GEO DataSets

Analysis of crown and growing point of salt-tolerant (FL478) and salt-sensitive (IR29) genotypes under control and salinity-stressed conditions during vegetative growth. Results provide insight into the genetic basis of salt tolerance in rice.

Organism:

Oryza sativa; Oryza sativa Indica Group

Type:

Expression profiling by array, count, 2 genotype/variation, 2 stress sets

Platform:

GPL2025

Series:

GSE3053

11 Samples

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(Submitter supplied) Crown and growing point tissue was used for expression analysis in control and salt stressed samples. Targets from biological replicates of both genotypes were generated and the expression profiles were determined using Affymetrix Rice Genome arrays. Keywords: repeat

Organism:

Oryza sativa; Oryza sativa Indica Group

Type:

Expression profiling by array

Dataset:

GDS1383

Platform:

GPL2025

11 Samples

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(Submitter supplied) Expression Data of Rice Crown and Growing Point Tissue Under Salt Stress imposed during the Panicle Initiation Stage Keywords: genotypes and growth conditions (control and salt stressed)

Organism:

Oryza sativa Japonica Group; Oryza sativa; Oryza sativa Indica Group

Type:

Expression profiling by array

Platform:

GPL2025

24 Samples

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

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13160

8 Samples

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(Submitter supplied) Soil salinity is one of the primary causes of yield decline in rice. Pokkali (Pok) is a highly salt-tolerant landrace whereas IR29, is salt-sensitive but a widely cultivated cultivar. Comparative analysis of these genotypes may offer better understandings of the salinity tolerance mechanism. The published reports largely underscored the importance of transcriptional regulation during salt stress in these genotypes, while, the regulation at translational level is also critically important. more...

Organism:

Oryza sativa

Type:

Other

Platform:

GPL13160

4 Samples

Download data: XLSX

(Submitter supplied) Soil salinity is one of the primary causes of yield decline in rice. Pokkali (Pok) is a highly salt-tolerant landrace whereas IR29, is salt-sensitive but a widely cultivated cultivar. Comparative analysis of these genotypes may offer better understandings of the salinity tolerance mechanism. The published reports largely underscored the importance of transcriptional regulation during salt stress in these genotypes, while, the regulation at translational level is also critically important. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13160

4 Samples

Download data: XLSX

(Submitter supplied) Analysis of root gene expression of salt-tolerant genotypes FL478, Pokkali and IR63731, and salt-sensitive genotype IR29 under control and salinity-stressed conditions during vegetative growth. Results provide insight into the genetic basis of salt tolerance in indica rice. Keywords: stress response

Organism:

Oryza sativa; Oryza sativa Indica Group

Type:

Expression profiling by array

Platform:

GPL2025

23 Samples

Download data: CEL

(Submitter supplied) To dissect the molecular mechanisms underlying drought tolerance (DT) in rice, transcriptome differences of a DT introgression line H471, the DT donor P28 and the drought sensitive recurrent parent HHZ under drought stress were investigated using deep transcriptome sequencing. Results revealed a differential constitutive gene expression prior to stress and distinct global transcriptome reprogramming among three genotypes under time-series drought stress, consistent with their differential genotypes and DT phenotypes.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13160

18 Samples

Download data: TXT

(Submitter supplied) Rice is sensitive to chilling stress, especially at the seedling stage. To elucidate the molecular genetic mechanisms of chilling tolerance in rice, comprehensive gene expressions of two rice genotypes (chilling-tolerant LTH and chilling-sensitive IR29) with contrasting responses to chilling stress were comparatively analyzed. Results revealed distinct global transcription reprogramming between the two rice genotypes under time-series chilling stress and subsequent recovery conditions. more...

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

36 Samples

Download data: CEL

(Submitter supplied) In present study we compared transcriptional response to salinity stress between susceptible CO 12 and tolerant genotype trichy 1 of finger millet. We found out that several functional group of genes like transporters, transcription factors, genes involved in cell signalling, osmotic homeostasis, compatible solutes biosynthesis were upregulated more in tolerant genotype as compared to susceptible genotype in response to salinity stress. more...

