TOP TEN perturbations for Q9ZQ85 (Arabidopsis thaliana)

Organism: Arabidopsis thaliana
Gene: Q9ZQ85
Selected probe(set): 265719_at
Platform: Affymetrix Arabidopsis ATH1 Genome Array

Expression of Q9ZQ85 (265719_at) across 3117 perturbations tested by GENEVESTIGATOR:

ambient CO2 (mature leaf 10) / ambient CO2 (leaf 10 primordia)

Relative Expression (log2-ratio):1.8234997
Number of Samples:4 / 4
Experimental ambient CO2 (mature leaf 10)
Fully expanded rosette leaf 10 samples of Col-0 grown for 30 days under ambient CO2 (370ppm). The rosette leaf 10 started to form at least 15 days after germination. 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 day 30 after germination.
Control ambient CO2 (leaf 10 primordia)
Rosette leaf 10 primordia samples of Col-0 grown for 16 days under ambient CO2 (370ppm). The rosette leaf 10 started to form at least 15 days after germination. 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 day 16 after germination, frozen in liquid N2, and used for dissection of the leaf 10 primordia.

circadian clock study 9 (17h dark+1h light) / circadian clock study 9 (18h dark)

Relative Expression (log2-ratio):1.5812302
Number of Samples:3 / 3
Experimental circadian clock study 9 (17h dark+1h light)
Shoot samples of Col plants grown for 13.5 days on soil under 12h light / 12h dark cycles at 22°C, then, starting at the beginning of the dark period on day 14, kept for 17h in darkness, and then placed for 1h to light (70µmol photons m-2 s-1).
Control circadian clock study 9 (18h dark)
Shoot samples of Col plants grown for 13.5 days on soil under 12h light / 12h dark cycles at 22°C, then, starting at the beginning of the dark period on day 14, kept for 18h in darkness (i.e. samples were harvested 6h after the beginning of the subjective light period on day 15).

ambient CO2 (expanding leaf 10) / ambient CO2 (leaf 10 primordia)

Relative Expression (log2-ratio):1.5195932
Number of Samples:3 / 4
Experimental ambient CO2 (expanding leaf 10)
Expanding rosette leaf 10 samples of Col-0 grown for 23 days under ambient CO2 (370ppm). The rosette leaf 10 started to form at least 15 days after germination. 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 day 23 after germination.
Control ambient CO2 (leaf 10 primordia)
Rosette leaf 10 primordia samples of Col-0 grown for 16 days under ambient CO2 (370ppm). The rosette leaf 10 started to form at least 15 days after germination. 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 day 16 after germination, frozen in liquid N2, and used for dissection of the leaf 10 primordia.

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

Relative Expression (log2-ratio):1.4878664
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.

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

Relative Expression (log2-ratio):1.4624863
Number of Samples:3 / 4
Experimental elevated CO2 study 3 (expanding leaf 10)
Expanding rosette leaf 10 samples of Col-0 grown for 7 days under ambient CO2 (370ppm), then transferred to elevated CO2 (750ppm) for 16 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 16 (day 23 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.

iron deficiency / protoplasting / iron deficiency study 8 (24h)

Relative Expression (log2-ratio):1.3671732
Number of Samples:2 / 3
Experimental iron deficiency / protoplasting
Col-0 seedlings were grown for 5 days on iron-sufficient medium (1x Murashige and Skoog salt mixture in which ferrous sulfate was replaced with 100mM Fe(III)-EDTA, 0.5g/L MES, 1% sucrose, 1% agar; pH 5.7), then transferred to iron deficient medium (1x Murashige and Skoog salt mixture in which ferrous sulfate was replaced with 300μM Ferrozine, 0.5g/L MES, 1% sucrose, 1% agar; pH 5.7) for 24h; protoplasts were then isolated from the whole roots and FACS-sorted (all protoplasts were taken after the sorting). FACS, Fluorescence Activated Cell Sorting.
Control iron deficiency study 8 (24h)
Whole root samples of Col-0 seedlings grown on iron-sufficient medium (1x Murashige and Skoog salt mixture in which ferrous sulfate was replaced with 100mM Fe(III)-EDTA, 0.5g/L MES, 1% sucrose, 1% agar; pH 5.7) for 5 days, then transferred to iron deficient medium (1x Murashige and Skoog salt mixture in which ferrous sulfate was replaced with 300μM Ferrozine, 0.5g/L MES, 1% sucrose, 1% agar; pH 5.7) for 24h.

