GEO DataSets

(Submitter supplied) In order to understand molecular mechanisms of salt stress tolerance in rice several researches have been reported, however there are still unclear processes involved in salt tolerance. For reaching to a better perspective of the molecular mechanisms, we designed a comprehensive transcriptome study consisting contrasting genotypes, different tissues and different sampling time points. Two contrasting genotypes were selected and grown in Yoshida hydroponic medium for 14 days under controlled conditions. more...

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22250

48 Samples

Download data: TXT

(Submitter supplied) Rice has evolved regulatory programs and specialized cell types that allow the plant to withstand different environments. To understand how rice root systems cope with water stresses, we profiled translatomes (ribosome-associated mRNAs) and accessible chromatin of developmentally-defined root cell populations from well-watered and drained control (aerobic control), water deficit, waterlogged, fully submerged plants and recovery conditions.  Whereas, the waterlogging responses are limited to specific root domains, water deficit and submergence signatures are extensive, and mostly reversible after 1 day of  recovery, relative to control roots. more...

Organism:

Oryza sativa Japonica Group

Type:

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

Platforms:

GPL22250 GPL26083

238 Samples

Download data: XLSX

(Submitter supplied) In this study we generated small RNA libraries from tissues rice plants infected with Meloidogyne graminicola (Mg)3 days postinoculation as well as from uninfected rice plants. The goal was to study the behaviour of small RNA (miRNA and siRNAs) in response to Mg infection. We combine the expression data gathered from this experiment together with degradome sequencing to predict the targets of differentially expressed miRNAs. more...

Organism:

Oryza sativa Japonica Group

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL22250

6 Samples

Download data: TXT

(Submitter supplied) Rice MERISTEM ACTIVITYLESS1 (MAL1) is an RING-H2 finger domain (RFD) contained gene. To elucidate the molecular functions of MAL1 during crown root development, we generated MAL1 knock-down transgenic plants. MAL1 RNA interfering (RNAi) transgenic plants exhibited shorter crown root length and less crown root number phenotype accompanied by low cell division rate.Here we sought to find the downstream genes of OsMAL1 in rice crown root tip

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22250

4 Samples

Download data: DIFF

(Submitter supplied) Staple crops in human and livestock diets suffer from deficiencies in certain “essential” amino acids including methionine. With the goal of increasing methionine in rice seed, we generated a pair of “PushxPull” double transgenic lines, each containing a methionine-dense seed storage protein (2S albumin from sunflower, HaSSA) and an exogenous enzyme for either methionine (feedback desensitized cystathionine gamma synthase from Arabidopsis, AtD-CGS) or cysteine (serine acetyltransferase from E. more...

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22250

22 Samples

Download data: TAB

(Submitter supplied) Climate change has increased the frequency and intensity of floods that impact global agricultural productivity. To better understand the response mechanisms and evolutionary history of gene family member regulation across angiosperm phyla, we studied the rapid submergence response of rice, the legume Medicago truncatula, and two Solanum species, domesticated tomato (S. lycopersicum cv. M82) and its dryland-adapted wild relative S. more...

Organism:

Solanum lycopersicum; Medicago truncatula; Solanum pennellii; Oryza sativa Japonica Group

Type:

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

8 related Platforms

231 Samples

Download data: BED, BW, TXT, XLSX

(Submitter supplied) Plants dynamically regulate chromatin architecture, transcription and post-transcriptional processes in accordance with developmental programs and environmental cues. Isolated nuclei can provide access to early steps in gene regulation involving chromatin as well as transcript production and processing. Here we describe transfer of the Isolation of Nuclei from TAgged specific Cell Types (INTACT) to the monocot rice (Oryza sativa L.). more...

Organism:

Oryza sativa Japonica Group

Type:

Other

Platform:

GPL22250

3 Samples

Download data: XLS

(Submitter supplied) WUSCHEL-related homeobox domain trancription factor WOX11 is a key regulator of crown root growth and development in rice (Oryza sativa. L). However, the gene regulatory network downstream of WOX11 remains largely unknown. To dissect WOX11 transcriptional regulatory framework, we determined the transcriptome of wox11 mutants and corresponding wild type (Hwayoung) by using RNA-seq technology.

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22250

4 Samples

Download data: DIFF, FPKM_TRACKING

(Submitter supplied) Shoot-borne crown roots are the major root system in cereals. Previous work has shown that the Wuschel-related homeobox gene WOX11 is necessary and sufficient to promote rice crown root emergence and elongation. Here, we show that WOX11 recruits the ADA2-GCN5 histone acetyltransferase (HAT) module to activate downstream target genes in crown root meristem. OsGCN5 and OsADA2 are highly expressed in root meristem. more...

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22250

8 Samples

Download data: DIFF

(Submitter supplied) H3K27me3 is a repressive chromatin mark of genes and is catalyzed by homologs of Enhancer of zeste [E(z)], a component of Polycomb-repressive complex 2 (PRC2), while DNA methylation that occurs in CG and non-CG (CHG and CHH, where H is A, C or T) contexts is a hallmark of transposon silencing in plants. However, relationship between H3K27me3 and DNA methylation in gene repression remains unclear. In addition, the mechanism of PRC2 recruitment to specific genes is not known in plants. more...

Organism:

Oryza sativa Japonica Group

Type:

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

Platforms:

GPL13834 GPL22250

7 Samples

Download data: TAR, TXT, WIG