The effect of OsWOX4 knockdown on the expression profile in rice the leaf primordia and the SAM
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE107463 | GEO | 2018/12/31
REPOSITORIES: GEO
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Project description:Transgenic Arabidopsis seedlings RV86-5 (contains a dexamethasone-inducible ubiquitin variant that contains Arg instead of Lys at position 48; ̈Schlögelhofer et al., 2005) were surface-sterilized and sown on Uhelon 120T (Silk & Progress, Czech Republic) mesh placed on 1% (w/v) agar containing a half-strength Murashige and Skoog medium (pH 5.7), stratified at 4 °C for 3 d, and cultivated at 21 °C/19 °C day/night temperatures, with a 16 h photoperiod (90 μmol m−2 s−1 light intensity) for 14 d. On the fourteenth day (after the first 2 h of the day period), the Uhelon mesh with the seedlings was transferred onto a new solid medium supplemented with (i) 5×10−4% (v/v) DMSO (mock); (ii) 0.7 or 7.0 μM dexamethasone (DEX) and rinsed with DMSO or DEX-supplemented water for mock and DEX-treated seedlings, respectively, and incubated for 24 hours.
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2019-02-21 | PXD007678 | Pride
Project description:Purpose: The goals of this study are screening the putative target genes regulated by OsNF-YA5 using DEX(dexamethason) inducible system. Methods: 10-day-old GOS2::OsNF-YA5-GR plants grown on MS solid media were treated with 50 μM dexamethasone (DEX) solution containing 0.02% (w/v) Silwet L-77. For mock treatments, 0.02% Silwet L-77 was sprayed into rice plants. To minimize the effect by the treatment, plants were pre-treated with 0.02% Silwet L-77 3 hours before DEX treatment). Total RNAs were extracted using the RNeasy plant mini kit (Qiagen, USA) according to the manufacturer’s instruction. cDNA libraries were prepared using the TruSeq RNA Sample Prep kit (v2) (Macrogen, Korea). Single-end sequences were obtained using IRGSP (v 1.0) and raw sequence reads were trimmed to remove adaptor sequence, and those with a quality lower than Q20 were removed using the Trimmomatic 0.32 software (Bolger et al., 2014). To map the reads to reference genome, all reads were assembled with annotated genes from the Rap-DB database [http://rapdb.dna.affrc.go.jp; IRGSP (v 1.0)] using TopHat software (https://ccb.jhu.edu/software/tophat/index.shtml). After mapping reads to a reference genome, differentially expressed genes (DEGs) were selected using a cut-off change of at least 2-fold change (DEX/mock) and Student’s t-test (P < 0.1). The selected DEGs were grouped by hierarchical clustering analysis (Complete Linkage). Results: RNA sequencing analysis revealed that 81 (3 hr DEX treatment) and 88 (9 hr DEX treatment) genes were up-regulated. In comparison, 61 (3 hr DEX treatment) and 45 (9 hr DEX treatment) genes were down-regulated in GOS2:OsNF-YA5-GR transgenic plants by DEX treatment compared to mock treatment. Among 161 up-regulated genes, 71 genes (44%) were also up-regulated in N starvation conditions. GO term analysis of up-regulated genes revealed that 59-76% of genes were involved in the metabolic process, and 10%-12% were transporter (Extended Data Fig. 4c). These results suggested that OsNF-YA5 regulated the genes involved in the metabolic process. Conclusions: OsNF-YA5 positively regulated the genes involved in the nitrogen metabolic process including amino acid and nitrate/peptide transporters.
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Project description:This experiment describes gene expression after the activation of APETALA1-GR, to study and identify AP1 target genes. We used a 35S:AP1-GR ap1 cal line to induce a synchronized response activating the AP1-GR fusion protein in ap1 cal inflorescence-like meristems through dexamethasone treatment. Tissue samples were collected immediately after the treatment, as well as subsequent timepoints. The expression profiles of the individual samples were then analyzed by gene expression profiling using whole-genome oligonucleotide arrays (non-commercial; Meyerowitz Lab Arabidopsis Operon Array v4). Keywords: time course Four sets of biologically independent tissue samples were collect at 0, 2, 4 ,8, and 12 hours after the application of dexamethasone (Dex-; activation of the AP1-GR fusion protein) or a mock solution (Mock-; control). In each of the biological replicates of the time course experiments, all the samples derived from dexamethasone (Dex)-treated plants were labeled with one dye (i.e., Cy3), and all the samples derived from the corresponding Mock-treated plants were labeled with the alternative dye (i.e., Cy5). The dyes used for labeling RNA from a given treatment type (Dex and Mock) were switched for two of the replicate experiments, to reduce dye-related artifacts. Dex- and Mock-derived samples for each timepoint and biological replicate were co-hybridized. This experimental setup resulted in a total of 5 hybridizations per set (0h, 2h, 4, 8h, and 12h; Dex vs. Mock at each timepoint), and two biological replicate sets labeled with each dye polarity (Mock-Cy3/Dex-Cy5, and vice versa). The combined ratio data results are available as a supplementary file on the Series record.
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Project description:This experiment describes gene expression after the activation of APETALA1-GR, to study and identify AP1 target genes. We used a 35S:AP1-GR ap1 cal line to induce a synchronized response activating the AP1-GR fusion protein in ap1 cal inflorescence-like meristems through dexamethasone treatment. Tissue samples were collected immediately after the treatment, as well as subsequent timepoints. The expression profiles of the individual samples were then analyzed by gene expression profiling using whole-genome oligonucleotide arrays (non-commercial; Meyerowitz Lab Arabidopsis Operon Array v4). Keywords: time course Four sets of biologically independent tissue samples were collect at 0, 2, 4 ,8, and 12 hours after the application of dexamethasone (Dex-; activation of the AP1-GR fusion protein) or a mock solution (Mock-; control). In each of the biological replicates of the time course experiments, all the samples derived from dexamethasone (Dex)-treated plants were labeled with one dye (i.e., Cy3), and all the samples derived from the corresponding Mock-treated plants were labeled with the alternative dye (i.e., Cy5). The dyes used for labeling RNA from a given treatment type (Dex and Mock) were switched for two of the replicate experiments, to reduce dye-related artifacts. Dex- and Mock-derived samples for each timepoint and biological replicate were co-hybridized. This experimental setup resulted in a total of 5 hybridizations per set (0h, 2h, 4, 8h, and 12h; Dex vs. Mock at each timepoint), and two biological replicate sets labeled with each dye polarity (Mock-Cy3/Dex-Cy5, and vice versa). The combined ratio data results are available as a supplementary file on the Series record.
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