GEO DataSets

(Submitter supplied) Iron (Fe) is an essential micronutrient for almost all organisms. However, Fe is frequently inaccessible to plants. To acquire insoluble Fe from soil, rice (Oryza sativa L.) plants employ a Combined Strategy, which is composed by all features of Strategy II, common to all Poaceae species, and some features of the Strategy I from non-Poaceae. To understand the evolution of Fe uptake mechanisms, we analyzed the root transcriptomic response to Fe deficiency in two species from the Oryza genus: O. more...

Organism:

Oryza rufipogon; Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL15800 GPL13160

8 Samples

Download data: TSV

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

Organism:

Oryza sativa; Oryza sativa aus subgroup; Oryza nivara; Oryza sativa Indica Group; Oryza rufipogon

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

5 related Platforms

50 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) are a class of 21 nt non-coding small RNAs (sRNAs) produced from endogenously expressed MIR genes. MiRNAs are mostly involved in development and disease resistance. To know the involvement of miRNAs during domestication of rice, sRNA sequencing of two wild species (O. nivara and O. rufipogon), one landrace (O. sativa chomala) and one cultivated species of rice (O. sativa indica Pusa Basmati-1) was carried out. more...

Organism:

Oryza sativa; Oryza sativa Indica Group; Oryza sativa aus subgroup; Oryza nivara; Oryza rufipogon

Type:

Non-coding RNA profiling by high throughput sequencing

5 related Platforms

30 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) are a class of 21 nt non-coding small RNAs (sRNAs) produced from endogenously expressed MIR genes. MiRNAs are mostly involved in development and disease resistance. To know the involvement of miRNAs during domestication of rice, sRNA sequencing of two wild species (O. nivara and O. rufipogon), one landrace (O. sativa chomala) and one cultivated species of rice (O. sativa indica Pusa Basmati-1) was carried out. more...

Organism:

Oryza sativa; Oryza sativa aus subgroup; Oryza sativa Indica Group; Oryza rufipogon; Oryza nivara

Type:

Expression profiling by high throughput sequencing

5 related Platforms

20 Samples

Download data: TXT

(Submitter supplied) Ecological speciation is a common mechanism by which new species arise. Despite great efforts, the role of gene expression in ecological divergence and speciation is poorly understood. Here, we conducted a genome-wide gene expression investigation of two Oryza species that are evolutionarily young and distinct in ecology and morphology. Using digital gene expression (DGE) technology and the paired-end RNA sequencing (RNA-Seq) method, we obtained 21,415 expressed genes across three reproduction-related tissues at two critical developmental stages. more...

Organism:

Oryza rufipogon; Oryza nivara

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL10246 GPL10245

42 Samples

Download data: TXT

(Submitter supplied) Dongxiang wild rice (Oryza rufipogon Griff.) is the progenitor of cultivated rice (Oryza sativa L.) and is well known for its superior level of tolerance against cold, drought and diseases. To date, however, little is known about the salt-tolerant character of Dongxiang wild rice. To elucidate the molecular genetic mechanisms of salt-stress tolerance in Dongxiang wild rice, the Illumina HiSeq 2000 platform was used to analyze the transcriptome profiles of the leaves and roots at the seedling stage under salt stress compared with those under normal conditions. more...

Organism:

Oryza rufipogon

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15800

4 Samples

Download data: TXT

(Submitter supplied) Canola (oilseed rape, Brassica napus L.), is susceptible to infection by the biotrophic protist Plasmodiophora brassicae, the causal agent of clubroot. To understand the roles of microRNAs (miRNAs) during the post-transcriptional regulation of disease initiation and progression, we have characterized the changes in miRNA expression profiles in canola roots during clubroot disease development and have compared these to uninfected roots. more...

