Oryza sativa Japonica Group
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ABSTRACT:
PROVIDER: PRJNA196691 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Knowledge of genes expression related to the growth-inhibition biological effects induced by low-energy N+ in plant. This study investigated the differentially expressed genes (DEGs) related to the growth-inhibition biological effects induced by low-energy N+ in plant by RNA-seq. Ion fluences (40Kev, curren intensity=3mA) of 1×1017N+/cm2，2×1017N+/cm2，4×1017N+/cm2，6×1017N+/cm2，8×1017N+/cm2 were used in the ion-implanted experiments. Biological effects with growht-inhibition were arised from the samples implanted by the ion fluences of 6×1017N+/cm2，8×1017N+/cm2 because of the inhibition of seedling height and root length. We sequenced mRNA from these damaged rice seedlings and others. We identified 776 transcripts as reliable DEGs at the growth inhibition sample campared with the control.The pathway enrichment analysis of these 776 DEGs showed that pathway of photosynthesis - antenna proteins was down-regulated. Meanwhile transcription factor analysis showed that genes related to AUX/IAA were also down-regulated. This study were contributed to a better understanding of molecular events responsible for adaption to the implantation of low-energy ion beam in plant.
2016-04-09 | GSE45908 | GEO
Project description:Analysis of 96-hours-old-rice seedlings with promoted-growth induced by implantation with low-energy nitrogen ion beam. Ion-beam implantation can induce changes in 351 up-regulated transcripts and 470 down-regulated transcripts, including signaling proteins, kinases, plant hormones, transposable elements, transcription factors, non-coding protein RNAs, secondary metabolites, resistance proteins, peroxidase, chromatin modification and even miRNAs. Results provide insight into the molecular basis of biological effects of plants that implanted by ion beam. Three sample groups—the controls, the ion-beam implanted samples and vacuum-treated samples. Three replicates were included in each sample group. Radiation induced gene expression rice seedlings was measured at 96 hours after germination of the seeds.
2012-03-01 | E-GEOD-36152 | biostudies-arrayexpress
Project description:Analysis of 96-hours-old-rice seedlings with promoted-growth induced by implantation with low-energy nitrogen ion beam. Ion-beam implantation can induce changes in 351 up-regulated transcripts and 470 down-regulated transcripts, including signaling proteins, kinases, plant hormones, transposable elements, transcription factors, non-coding protein RNAs, secondary metabolites, resistance proteins, peroxidase, chromatin modification and even miRNAs. Results provide insight into the molecular basis of biological effects of plants that implanted by ion beam.
2012-03-01 | GSE36152 | GEO
Project description:Phosphate starvation/sufficient rice seedling, root or shoot Pi-starvation or Pi-sufficient stresses responsible rice genes, including previously unannotated genes were identified by Illumina mRNA-seq technology. 53 million reads from Pi-starvation or Pi-sufficient root or shoot tissues were uniquely mapped to the rice genome, and these included 40574 RAP3 transcripts in root and 39748 RAP3 transcripts in shoot. We compared our mRNA-seq expression data with that from Rice 44K oligomicroarray, and about 95.5% (root) and 95.4% (shoot) transcripts supported by the array were confirmed expression both by the array and by mRNA-seq, Moreover, 11888 (root) and 11098 (shoot) RAP genes which were not supported by array, were evidenced expression with mRNA-seq. Furthermore, we discovered 8590 (root) and 8193 (shoot) previously unannotated transcripts upon Pi-starvation and/or Pi-sufficient.
2012-01-06 | E-MTAB-4302 | biostudies-arrayexpress
Project description:Nitrogen-ion-beam implantation effect on rice dry seeds
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Project description:Gene expression profiling of rice seedling with 2-azahypoxanthine
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Project description:Expression data from shoot bases of rice seedling after gravistimulation
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Project description: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. The probes were synthesized via maskless photolithography at a feature density of approximately 389,000 probes per slide. The arrays were hybridized with fluorescence-labeled cDNA reverse-transcribed from equal amounts of four selected poly(A)+ RNA populations, namely, seedling roots, seedling shoots, panicles, and suspension cultured cells of the respective rice subspecies. Keywords: other
2005-04-09 | GSE2500 | GEO
Project description:Genome-wide Gene Expression Profiling Associated with Seedling Cold Tolerance Improvement in Japonica Rice Background
| PRJNA167155 | ENA
Project description:This experiment was designed to identify transcribed regions of japonica subspecies of the rice genome. A series of high-density oligonucleotide tiling arrays that represent sense and antisense strands of the entire nonrepetitive sequence of all the 12 chromosomes were designed to measure genome-wide transcription. A total of 12253842 36mer oligonucleotide probes positioned every 46 nt on average were used for this purpose. The probes were synthesized via maskless photolithography at a feature density of approximately 389,000 probes per slide. The arrays were hybridized with fluorescence-labeled cDNA reverse-transcribed from equal amounts of four selected poly(A)+ RNA population (seedling root, seedling shoot, panicle, and suspension cultured cells). Keywords: tiling array, genome-wide transcription
2007-02-21 | GSE6996 | GEO