GEO DataSets

(Submitter supplied) In this study, we provide a global overview of genome-wide OsHOX24 binding sites in rice under control and desiccation stress conditions in wild-type and OsHOx24 overexpressing rice plants (H49 line) via chromatin immunoprecipitation sequencing (ChIP-sequencing) approach. We identified numerous downstream targets of OsHOX24 under desiccation stress and control by analyzing the comprehensive binding site map of OsHOX24 at whole genome level in rice.

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9316

16 Samples

Download data: BED

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19290

16 Samples

Download data: TXT

(Submitter supplied) Plant stress response and tolerance mechanisms are controlled by diverse genes. Transcription factors have been implicated in drought tolerance under drought stress conditions. Identification of target genes of such transcription factors could offer molecular regulatory networks by which the tolerance mechanisms orchestrated. Previously, we generated transgenic rice plants with 4 rice transcription factors OsNAC5, 6, 9, and 10 under the root-specific promoter RCc3 that were tolerant to drought stress with less loss of grain yield under drought conditions. more...

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19290

6 Samples

Download data: TXT

(Submitter supplied) To understand the molecular mechanisms of drought tolerance, we performed ChIP-Seq and RNA-Seq analyses to identify direct target genes of the OsNACs using the RCc3:MYC-OsNACs roots. A total of 475 binding loci of 4 OsNACs were identified by cross-referencing the binding occupancy of OsNACs at promoter regions and expression levels of corresponding genes. The binding loci are distributed on promoter regions of 391 target genes that were directly up-regulated by OsNACs in four RCc3:MYC-OsNAC transgenic roots. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19290

10 Samples

Download data: TXT

(Submitter supplied) Homeobox transcription factors are known to regulate plant growth and development. Recently, they have also been implicated in abiotic stress responses. To analyze the role of HD-ZIP I subfamily member, OsHOX24, we constitutively overexpressed it in Arabidopsis. The physiological analyses revealed that overexpression of OsHOX24 gene severely reduced abiotic stress tolerance in transgenic plants as compared to wild-type. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

6 Samples

Download data: CEL

(Submitter supplied) Several homeobox genes belonging to HD-ZIP I subfamily are highly induced by drought stress at various developmental stages in rice. To analyze the role of a candidate HD-ZIP I subfamily member, OsHOX24, we constitutively overexpressed it in rice. The physiological analyses revealed that overexpression of OsHOX24 gene reduced drought stress tolerance in transgenic plants as compared to wild-type. We used microarrays to study the global effect of OsHOX24 overexpression in rice as compared to wild-type under control and drought stress condition.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL21593

12 Samples

Download data: CEL

(Submitter supplied) Overexpression of a transcription factor OsEREBP1 results in attenuation of disease symptoms upon infection with bacterial pathogen Xanthomonas oryzae pv. oryzae and tolerance to drought stress in transgenic rice plants. Microarray analysis was performed to identify genes regulated by the rice transcription factor OsERBP1.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

6 Samples

Download data: CEL

(Submitter supplied) In this study, we aim to present a global view of transcriptome dynamics in different rice cultivars (IR64, Nagina 22 and Pokkali) under control and stress conditions. More than 50 million high quality reads were obtained for each tissue sample using Illumina platform. Reference-based assembly was performed for each rice cultivar. The transcriptome dynamics was studied by differential gene expression analyses between stress treatment and control sample.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9316

7 Samples

Download data: TXT

(Submitter supplied) Heat stress along with other abiotic stresses is one of the major factors affecting crop health and overall yield in a tropical country like India. Thus, there is an urgent need to understand the dynamics of heat responsiveness at the molecular as well as physiological level. Fortunately, India has a number of indigenous varieties that show tolerance to extremes in temperature during the scorching summer months. more...

Organism:

Oryza sativa; Oryza sativa Indica Group

Type:

Expression profiling by array

Platform:

GPL2025

18 Samples

Download data: CEL

(Submitter supplied) Aluminum (Al) toxicity in plants is one of the primary constraints in crop production. Al³⁺, the most toxic form of Al, is released into soil under acidic conditions and causes extensive damage to plants, especially in the roots. In rice, Al tolerance requires the ASR5 gene, but the molecular function of ASR5 has remained unknown. This data establish a comparative study of miRNAome profiles in ASR5 knockdown rice plants (ssp. more...