Organism:

Picea glauca; Populus tremuloides; Populus trichocarpa; Prunus persica; Medicago truncatula; Nicotiana benthamiana; Hordeum vulgare; Ipomoea nil; Prunus armeniaca; Peridictyon sanctum; Oryza barthii; Hordeum vulgare subsp. vulgare; Oenocarpus bataua; Picea sitchensis; Brassica napus; Lupinus luteus; Phaseolus coccineus; Manihot esculenta; Ricinus communis; Oryza brachyantha; Cenchrus americanus; Phleum pratense; Panicum virgatum; Nuphar advena; Physcomitrium patens; Persea americana; Populus trichocarpa x Populus deltoides; Malus domestica; Nicotiana sylvestris; Nicotiana tabacum; Petunia x hybrida; Oryza sativa; Lolium arundinaceum; Lotus japonicus; Cenchrus ciliaris; Populus tremula x Populus tremuloides; Nasturtium officinale; Pinus taeda; Liriodendron tulipifera; Phaseolus vulgaris; Ipomoea batatas; Lactuca sativa; Oryza rufipogon; Oryza nivara; Sorghum bicolor; Rorippa indica; Prunus salicina; Populus tremula; Malcolmia maritima

Type:

Non-coding RNA profiling by array

Platform:

GPL17805

4 Samples

Download data: TXT

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

Organism:

Oryza rufipogon

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL10246 GPL15800

4 Samples

Download data: FA, FASTA

(Submitter supplied) The lack of MIRNA set and genome sequence of O. rufipogon (the ancestor of the cultivated rice) has limited to answer the role of MIRNA genes in rice domestication. In this study, a genome, three small RNA populations and a degradome of O.rufipogon were sequenced by Illumina platform and miRNA expression were investigated by miRNA chips. A de novo genome was assembled using ~55x coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. more...

Organism:

Oryza rufipogon

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15800

3 Samples

Download data: FASTA

(Submitter supplied) The lack of MIRNA set and genome sequence of O. rufipogon (the ancestor of the cultivated rice) has limited to answer the role of MIRNA genes in rice domestication.In this study, a genome, three small RNA populations and a degradome of O.rufipogon were sequenced by Illumina platform and miRNA expression were investigated by miRNA chips. A de novo genome was assembled using ~55x coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. more...

Organism:

Oryza rufipogon

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10246

1 Sample

Download data: FA

(Submitter supplied) To examine the rice genome methylation landscape and assess its functional significance, we generated the first single-base resolution genome methylation maps for Oryza sativa ssp. japonica, indica and their wild relatives, Oryza rufipogon and Oryza nivara. The methylation level of rice genomes is four times higher than that of Arabidopsis. Methylation in the promoter and gene body regions have similar patterns and effects on gene expression as those in Arabidopsis but different from a previous study on rice chromosomes 4 and 10. more...

Organism:

Oryza rufipogon; Oryza nivara; Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL10245 GPL9147 GPL10246

4 Samples

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(Submitter supplied) plant miRNA microarray with 100% coverage of mature plant miRNAs listed in miRBase version 15.0. Arrays are made based µParaflo microfluidic technology (Atactic Technologies). On the µParaflo microfluidic chip, each detection probe consists of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. more...

Organism:

Physcomitrium patens; Picea glauca; Picea sitchensis; Pinus taeda; Liriodendron tulipifera; Persea americana; Populus tremuloides; Populus trichocarpa; Populus trichocarpa x Populus deltoides; Malus domestica; Prunus persica; Lupinus luteus; Medicago truncatula; Phaseolus vulgaris; Phaseolus coccineus; Manihot esculenta; Ricinus communis; Nicotiana sylvestris; Nicotiana tabacum; Nicotiana benthamiana; Petunia x hybrida; Ipomoea batatas; Lactuca sativa; Hordeum vulgare; Oryza rufipogon; Oryza sativa; Oryza brachyantha; Oryza nivara; Cenchrus americanus; Sorghum bicolor; Lolium arundinaceum; Phleum pratense; Lotus japonicus; Cenchrus ciliaris; Ipomoea nil; Prunus armeniaca; Peridictyon sanctum; Panicum virgatum; Populus tremula x Populus tremuloides; Rorippa indica; Oryza barthii; Nasturtium officinale; Nuphar advena; Prunus salicina; Hordeum vulgare subsp. vulgare; Populus tremula; Oenocarpus bataua; Malcolmia maritima

1 Series

4 Samples

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