arabidopsis ath1 microarray  (Thermo Fisher)

Journal: International Journal of Molecular Sciences

Article Title: Modulation of the Arabidopsis Starch Metabolic Network by the Cytosolic Acetyl-CoA Pathway in the Context of the Diurnal Illumination Cycle

doi: 10.3390/ijms251910850

Figure Lengend Snippet: Expression profiles of genes encoding enzymes related to starch metabolism during the SD diurnal cycle. Genes are grouped by their biochemical activity: ( A ) starch synthases (SSs), ( B ) starch branching enzymes (BEs), ( C ) starch debranching enzymes (DBEs), ( D ) starch disproportionating enzymes (DPEs), ( E ) β-amylases (BAMs), ( F ) α-amylases (AAMs), ( G ) starch phosphorylases (PHSs), and ( H ) other enzymes related to starch metabolism. Leaves from WT plants cultivated under short day (SD) conditions, consisting of 8 h of light followed by 16 h of dark, were collected at various times throughout the 24-h cycle. RNA from these samples was then examined using the Affymetrix Arabidopsis ATH1 chip. The average normalized intensity for each microarray chip is 1. RNA was analyzed using GeneChip. The analysis was repeated in two independent experiments.

Article Snippet: These data were collected from nearly 1000 chips representing 70 Arabidopsis Affymetrix ATH1 microarray experiments.

Techniques: Expressing, Starch, Activity Assay, Microarray

Journal: International Journal of Molecular Sciences

Article Title: Modulation of the Arabidopsis Starch Metabolic Network by the Cytosolic Acetyl-CoA Pathway in the Context of the Diurnal Illumination Cycle

doi: 10.3390/ijms251910850

Figure Lengend Snippet: Expression correlations among genes within the starch metabolic network. Expression correlations among starch metabolic genes were evaluated by 963 Affymetrix ATH1 microarray chips representing 70 different Arabidopsis experiments and analyzed by MOG . Pearson correlation values are color-coded. Vertical bars (labeled #1, group 1; #2, group 2; and #3, group 3) denote the three groups of genes with the highest correlations. Group 1 represents genes involved in starch degradation, Group 2 includes genes primarily associated with starch synthesis, and Group 3 comprises genes involved in both starch synthesis and carbohydrate metabolism. Details for each group are described in the text.

Article Snippet: These data were collected from nearly 1000 chips representing 70 Arabidopsis Affymetrix ATH1 microarray experiments.

Techniques: Expressing, Starch, Microarray, Labeling

Journal: International Journal of Molecular Sciences

Article Title: Modulation of the Arabidopsis Starch Metabolic Network by the Cytosolic Acetyl-CoA Pathway in the Context of the Diurnal Illumination Cycle

doi: 10.3390/ijms251910850

Figure Lengend Snippet: Gene expression correlated with the expression of the DPE2 gene. Gene-expression profiles of nine genes ( PTPKIS1 / SEX4 , GWD1 , ISA3 , GWD3 , ISA2 , PHS2 , PHS1 , AT1G06460, and AT2G31040) correlated to the expression profile of DPE2 (Pearson’s correlation coefficients of between 0.72 and 0.84). Gene expression was evaluated at the level of RNA accumulation from 963 Affymetrix ATH1 microarray chips representing 70 different Arabidopsis experiments and analyzed by MOG ; the average expression level for each chip is 6.6.

Article Snippet: These data were collected from nearly 1000 chips representing 70 Arabidopsis Affymetrix ATH1 microarray experiments.

Techniques: Expressing, Microarray

Journal: BMC Plant Biology

Article Title: Transcriptome profiling of genes and pathways associated with arsenic toxicity and tolerance in Arabidopsis

doi: 10.1186/1471-2229-14-94

Figure Lengend Snippet: Microarray expression of genes in Arabidopsis Col-0 and Ws-2 plants exposed to As stress. (a) Venn diagram of regulated As-responsive genes extracted by comparing microarray probe sets of the 2 Arabidopsis accessions. The number of overlapping and non-overlapping genes early (1.5 to 3 h) after treatment with 100 or 200 μM As is shown. The probe sets were selected on the basis of an adjusted P-value of <0.05 and a >2-fold change in gene expression. The area of the diagram is proportional to the number of genes that are up- or downregulated in response to As stress. To clearly differentiate As-regulated genes in Col-0 from that in Ws-2, the Col-0-specific set contains only those genes with both >2-fold change in abundance (compared with control treatment) in Col-0 and <1.4-fold change in Ws-2. Likewise, the Ws-2-specific set contains genes with both > 2-fold change in abundance in Ws-2 and < 1.4-fold change in Col-0. The general As-regulated gene set contains genes displaying > 2-fold change in abundance in Col-0 or Ws-2 and >1.4-fold change in another accession. (b) Displayed are genes associated with ubiquitin pathways and abiotic stress responses using MapMan software. Both sets of material were harvested from roots tissues treated with or without As stress (100 and 200 μM for Ws-2 and Col-0, respectively). Red and blue signals represent a decrease and increase in transcript abundance, respectively, relative to water-treated control samples. The scale used for coloration of signals (log 2 ratios) is presented. (c) Validation of representative As-induced genes by semi-quantitative RT-PCR analysis. Total RNA was extracted from root tissues of Arabidopsis plants with different accessions with As treatment. The As-treated roots were harvested at 1 and 3 h. The samples were pooled together. The transcript level of actin served as an equal loading control.

Article Snippet: Microarray analysis involved Affymetrix microarrays (GeneChip Arabidopsis ATH1 genome array) containing 22,810 probe sets on a single chip.