Organism:

Eleusine coracana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18352

4 Samples

Download data: TXT

(Submitter supplied) We analyzed the transcriptional activity of rice chromosom 4 using a tiling path microarray based on PCR-generated genomic DNA fragments. Five organ samples from various developmental stages and cultured cells were examined. Keywords: ordered

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL1722

15 Samples

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(Submitter supplied) The array represents a minimal tilling-path covering rice chromosome 4. This tilling-path was assembled using 15,141 BAC subclone fragments. All subclone fragments were PCR amplified using universal primers and plasmids containing the genomic DNA fragment as the template. DNA gel electrophoresis was performed for all fragments and poor amplifications were not included here. This tiling array covers 33.8 Mb or 96% of rice Nipponbare chromosome 4. more...

Organism:

Oryza sativa

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(Submitter supplied) Changes in the gene expression during exposure to salinity stress were compared among nodal roots, S-type lateral roots, and L-type lateral roots.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19290

6 Samples

Download data: FPKM_TRACKING, TXT, XLSX

(Submitter supplied) Changes in the gene expression during exposure to salinity stress were compared among nodal roots, S-type lateral roots, and L-type lateral roots.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19290

6 Samples

Download data: FPKM_TRACKING, TXT

(Submitter supplied) Rice is the most salt sensitive cereal crop and its cultivation is particularly threatened by salt stress. This study reports the development of salt tolerant introgressed lines (ILs) derived from crosses between the salt tolerant indica rice variety FL478, which harbors the Saltol QTL, and the salt-sensitive japonica elite cultivar  PL12. Although the introgression of the Saltol QTL has been widely used to improve salinity tolerance, the molecular basis underlying the salinity tolerance conferred by Saltol remains poorly understood. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27660

12 Samples

Download data: XLSX

(Submitter supplied) The aim of this study was to minimize the number of candidate genes responsible for salt tolerance between a pair of rice varieties (CSR27 and MI48) with contrasting level of salt tolerance by bulked segregant analysis of their recombinant inbred lines. Microarray analysis of RNA extracted from the tolerant and susceptible parents without and with stress showed 798 and 2407 differentially expressed genes, respectively. more...

Organism:

Oryza sativa; Oryza sativa Indica Group

Type:

Expression profiling by array

Platform:

GPL2025

16 Samples

Download data: CEL, CHP

(Submitter supplied) We designed an array based on the release 7 of Michigan State University (MSU) rice genome annotation database (http://rice.plantbiology.msu.edu). The array was used for investigating the expression divergence and regulation between two contrasting rice genotypes under high salinity stress.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL17380

8 Samples

Download data: TXT

(Submitter supplied) Low temperature exposure during early vegetative stages limits rice plant’s growth and development. Most genes previously related to cold tolerance in rice are from the japonica subspecies. To help clarify the mechanisms that regulate cold tolerance in young indica rice plants, comparative transcriptome analysis of 6 h cold-treated leaves from two genotypes, cold-tolerant and cold-sensitive, was performed. more...

Organism:

Oryza sativa Indica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14553

2 Samples

Download data: TXT

(Submitter supplied) This experiment was designed to identify transcribed regions of both japonica and indica rice chromosome 10. A series of high-density oligonucleotide tiling arrays that represent sense and antisense strands of the entire nonrepetitive sequence of the chromosome were used to measure transcriptional activities. A total of 750,282 and 838,816 36mer oligonucleotide probes, positioned every 46 nt on average, were designed to interrogating the japonica and the indica chromosome, respectively. more...

Organism:

Oryza sativa

Type:

Expression profiling by genome tiling array

Platforms:

GPL1933 GPL1938 GPL1937

6 Samples

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

Organism:

Cicer arietinum; Lens culinaris; Lathyrus sativus

Type:

Expression profiling by array

Platform:

GPL3649

32 Samples

Download data: TXT