TOP TEN perturbations for At5g17820 (Arabidopsis thaliana)

Organism: Arabidopsis thaliana
Gene: At5g17820
Selected probe(set): 250059_at
Platform: Affymetrix Arabidopsis ATH1 Genome Array

Expression of At5g17820 (250059_at) across 3243 perturbations tested by GENEVESTIGATOR:

germination (48h) / stratification (48h)

Relative Expression (log2-ratio):7.10168
Number of Samples:3 / 3
Experimental germination (48h)
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 48h.
Control stratification (48h)
Col-0 seeds were harvested, allowed to dessicate for 15 days in darkness, then sterilized, plated on Murashige and Skoog medium (containing 3% sucrose), and stratified at 4°C in darkness for 48h.

germination (48h) / seed desiccation

Relative Expression (log2-ratio):6.5328655
Number of Samples:3 / 3
Experimental germination (48h)
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 48h.
Control seed desiccation
Col-0 seeds were harvested and allowed to dessicate for 15 days in darkness.

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

Relative Expression (log2-ratio):5.351736
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.

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

Relative Expression (log2-ratio):5.1852093
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.

ckh1-1 / Ler

Relative Expression (log2-ratio):-4.6264467
Number of Samples:2 / 2
Experimental ckh1-1
EMS-generated mutant carrying recessive nonsense mutation (319C → T) in the first exon of CKH1 (At1g17440; AtTAF12b; EER4). CKH1 (Cytokinin hypersensitive 1) is similar to yeast TAF12, a component of general transcription factor TFIID (needed for core promoter recognition and nucleation of the pre-initiation complex for RNA polymerase II) and histone acetyltransferase-containing complexes. Compared to Ler wild type, the ckh1-1 mutant requires less cytokinin to produce green and rapidly growing calli, e.g. when hypocotyl segments are placed on medium containing 25ng/ml kinetin and 100ng/ml 2,4-D (synthetic auxin), ckh1-1 produces green calli whereas the wild type forms root-like structures. The ckh1-1 mutant does not accumulate more cytokinins than the wild type (Kubo et al., 2011, Plant and Cell Physiol. 52: 629-637; Kubo and Kakimoto, 2000, Plant J. 23: 385-394).
Control Ler
Arabidopsis accession: Landsberg erecta

ABA study 11 (3h) / solvent treated cell samples (3h)

Relative Expression (log2-ratio):-4.486208
Number of Samples:2 / 2
Experimental ABA study 11 (3h)
Cell samples of T87 cell suspension that was grown in modified JPL medium (Axelos et al., 1992, Plant Physiol Biochem. 30: 123-128) under 16h light / 8h dark cycles, 24°C, on a rotary shaker at 100rpm with subculturing every 7 days and then, at the exponential phase of growth, exposed to 25μM ABA (abscisic acid) for 3h.
Control solvent treated cell samples (3h)
Cell samples of T87 cell suspension that was grown in modified JPL medium (Axelos et al., 1992, Plant Physiol Biochem. 30: 123-128) under 16h light / 8h dark cycles, 24°C, on a rotary shaker at 100rpm with subculturing every 7 days and then, at the exponential phase of growth, exposed to 0.6% ethanol for 3h.

C24 / Col

Relative Expression (log2-ratio):-4.4050674
Number of Samples:2 / 2
Experimental C24
Arabidopsis accession comparatively tolerant to ozone: ozone treated (400nl L-1 O3 for 6h) C24 shows less cell death than ozone treated Te-0 accession. When plants are exposed to 400nl L-1 ozone for 4h, both stomatal O3 uptake rate and cumulative O3 dose received by the plants during the treatment are lower in C24 than in Te-0 (Xu et al., 2015, Plant Cell Environ. 38: 1418-1433).
Control Col

ckh1-1 / Ler

Relative Expression (log2-ratio):-4.2380247
Number of Samples:2 / 2
Experimental ckh1-1
EMS-generated mutant carrying recessive nonsense mutation (319C → T) in the first exon of CKH1 (At1g17440; AtTAF12b; EER4). CKH1 (Cytokinin hypersensitive 1) is similar to yeast TAF12, a component of general transcription factor TFIID (needed for core promoter recognition and nucleation of the pre-initiation complex for RNA polymerase II) and histone acetyltransferase-containing complexes. Compared to Ler wild type, the ckh1-1 mutant requires less cytokinin to produce green and rapidly growing calli, e.g. when hypocotyl segments are placed on medium containing 25ng/ml kinetin and 100ng/ml 2,4-D (synthetic auxin), ckh1-1 produces green calli whereas the wild type forms root-like structures. The ckh1-1 mutant does not accumulate more cytokinins than the wild type (Kubo et al., 2011, Plant and Cell Physiol. 52: 629-637; Kubo and Kakimoto, 2000, Plant J. 23: 385-394).
Control Ler
Arabidopsis accession: Landsberg erecta

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

Relative Expression (log2-ratio):4.2208796
Number of Samples:3 / 3
Experimental two-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 Two-Cycle Eukaryotic Target Labeling Assay kit.
Control two-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 Two-Cycle Eukaryotic Target Labeling Assay kit.

circadian clock (Ca2+)cyt / nicotinamide (81h) / circadian clock (Ca2+)cyt study 9 (C24_LUC_AEQ)

Relative Expression (log2-ratio):-4.125086
Number of Samples:2 / 2
Experimental circadian clock (Ca2+)cyt / nicotinamide (81h)
Aeral tissue samples of C24 plants (containing LUC and AEQ transgenes) grown under 12h light / 12d dark cycles, 70μmolm-2s-1, 19°C for 11 days, on day 12 transferred to constant light (100μmolm-2s-1) and treated with 50mM nicotinamide every 2 hours over a period of 81h.
Control circadian clock (Ca2+)cyt study 9 (C24_LUC_AEQ)
Aeral tissue samples of C24 plants (containing LUC and AEQ transgenes) grown under 12h light / 12d dark cycles, 70μmolm-2s-1, 19°C for 11 days and on day 12 transferred to constant light (100μmolm-2s-1) for 81h.