TOP TEN perturbations for AT3G10410 (Arabidopsis thaliana)

Organism: Arabidopsis thaliana
Gene: AT3G10410
Selected probe(set): 258970_at
Platform: Affymetrix Arabidopsis ATH1 Genome Array

Expression of AT3G10410 (258970_at) across 3240 perturbations tested by GENEVESTIGATOR:

oxt6:AtCPSF30 / Col-0

Relative Expression (log2-ratio):3.1498957
Number of Samples:4 / 3
Experimental oxt6:AtCPSF30
Oxt6 (polyadenylation factor subunit) transformant that carries a gene encoding just the smaller of the two At1g30460-encoded proteins.
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).

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

Relative Expression (log2-ratio):-2.900773
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.

P. syringae pv. tomato study 15 (DC3000 hrpA) / P. syringae pv. tomato study 13 (DC3000 hrpA)

Relative Expression (log2-ratio):-2.804349
Number of Samples:3 / 3
Experimental P. syringae pv. tomato study 15 (DC3000 hrpA)
Systemic leaf samples of Col-5(gl1-1) grown for 4-5 weeks, then inoculated with mutant Pseudomonas syringae pv. tomato DC3000 hrpA (10e8 cfu/ml) by infiltrating at least 5 leaves per plant. Not infiltrated (systemic) leaves from inner rosette were harvested 21h after the treatment. Plant growth conditions: 10h light (150µmolm-2s-1) / 14h dark; 22°C-20°C.
Control P. syringae pv. tomato study 13 (DC3000 hrpA)
Systemic leaf samples of Col-5(gl1-1) grown for 4-5 weeks, then inoculated with mutant Pseudomonas syringae pv. tomato DC3000 hrpA (10e8 cfu/ml) by infiltrating at least 5 leaves per plant. Not infiltrated (systemic) leaves from inner rosette were harvested 8h after the treatment. Plant growth conditions: 10h light (150µmolm-2s-1) / 14h dark; 22°C-20°C.

long day (Col-0) / short day study 2 (Col-0)

Relative Expression (log2-ratio):2.803978
Number of Samples:3 / 3
Experimental long day (Col-0)
Leaf samples of Col-0 grown on soil (supplemented with Hoagland medium) under long day conditions (16h light (120 -160μmol photons m-2 s-1) at 20°C / 8h darkness at 18°C) for 21 day.
Control short day study 2 (Col-0)
Leaf samples of Col-0 grown on soil (supplemented with Hoagland medium) under short day conditions (8h light (140 -160μmol photons m-2 s-1) at 20°C / 16h darkness at 18°C) for 35 days.

cold study 19 (Col-0) / untreated Col-0 rosette samples

Relative Expression (log2-ratio):2.736497
Number of Samples:3 / 3
Experimental cold study 19 (Col-0)
Rosette samples of Col-0 grown for 23 days on soil under 12h light (120μmol photons m-2 s-1) / 12h dark cycles at 22°C, then placed for 3 weeks at 4°C under 12h light (35μmol photons m-2 s-1) / 12h dark cycles. Rosettes were harvested at ZT4 (4h after the start of the light period).
Control untreated Col-0 rosette samples
Rosette samples of Col-0 grown for 23 days on soil under 12h light (120μmol photons m-2 s-1) / 12h dark cycles at 22°C. Rosettes were harvested at ZT4 (4h after the start of the light period).

P. syringae pv. tomato study 15 (DC3000) / P. syringae pv. tomato study 13 (DC3000)

Relative Expression (log2-ratio):-2.7319813
Number of Samples:3 / 3
Experimental P. syringae pv. tomato study 15 (DC3000)
Systemic leaf samples of Col-5(gl1-1) grown for 4-5 weeks, then inoculated with virulent Pseudomonas syringae pv. tomato DC3000 (10e8 cfu/ml) by infiltrating at least 5 leaves per plant. Not infiltrated (systemic) leaves from inner rosette were harvested 21h after the treatment. Plant growth conditions: 10h light (150µmolm-2s-1) / 14h dark; 22°C-20°C.
Control P. syringae pv. tomato study 13 (DC3000)
Systemic leaf samples of Col-5(gl1-1) grown for 4-5 weeks, then inoculated with virulent Pseudomonas syringae pv. tomato DC3000 (10e8 cfu/ml) by infiltrating at least 5 leaves per plant. Not infiltrated (systemic) leaves from inner rosette were harvested 8h after the treatment. Plant growth conditions: 10h light (150µmolm-2s-1) / 14h dark; 22°C-20°C.

RBR depletion (RNAi; 12h) / untreated leaf samples (0h)

Relative Expression (log2-ratio):2.7216806
Number of Samples:3 / 3
Experimental RBR depletion (RNAi; 12h)
Leaf samples from transgenic Col-0 seedlings, carrying an estradiol inducible RNA interference system against retinoblastoma-related-protein (RBR) mRNA. The leaf samples were harvested 12h after RNAi induction with estradiol.
Control untreated leaf samples (0h)
Leaf samples from transgenic Col-0 seedlings, carrying an estradiol inducible RNA interference system against retinoblastoma-related-protein (RBR) mRNA. The leaf samples were harvested before estradiol induction.

H. arabidopsidis (rpp4; 0.5dpi) / untreated shoot samples (rpp4)

Relative Expression (log2-ratio):2.6925468
Number of Samples:2 / 2
Experimental H. arabidopsidis (rpp4; 0.5dpi)
Shoot samples of rpp4 grown for 10 days (12h light / 12h darkness, 16-18°C, 80-100% relative humidity), then spray-inoculated with spore suspension of Hyaloperonospora arabidopsidis isolate Emwa1 (500 000 spores / ml), and incubated for 12h. Inoculation was performed at the beginning of the light period.
Control untreated shoot samples (rpp4)
Shoot samples of rpp4 grown for 10 days under 12h light / 12h dark cycles, 16-18°C, 80-100% relative humidity.

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

Relative Expression (log2-ratio):-2.6149292
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.

high light study 2 (8h) / untreated leaf samples (Col-4)

Relative Expression (log2-ratio):2.587988
Number of Samples:2 / 2
Experimental high light study 2 (8h)
Middle-aged leaf samples of 6-week-old Col-4 plants, exposed to continuous HL irradiation (photosynthetically active radiation 400 to 700 nm at approximately 1,600 to 1,800 µmol m–2 s–1) for 8h.
Control untreated leaf samples (Col-4)
Untreated middle-aged leaf samples of 6-week-old Col-4 plants.