system. Long Ashton nutrient solution as described in (Hewitt and Smith, 1975, Plant Mineral Nutrition, John Wiley and Sons, New York, NY, USA). Whole rosettes were harvested 7h after the beginning of the dark period on the treatment day 9 (day 16 after germination), frozen in liquid N2, and used for dissection of the leaf 10 primordia.