Techniques: Microarray, Expressing, Software, Quantitative RT-PCR

Journal: PLoS ONE

Article Title: A Role for Gene Duplication and Natural Variation of Gene Expression in the Evolution of Metabolism

doi: 10.1371/journal.pone.0001838

Figure Lengend Snippet: The variation of each aliphatic glucosinolate biosynthetic transcript across seven Arabidopsis accessions from the Accession I dataset is plotted. Accumulation of each transcript within each accession was standardized to the average transcript level across the accessions. Accession coding is shown in the legend. Genes for the different transcripts are ordered from first to last (left to right) biosynthetic step. Arrows group genes for different biosynthetic steps. ‘Duplication’ indicates whether each gene was classified as being a tandem (T), segmental (S) or unique (U) gene . ‘Activity’ shows whether each gene has a unique (U), redundant (R), semi-redundant (SR) or unvalidated (?) activity. Activity was defined via analysis of published literature such that if a loss of the gene abolished the biosynthetic reaction it was classified as unique, if the loss partially abolished the reaction it was classified as semi-redundant, and if gene loss had no effect on the reaction it was deemed redundant. A question mark means that gene loss has not yet been evaluated. As there is only one probeset on the ATH1 microarray for CYP79F1 and CYP79F2 , they are jointly annotated as CYP79F in this study.

Article Snippet: Four previously published datasets encompassing a large number of transcriptomic analysis utilizing Arabidopsis Affymetrix ATH1 microarrays were used for this experiment.

Techniques: Activity Assay, Microarray

Journal: International Journal of Molecular Sciences

Article Title: Signalling Overlaps between Nitrate and Auxin in Regulation of The Root System Architecture: Insights from the Arabidopsis thaliana

doi: 10.3390/ijms21082880

Figure Lengend Snippet: Signalling mechanism of nitrate mediated auxin modulation induces lateral root growth; ( A ) ( a ) NRT1.1 initially senses, taken up and transport by the NRT1.1 transporter, thereby changing its uptake affinity and modulating phosphorylation to activate signalling pathway. In low nitrate conditions, the phosphorylation switches NRT1.1 into the high-affinity system. This sensing ability of NO 3 − altering NRT1.1 phosphorylation causes calcium (Ca 2+ ) efflux by the activation of phospholipase C (PLC). This results in varying the expression of (TGA1/4*) and nitrate transporter genes ( NRT2.1, NRT2.2, NRT3.1 ) and nitrate assimilation genes ( NIA1 and NiR ). ( b ) T101A/chl1 mutant triggers Ca 2+ -ANR1 signalling from the endosomes under high NO 3 − supply. ( c ) Under adequate NO 3 − supply, AFB3 regulates NAC4 and OBP4 expression, which as a result affect the root renovation. ( d ) Finally, as a result of nitrate assimilation organic nitrogen is produced, this system includes miR167 and miR393, which regulates AFB3 and ARF8 , respectively ( B ) In Auxin response network; Class ARF directly connects to the AuxRE (red arrow). Under low nitrate conditions, AUX/IAAs and TPLs repress transcriptional activation by class-ARFs. The degradation of Aux/IAA released this inhibition by connecting auxin and TIR1/AFB. (See text for further details).*TGA1/4 regulatory factors mediate nitrate response inside Arabidopsis root, and while the link of TGA4 to PLC is not approved. Other transcription factors, for instance, NRG2 , NLP7 , connection to Ca 2+ signalling is currently unknown.

Article Snippet: Affymetrix Arabidopsis ATH1 Genome Microarray of Anatomical Part: Root.

Techniques: Activation Assay, Expressing, Mutagenesis, Produced, Inhibition

Journal: International Journal of Molecular Sciences

Article Title: Signalling Overlaps between Nitrate and Auxin in Regulation of The Root System Architecture: Insights from the Arabidopsis thaliana

doi: 10.3390/ijms21082880

Figure Lengend Snippet: The schematic model represents NO 3 − dependent shoot-root auxin transport and accumulation inside the Arabidopsis root. “A” represents auxin (IAA).

Article Snippet: Affymetrix Arabidopsis ATH1 Genome Microarray of Anatomical Part: Root.

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: Signalling Overlaps between Nitrate and Auxin in Regulation of The Root System Architecture: Insights from the Arabidopsis thaliana

doi: 10.3390/ijms21082880

Figure Lengend Snippet: Molecular players involved in nitrate signalling regulating the primary and lateral roots; Schematic presentation of a regulatory module involved in the nitrate-mediated auxin response in Arabidopsis root. For clarity purposes, all players and their secondary transcription factors (both upstream and downstream) are presented with blue and black colors respectively, which might not be the case in a plant cell. Auxin fluxes and accumulations contribute to primary and lateral root growth are indicated with the black arrow. However, the detailed mechanism and other transcripts are still unknown.

Article Snippet: Affymetrix Arabidopsis ATH1 Genome Microarray of Anatomical Part: Root.

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: Signalling Overlaps between Nitrate and Auxin in Regulation of The Root System Architecture: Insights from the Arabidopsis thaliana

doi: 10.3390/ijms21082880

Figure Lengend Snippet: Affymetrix Arabidopsis ATH1 genome microarray analysis of the root; The schematic model represents the absolute expression level of the different nitrate transcription factors in the root of Arabidopsis , under nitrate (NO 3 − ) and auxin treatment, the red bar represents the gene expression for nitrate treatment, while the green bar represents the expression level for auxin treatments. (See text for further detail).

Article Snippet: Affymetrix Arabidopsis ATH1 Genome Microarray of Anatomical Part: Root.

Techniques: Microarray, Expressing