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13160

4 Samples

Download data: TXT

(Submitter supplied) Background The homeodomain leucine zipper (HD-Zip) transcription factor family is one of the largest plant specific superfamilies, and includes genes with roles in modulation of plant growth and response to environmental stresses. Many HD-Zip genes are characterized in Arabidopsis (Arabidopsis thaliana), and members of the family are being investigated for abiotic stress responses in rice (Oryza sativa), maize (Zea mays), poplar (Populus trichocarpa) and cucumber (Cucmis sativus). more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

21 Samples

Download data: TXT

(Submitter supplied) Opaque2 (O2) is a transcription factor that plays important roles during maize endosperm development. Mutation of the O2 gene improves the nutritional value of maize seeds, but also confers pleiotropic effects that result in reduced agronomic quality. To reveal the transcriptional regulatory framework of O2, we determined O2 DNA binding targets using chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq). more...

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15463

2 Samples

Download data: BED, TXT

(Submitter supplied) Analysis of gene expression level. The hypothesis tested in the present study was that opaque2 mutant influence the expression of storage proteins. Results provide important information of the gene expression level regulation of storage proteins and other biological processes.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17628

2 Samples

Download data: TXT

(Submitter supplied) Glutaredoxins (GRXs) are the ubiquitous oxidoreductase enzymes, which play important role in defense against various stresses. To analyze the function of a CC-type rice GRX gene, OsGRX8, we overexpressed it into Arabidopsis constitutively. The physiological analyses revealed that overexpression of GRX gene enhanced abiotic stress tolerance in transgenic plants as compared to wild-type. We used microarrays to study the global effect of overexpression of OsGRX8 in Arabidopsis under control and various treatments.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

16 Samples

Download data: CEL

(Submitter supplied) The AP2/ERF family is one of the plant-specific transcription factors (TFs) whose members have been associated with various developmental processes and stress tolerance. Here, we functionally characterized the drought-inducible OsERF48, a group Ib member of the rice ERF family that contains four conserved motifs, CMI-1, 2, 3 and 4. Transactivation assay in yeast revealed that the CMI-1 at the C-terminal end was essential for its transcriptional activity. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19290

8 Samples

Download data: TXT

(Submitter supplied) Lateral Organ Boundary Domain (LBD) transcription factors are specific of plants and are involved in the control of development. One LBD clade is related to the control of root development (Coudert et al., 2013, Mol. Biol. Evol. 30, 569-572). Belonging to this clade, CROWN ROOTLESS 1 controls the initiation of crown roots in rice (Inukai Plant Cell, 17, 1387-1396, Liu et al., 2005, Plant J., 43, 47-56). more...

Organism:

Oryza sativa Japonica Group; Oryza sativa

Type:

Expression profiling by array

Platform:

GPL25932

96 Samples

Download data: CEL, CHP

(Submitter supplied) The OsbZIP23 transcription factor has been characterized for its essential role in drought resistance in rice, but the mechanism is unknown. Here, we performed genome-wide identification of OsbZIP23 targets by immunoprecipitation sequencing (ChIP-seq) and RNA Sequencing (RNA-Seq) analyses in the OsbZIP23-overexpression, osbzip23 mutant, and wild-type rice under normal and drought stress conditions. OsbZIP23 directly regulates a large number of reported genes that function in stress response, hormone signaling, and developmental processes. Among these targets, we found that OsbZIP23 could positively regulate OsPP2C49, and overexpression of OsPP2C49 in rice resulted in significantly decreased sensitivity of the ABA response and rapid dehydration. Moreover, OsNCED4 (9-cis-epoxycarotenoid dioxygenase 4), a key gene in ABA biosynthesis, was also positively regulated by OsbZIP23. Together, our results suggest that OsbZIP23 acts as a central regulator in ABA signaling and biosynthesis, and drought resistance in rice.

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13834

9 Samples

Download data: TAR, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19290

32 Samples

Download data: BEDGRAPH, TXT, XLS

(Submitter supplied) To identify the differetially expressed sRNAs under nitrate stress, sRNA-seq was performed using total RNA extracted from root and seedling tissues from plants were grown in both low (0 mM) and high (100 mM) nitrate conditions. The analysis was performed in duplicates and the reads were processed and analysed using UEA sRNA workbench.

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19290

12 Samples

Download data: TXT

(Submitter supplied) To identify the differetially expressed genes under nitrate stress, RNA-seq was performed using total RNA extracted from root and seedling tissues from plants were grown in both low (0 mM) and high (100 mM) nitrate conditions. The analysis was performed in duplicates and the reads were mapped to rice (IRGSP-1) genome.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19290

12 Samples

Download data: XLSX