M. incognita study 2 (Pico) / non-infested root cell samples (Pico)

Relative Expression (log2-ratio):-1.2514591
Number of Samples:4 / 5
Experimental M. incognita study 2 (Pico)
Giant cell samples isolated from Col grown for 3 weeks on plates with solid medium (0.3% Gamborg's basal salts, 2% sucrose, 0.6 % Phytagel, pH 6.1; plates placed at 45° angle; 5 plants per plate), then inoculated with 1000 stage 2 juveniles of Meloidogyne incognita per plate, and grown for further 21 day. Approx. 80 giant cells per biological replicate were harvested from an area of approx. 5000000µm2 using LCM (laser capture microdissection). WT-Ovation Pico kit (NuGEN Technologies Inc.) was used for RNA amplification. Other plant growth conditions: 8h light / 16h dark cycles; 23°C.
Control non-infested root cell samples (Pico)
Root cell samples isolated from Col grown for 3 weeks on plates with solid medium (0.3% Gamborg's basal salts, 2% sucrose, 0.6 % Phytagel, pH 6.1; plates placed at 45° angle; 5 plants per plate), then inoculated with 1000 stage 2 juveniles of Meloidogyne incognita per plate, and grown for further 21 day. Approx. 150 root cells (not undergoing giant cell formation) per biological replicate were harvested from a not infested area of approx. 13000000µm2 using LCM (laser capture microdissection). WT-Ovation Pico kit (NuGEN Technologies Inc.) was used for RNA amplification. Other plant growth conditions: 8h light / 16h dark cycles; 23°C.

mpk4: ctr1 / Ler

Relative Expression (log2-ratio):-1.2059498
Number of Samples:3 / 2
Experimental mpk4: ctr1
Control Ler
Arabidopsis accession: Landsberg erecta

IVT-E RNA labeling (root elongation zone) / IVT-E RNA labeling (root tip)

Relative Expression (log2-ratio):1.0421591
Number of Samples:3 / 3
Experimental IVT-E RNA labeling (root elongation zone)
Root elongation zone samples of Col-0 grown for 7 days on vertically oriented plates containing solid 0.5x Murashige and Skoog medium under continuous light (150µmol photons m-1 s-1) at 24°C. For microarrays RNA was labeled using Affymetrix GeneChip 3' IVT-Express Kit.
Control IVT-E RNA labeling (root tip)
Root tip samples of Col-0 grown for 7 days on vertically oriented plates containing solid 0.5x Murashige and Skoog medium under continuous light (150µmol photons m-1 s-1) at 24°C. For microarrays RNA was labeled using Affymetrix GeneChip 3' IVT-Express Kit.

one-cycle RNA labeling (root elongation zone) / one-cycle RNA labeling (root tip)

Relative Expression (log2-ratio):1.039712
Number of Samples:3 / 3
Experimental one-cycle RNA labeling (root elongation zone)
Root elongation zone samples of Col-0 grown for 7 days on vertically oriented plates containing solid 0.5x Murashige and Skoog medium under continuous light (150µmol photons m-1 s-1) at 24°C. For microarrays RNA was labeled using Affymetrix One-Cycle Eukaryotic Target Labeling Assay kit.
Control one-cycle RNA labeling (root tip)
Root tip samples of Col-0 grown for 7 days on vertically oriented plates containing solid 0.5x Murashige and Skoog medium under continuous light (150µmol photons m-1 s-1) at 24°C. For microarrays RNA was labeled using Affymetrix One-Cycle Eukaryotic Target Labeling Assay kit.