GEO DataSets

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to investigate NGS-derived rice leaf transcriptome profiling (RNA-seq) exposed to green rice leafhopper (GRH) and validated RNA-Seq results using quantitative reverse transcription polymerase chain reaction (qRT–PCR). Methods: Rice leaf mRNA profiles of 21-day-old wild-type (WT) and Near Isogenic Line (NIL) rice were generated by deep sequencing, in triplicate, using Illumina’s HiSeq™ 4000 Sequencing System. more...

Organism:

Oryza sativa Japonica Group; Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21812 GPL23013

4 Samples

Download data: GTF, TAB, TXT, XLS

(Submitter supplied) We exposed Kavya rice seedlings to different gall midge biotypes, GMB1 and GMB4M, which exhibit incompatible and compatible interactions, respectively.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

9 Samples

Download data: CEL, CHP

(Submitter supplied) Purpose: The aim of this study was to compare transcriptome profiling (RNA-seq) of rice panicle tissue from resistant and suceptible lines at different time intervals infected with M.oryzae. The results were validated using Semi-quantitative PCR. Methods: Panicles from resistant and suceptible rice lines were inoculated with suspension having double distill water, Tween-20 without spores for 0 hour and same suspension with spores was used to inoculate for 48, 72 and 96 hour samples. more...

Organism:

Oryza sativa Indica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14553

16 Samples

Download data: GTF

(Submitter supplied) In order to reveal the molecular foundation of BPH resistance of RH, the whole genome expressional profiles of RH together with the control TN1 under BPH infestation were determined using cDNA microarray analysis.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

36 Samples

Download data: CEL

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

Organism:

Oryza sativa Japonica Group

Type:

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

Platform:

GPL23876

44 Samples

Download data

(Submitter supplied) Here, a combined small RNA and transcriptome sequencing analysis was performed on the BPH6-transgenic and Nipponbare plants sheath samples at the different feeding stage by BPH, and differentially expressed microRNAs (DEMs) and genes (DEGs) were identified and further analyzed for a possible involvement in BPH6 mediated resistance mechanism. A total of 217 DEMs and 7,874 DEGs were identified in the BPH6-transgenic and Nipponbare plants after BPH feeding. more...

Organism:

Oryza sativa Japonica Group

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23876

26 Samples

Download data: XLS

(Submitter supplied) Here, a combined small RNA and transcriptome sequencing analysis was performed on the BPH6-transgenic and Nipponbare plants sheath samples at the different feeding stage by BPH, and differentially expressed microRNAs (DEMs) and genes (DEGs) were identified and further analyzed for a possible involvement in BPH6 mediated resistance mechanism. A total of 217 DEMs and 7,874 DEGs were identified in the BPH6-transgenic and Nipponbare plants after BPH feeding. more...

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23876

18 Samples

Download data: XLS

(Submitter supplied) Autotoxicity plays an important mechanism in regulating plant productivity. Ferulic acid (FA) is phytotoxic and was identified in extracts and residues of rice plants as a candidate for rice allelochemicals. To help characterize the autotoxicity mechanism of rice, we present the first large-scale, transcriptomic analysis of rice root responses to ferulic acid.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL8852

6 Samples

Download data: TXT

(Submitter supplied) Purpose: The aim of this study was to compare transcriptome profiling (RNA-seq) of rice leaf tissue infected with M.oryzae of resistant and suceptible line. The results were validated using real time PCR. Methods: Rice leaves were collected 24 hours after M. Oryza (Mo-nwi-53) infection from resistant and suceptible line, frozen on liquid nitrogen, and RNA was extracted using Spectrum™ Plant Total RNA Kit (Sigma). more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21945

12 Samples

Download data: GTF

(Submitter supplied) Host-pathogen interactions, in particular during the early stages of infection, are important for the fate of both the invading pathogen and host. In pathogens, these interactions activate diverse pathogenic signals to cause disease in the host and evade the inevitably activated immune responses of the infected host. In this study, we used in vitro assay system and RNA-seq to analyze the time-resolved genome-wide gene expressions of Xanthomonas oryzae pv. more...

Organism:

Xanthomonas oryzae pv. oryzae KACC 10331

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19216

14 Samples

Download data: TXT

(Submitter supplied) Rice blast disease is a major threat to rice production worldwide, but the mechanisms underlying rice resistance to the causal agent Magnaporthe oryzae remain elusive. In this whole-genome transcriptome study of rice early defense response to M. oryzae, we applied Affymetrix Rice Genome Genechip to compare the compatible and incompatible rice-M. oryzae interactions in 24 hours post-inoculation.

