TOP TEN perturbations for AT3G27080 (Arabidopsis thaliana)

Organism: Arabidopsis thaliana
Gene: AT3G27080
Selected probe(set): 257792_at
Platform: Affymetrix Arabidopsis ATH1 Genome Array

Expression of AT3G27080 (257792_at) across 3240 perturbations tested by GENEVESTIGATOR:

cycloheximide / dexamethasone study 2 (pBeaconRFP_GR-ABI3) / mock treated root protoplast samples (pBeaconRFP_GR-ABI3)

Relative Expression (log2-ratio):-2.1024323
Number of Samples:3 / 3
Experimental cycloheximide / dexamethasone study 2 (pBeaconRFP_GR-ABI3)
Col-0 root protoplasts were transfected with the pBeaconRFP_GR-ABI3 vector (50μg plasmid DNA / 10^6 protoplasts; polyethylene glycol method), incubated for 16h at room temperature, then treated with 35μM cycloheximide (an inhibitor of protein synthesis) and 10μM dexamethasone for 16h (cycloheximide was added to the protoplasts 30min prior adding dexamethasone). Prior RNA isolation, the successfully transfected protoplasts were harvested using FACS (Fluorescence Activated Cell Sorting), possible due to the expression of mRFP (monomeric red fluorescent protein) from the pBeaconRFP_GR-ABI3 vector.
Control mock treated root protoplast samples (pBeaconRFP_GR-ABI3)
Col-0 root protoplasts were transfected with the pBeaconRFP_GR-ABI3 vector (50μg plasmid DNA / 10^6 protoplasts; polyethylene glycol method), incubated for 16h at room temperature, then mock-treated with solvents, ethanol and DMSO, for 16h. Prior RNA isolation, the successfully transfected protoplasts were harvested using FACS (Fluorescence Activated Cell Sorting), possible due to the expression of mRFP (monomeric red fluorescent protein) from the pBeaconRFP_GR-ABI3 vector.

cycloheximide study 4 (pBeaconRFP_GR-ABI3) / mock treated root protoplast samples (pBeaconRFP_GR-ABI3)

Relative Expression (log2-ratio):-2.065013
Number of Samples:3 / 3
Experimental cycloheximide study 4 (pBeaconRFP_GR-ABI3)
Col-0 root protoplasts were transfected with the pBeaconRFP_GR-ABI3 vector (50μg plasmid DNA / 10^6 protoplasts; polyethylene glycol method), incubated for 16h at room temperature, then treated with 35μM cycloheximide (an inhibitor of protein synthesis) for 16h. Prior RNA isolation, the successfully transfected protoplasts were harvested using FACS (Fluorescence Activated Cell Sorting), possible due to the expression of mRFP (monomeric red fluorescent protein) from the pBeaconRFP_GR-ABI3 vector.
Control mock treated root protoplast samples (pBeaconRFP_GR-ABI3)
Col-0 root protoplasts were transfected with the pBeaconRFP_GR-ABI3 vector (50μg plasmid DNA / 10^6 protoplasts; polyethylene glycol method), incubated for 16h at room temperature, then mock-treated with solvents, ethanol and DMSO, for 16h. Prior RNA isolation, the successfully transfected protoplasts were harvested using FACS (Fluorescence Activated Cell Sorting), possible due to the expression of mRFP (monomeric red fluorescent protein) from the pBeaconRFP_GR-ABI3 vector.

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

Relative Expression (log2-ratio):1.8507557
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.

pollen tube growth (semi in vivo) / dry mature pollen samples

Relative Expression (log2-ratio):1.8093452
Number of Samples:3 / 4
Experimental pollen tube growth (semi in vivo)
Col-0 pollen grains were placed on stigmata of excised pistils lacking the ovaries and pollen tubes were allowed to grow through the stigmata and styles that first were kept vertically for 1h, then laid horizontally on solid pollen growth medium (Palanivelu et al., 2003, Cell. 114: 47–59). Pollen tubes that emerged from the styles (approx.3h after pollination) were allowed to grow along the medium surface for 5h and then harvested by cutting.
Control dry mature pollen samples
Mature dry pollen grains of Col-0 were collected using vacuum method (Johnson-Brousseau and McCormick, 2004, Plant J. 39: 761–775).

callus formation study 3 (7d + 1d) / untreated hypocotyl samples (7d)

Relative Expression (log2-ratio):1.7684422
Number of Samples:3 / 3
Experimental callus formation study 3 (7d + 1d)
Hypocotyl segments (0.5cm just above the root-hypocotyl junction) were cut out from 7-days-old Col-0 seedlings, 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 (7d)
Hypocotyl samples (0.5cm-long segments just above the root-hypocotyl junction) of 7-days-old Col-0 seedlings 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.

oxt6 / Col-0

Relative Expression (log2-ratio):1.708601
Number of Samples:3 / 3
Experimental oxt6
The oxt6 mutant is an oxidative stress-tolerant Arabidopsis mutant that is deficient in a polyadenylation factor subunit.
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).

