Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA173228 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Identification of WRKY22 targets under submergence in Arabidopsis (mRNA)
| PRJNA173229 | ENA
Project description:We analyzed global transcriptional changes in submerged Arabidopsis seedlings comparing control untreated seedlings. The same analysis were also applied on wrky22-ko2 seedling to identify WRKY22 targets under submergence.
2013-07-03 | GSE40139 | GEO
Project description:To identify direct targets of WRKY22, we created a transgenic Arabidopsis line that expresses a c-myc epitope-tagged WRKY22 and used ChIP followed by microarray hybridization (ChIP-chip) to screen for candidates and validate the in vivo protein-DNA interactions with ChIP followed by quantitative PCR (ChIP-Q-PCR). The WRKY22 and c-myc epitope tag fusion construct was generated and transformed into wrky22-ko2 plants. The resulting transgenic lines should have better ChIP efficiency than the wild-type background, due to the reduced competition for WRKY22 binding sites from endogenous WRKY22. ChIP-enriched DNA fragments were identified using criteria of a window of +300 to M-oM-<M-1200 of a gene for a promoter, a width of 4 probes or more, and a false discovery rate (FDR) < 0.1. The ChIP-chip experiments were repeated six times, i.e., six biological replicas. Candidates were defined by the presence of the promoter in three out of six biological replicas. Candidates were then classified based on their hypoxic responsiveness with a positive response defined as gene expression levels exhibiting > 2 or < 0.5-fold induction in any time point under submergence treatments in expression array data. Comparison of c-myc tagged WRKY22 transgenic plants vs wild-type (Columbia) plants. Both materials were submergence treated for 3 hours.
2013-07-03 | E-GEOD-40138 | biostudies-arrayexpress
Project description:To identify direct targets of WRKY22, we created a transgenic Arabidopsis line that expresses a c-myc epitope-tagged WRKY22 and used ChIP followed by microarray hybridization (ChIP-chip) to screen for candidates and validate the in vivo protein-DNA interactions with ChIP followed by quantitative PCR (ChIP-Q-PCR). The WRKY22 and c-myc epitope tag fusion construct was generated and transformed into wrky22-ko2 plants. The resulting transgenic lines should have better ChIP efficiency than the wild-type background, due to the reduced competition for WRKY22 binding sites from endogenous WRKY22. ChIP-enriched DNA fragments were identified using criteria of a window of +300 to －1200 of a gene for a promoter, a width of 4 probes or more, and a false discovery rate (FDR) < 0.1. The ChIP-chip experiments were repeated six times, i.e., six biological replicas. Candidates were defined by the presence of the promoter in three out of six biological replicas. Candidates were then classified based on their hypoxic responsiveness with a positive response defined as gene expression levels exhibiting > 2 or < 0.5-fold induction in any time point under submergence treatments in expression array data.
2013-07-03 | GSE40138 | GEO
Project description:We analyzed global transcriptional changes in submerged Arabidopsis seedlings comparing control untreated seedlings. The same analysis were also applied on wrky22-ko2 seedling to identify WRKY22 targets under submergence. Time course experiments (1, 3, and 6 for Columbia and wrky22-ko2). Tissues from submerged seedlings vs. Tissues from un-submerged seedlings. Biological replicates: 4 replicates for each time point, independently grown, treated, and harvested. One replicate per array. 2 of 4 replicates are dye-swapped.
2013-07-03 | E-GEOD-40139 | biostudies-arrayexpress
Project description:Identification of NLP7 direct targets using ChIP-chip in Arabidopsis thaliana
| PRJNA156735 | ENA
Project description:Autophagy involves massive degradation of intracellular components and functions as a conserved system that helps cells to adapt to adverse conditions. In Arabidopsis thaliana, submergence induces the transcription of autophagy-related (ATG) genes and the formation of autophagosomes. To study the role of autophagy during submergence, we performed transcriptome analysis with atg5, an autophagy-defective mutant, under submergence conditions. Our data showed that submergence changed the expression profile of DEG in the atg5 versus wild-type.
2021-09-20 | GSE184340 | GEO
Project description:Identification of direct targets of Arabidopsis JAGGED in floral buds
| PRJNA223391 | ENA
Project description:FLP and MYB88 are two paralogous MYB proteins, regulating the symmetric division of guard mother cell during Arabidopsis stomatal development. To understand their molecular functions, we performed genome-wide identification of FLP/MYB88 binding targets using ChIP-chip with FLP/MYB88 antibody. By comparing ChIP-chip between wild-type and flp-1 myb88 lines, a total genes were identified as putative direct targets for FLP/MYB88.
2010-09-01 | GSE19763 | GEO