Organism:

Oryza sativa Japonica Group; Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

18 Samples

Download data: CEL

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

Organism:

Oryza sativa; Oryza sativa Indica Group

Type:

Expression profiling by array

Platform:

GPL7252

90 Samples

Download data: TXT

(Submitter supplied) The current knowledge of drought stress transcriptomes in rice are mostly relying on comparative studies of diverse genetic background under drought. A more reliable approach is to use near-isogenic lines (NILs) with a common genetic background (Donar parent: Aday Sel, Recurrent parent: IR64), but contrasting levels of resistance to drought stress under initial exposure to water deficit. Here, we examined two pairs of NILs in IR64 background with contrasting drought tolerance. more...

Organism:

Oryza sativa Indica Group; Oryza sativa

Type:

Expression profiling by array

Platform:

GPL7252

30 Samples

Download data: TXT

(Submitter supplied) The current knowledge of drought stress transcriptomes in rice are mostly relying on comparative studies of diverse genetic background under drought. A more reliable approach is to use near-isogenic lines (NILs) with a common genetic background (Donar parent: Aday Sel, Recurrent parent: IR64), but contrasting levels of resistance to drought stress under initial exposure to water deficit. Here, we examined two pairs of NILs in IR64 background with contrasting drought tolerance. more...

Organism:

Oryza sativa Indica Group; Oryza sativa

Type:

Expression profiling by array

Platform:

GPL7252

30 Samples

Download data: TXT

(Submitter supplied) The current knowledge of drought stress transcriptomes in rice are mostly relying on comparative studies of diverse genetic background under drought. A more reliable approach is to use near-isogenic lines (NILs) with a common genetic background (Donar parent: Aday Sel, Recurrent parent: IR64), but contrasting levels of resistance to drought stress under initial exposure to water deficit. Here, we examined two pairs of NILs in IR64 background with contrasting drought tolerance. more...

Organism:

Oryza sativa Indica Group; Oryza sativa

Type:

Expression profiling by array

Platform:

GPL7252

30 Samples

Download data: TXT

(Submitter supplied) Background: Plant disease is a major challenge to agriculture worldwide, and it is often exacerbated by abiotic environmental factors. During some plant-pathogen interactions, heat stress increases host susceptibility, a tendency which could spell disaster in light of the global warming trends associated with climate change. Despite the importance of this phenomenon, little is known about the molecular mechanisms that cause it. more...

Organism:

Oryza sativa Indica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21027

28 Samples

Download data: TXT

(Submitter supplied) MicroRNAs (miRNAs) regulate a spectrum of development and defense response processes in plants. The brown planthopper (BPH) is the most devastating insect pest of rice, BPH resistance gene BPH15 has a strong resistance to BPH. In this study, we analyzed six miRNA profiles of BPH15 introgression line (P15) and susceptible recipient line (PC) in 3 time points (0h, 6h and 48h) after BPH attacked, and identified 464 known miRNAs and 183 novel miRNAs. more...

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13160

6 Samples

Download data: XLS

(Submitter supplied) Comparative transcriptome profiles of cotton (G. hirsutum L. cv. Bikaneri narma) during boll development stages (0, 2, 5 and 10 dpa) under bollworm infested biotic stress. Cotton is one of the most commercially important fibre crops in the world and used as a source for natural textile fibre and cottonseed oil. The biotic stress is one of the major constraints for crop production. Cotton bollworm (Helicoverpa armigera) is one the major insect pest in cotton and drastically damages the cotton boll. more...

Organism:

Gossypium hirsutum; Gossypium arboreum; Gossypium barbadense; Gossypium raimondii

Type:

Expression profiling by array

Platform:

GPL8672

24 Samples

Download data: CEL, CHP

(Submitter supplied) Using rice cultivars Nipponbare, which exhibits resistance to Striga hermonthica (a root parasitic plant that causes devastating loss of yield), and IAC165, which is susceptible, we aim to identify suites of genes underlying susceptibility and resistance to S. hermonthica by profiling changes in gene expression using rice whole genome microarrays. In addition to a functional categorisation of changes in gene expression, genes that were significantly differentially regulated within regions predicted to contain Nipponbare quantitative trait loci for resistance were identified. more...

Organism:

Oryza sativa; Oryza sativa Japonica Group

Type:

Expression profiling by array

Platform:

GPL2025

24 Samples

Download data: CEL

(Submitter supplied) This study provides comprehensive information about plant responses to nitrosative stress at transcript level and would prove helpful in understanding and incorporating mechanisms associated with nitrosative stress responses in plants.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

6 Samples

Download data: TXT