glucose study 2 (dark) / mock treated seedling samples

Relative Expression (log2-ratio):1.5533991
Number of Samples:2 / 3
Experimental glucose study 2 (dark)
Seedling samples of Col grown for 5 days on solid medium (0.5x Murashige and Skoog (MS) salts, 1% sucrose, 0.8% agar) under 16h light (80µmol photons m-2 s-1) / 8h dark cycles at 22°C, then washed seven times with water and once with liquid medium (0.5x MS salts), incubated for 24h in liquid medium (0.5x MS salts) in darkness at 22°C with shaking at 140rpm, and then incubated in liquid medium containing 3% glucose and 0.5x MS salts for 3h in darkness at 22°C with shaking at 140rpm.
Control mock treated seedling samples
Seedling samples of Col grown for 5 days on solid medium (0.5x Murashige and Skoog (MS) salts, 1% sucrose, 0.8% agar) under 16h light (80µmol photons m-2 s-1) / 8h dark cycles at 22°C, then washed seven times with water and once with liquid medium (0.5x MS salts), and incubated for 27h in liquid medium (0.5x MS salts) in darkness at 22°C with shaking at 140rpm.

24-eBL + glucose (dark) / 24-eBL (dark)

Relative Expression (log2-ratio):1.5510044
Number of Samples:3 / 3
Experimental 24-eBL + glucose (dark)
Seedling samples of Col grown for 5 days on solid medium (0.5x Murashige and Skoog (MS) salts, 1% sucrose, 0.8% agar) under 16h light (80µmol photons m-2 s-1) / 8h dark cycles at 22°C, then washed seven times with water and once with liquid medium (0.5x MS salts), incubated for 24h in liquid medium (0.5x MS salts) in darkness at 22°C with shaking at 140rpm, and then incubated in liquid medium containing 0.1µM 24-epibrassinolide, 3% glucose, and 0.5x MS salts for 3h in darkness at 22°C with shaking at 140rpm.
Control 24-eBL (dark)
Seedling samples of Col grown for 5 days on solid medium (0.5x Murashige and Skoog (MS) salts, 1% sucrose, 0.8% agar) under 16h light (80µmol photons m-2 s-1) / 8h dark cycles at 22°C, then washed seven times with water and once with liquid medium (0.5x MS salts), incubated for 24h in liquid medium (0.5x MS salts) in darkness at 22°C with shaking at 140rpm, and then incubated in liquid medium containing 0.1µM 24-epibrassinolide and 0.5x MS salts for 3h in darkness at 22°C with shaking at 140rpm.

pollen tube growth (semi in vivo) / pollen tube growth (in vitro)

Relative Expression (log2-ratio):1.536623
Number of Samples:3 / 4
Experimental pollen tube growth (semi in vivo)
Col-0 pollen grains were placed on stigmata of excised pistils lacking the ovaries and pollen tubes were allowed to grow through the stigmata and styles that first were kept vertically for 1h, then laid horizontally on solid pollen growth medium (Palanivelu et al., 2003, Cell. 114: 47–59). Pollen tubes that emerged from the styles (approx.3h after pollination) were allowed to grow along the medium surface for 5h and then harvested by cutting.
Control pollen tube growth (in vitro)
Mature dry pollen grains of Col-0 were collected using vacuum method (Johnson-Brousseau and McCormick, 2004, Plant J. 39: 761–775) and incubated in 250µl liquid pollen growth medium (Palanivelu et al., 2003, Cell. 114: 47–59) for 4h at 24°C (58.3±6.0% of the pollen grains germinated and formed tubes of 383.8±32.1µm average length).

24-eBL + glucose (dark) / mock treated seedling samples

Relative Expression (log2-ratio):1.4746246
Number of Samples:3 / 3
Experimental 24-eBL + glucose (dark)
Seedling samples of Col grown for 5 days on solid medium (0.5x Murashige and Skoog (MS) salts, 1% sucrose, 0.8% agar) under 16h light (80µmol photons m-2 s-1) / 8h dark cycles at 22°C, then washed seven times with water and once with liquid medium (0.5x MS salts), incubated for 24h in liquid medium (0.5x MS salts) in darkness at 22°C with shaking at 140rpm, and then incubated in liquid medium containing 0.1µM 24-epibrassinolide, 3% glucose, and 0.5x MS salts for 3h in darkness at 22°C with shaking at 140rpm.
Control mock treated seedling samples
Seedling samples of Col grown for 5 days on solid medium (0.5x Murashige and Skoog (MS) salts, 1% sucrose, 0.8% agar) under 16h light (80µmol photons m-2 s-1) / 8h dark cycles at 22°C, then washed seven times with water and once with liquid medium (0.5x MS salts), and incubated for 27h in liquid medium (0.5x MS salts) in darkness at 22°C with shaking at 140rpm.