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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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DNA microarray data from root of transgenic rice Huahui 1 (HH1) and its parent Minghui 63 (MH63)

ABSTRACT: DNA microarray analysis has been proved to be an effective method in investigating unintended effects in genetically modified (GM) crops. However, unintended effects of GM plants in leaves through DNA microarray analysis has many researches, but research of unintended effects of GM plants of the underground portion has few. In this study, DNA microarray analysis was used to detect DEG in underground portions between transgenic rice HH1 and its non-transgenic control MH63. We used microarrays to study unintended effects in root of transgenic rice Huahui 1. Samples were collected from root of HH1 and MH63 at 30-day old and were used for RNA extraction and hybridization on Affymetrix microarrays. We selected diferentially expressed genes and common significantly changed pathways hoping to as a clue to investigate unintended effects of HH1 root.

ORGANISM(S): Oryza sativa

SUBMITTER: Jie Zhao

PROVIDER: E-GEOD-46086 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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DNA microarray data from root of transgenic rice Huahui 1 (HH1) and its parent Minghui 63 (MH63)

Project description:DNA microarray analysis has been proved to be an effective method in investigating unintended effects in genetically modified (GM) crops. However, unintended effects of GM plants in leaves through DNA microarray analysis has many researches, but research of unintended effects of GM plants of the underground portion has few. In this study, DNA microarray analysis was used to detect DEG in underground portions between transgenic rice HH1 and its non-transgenic control MH63. We used microarrays to study unintended effects in root of transgenic rice Huahui 1.

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DNA microarray data from transgenic rice Huahui 1 (HH1) and its parent Minghui 63 (MH63)

Project description:DNA microarray analysis has been proved to be an effective method in investigating unintended effects in genetically modified (GM) crops. But the distribution of differentially expressed genes in GM crops remains unclear. So the results of microarray analysis might be invalid for assessment of unintended effects if differentially expressed genes are extremely distributed. We used microarrays to study the distribution pattern of differentially expressed genes in HH1 at different developmental stages and environmental conditions. Samples were collected from both HH1 and MH63 at different developmental stages and environmental conditions and were used for RNA extraction and hybridization on Affymetrix microarrays. We selected differentially expressed genes, common differentially expressed genes and common significantly changed pathways hoping to clarify the distributions of differentially expressed genes in HH1.

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Expression data from brown planthhoper (BPH) infested and non-infested rice

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Project description:KMD is genetically engenered to be highly resistant to lepidopteran pests through expressing a synthetic cry1Ab gene and its parent non-transgenic rice is Xiushui 11 (XS11). Many unintended effects have been discovered in KMD. We used microarrays to study the molecular basis for unintended effects of KMD rice.

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iTRAQ-based proteomic analysis reveals genome-wide protein expression patterns in allohexaploid bread wheat in adaptation to potassium deficiency and an important role of jasmonic acid

Project description:Two-week old bread wheat seedlings hydroponically grown Hoagland solution were transferred to potassium (K+)-free conditions for 8 d, their root and leaf proteome profiles were assessed using iTRAQ proteome method, and NCBInr database combined with the recently published bread wheat genome information were used to analyze the identified protein species. Over 4,000 unique proteins were identified, 818 K+-responsive protein species showed significant abundance regulation. The most majority of the identified K+-responsive protein species had exact gene loci, and showed no global but tissue- and chromosome- dependent genome distributions. The identified protein species were associated with diverse functions and exhibited organ-specific differences. Most of identified protein species associated with hormone synthesis were the enzymes involved in the synthesis of jasmonic acid (JA). Allene oxide synthase (AOS), a key JA synthesis-related enzyme, was significantly induced in both root and leaf organs of K+-deficient wheat seedlings, and its overexpression in rice enhanced the tolerance to low K+ or K+ deficiency, increased contents of K+ and JA and transcription levels of some K+-responsive genes. However, rice AOS T-DNA inserted mutant (osaos) exhibited more sensitivity to K+ deficiency. K+ deficiency significantly increased abundance of a high affinity K+ transporter (TaAHAK1), TaAHAK1 transgenic rice seedlings markedly alleviated sensitivity to K+ deficiency, and K+ deficiency also upregulated expression of homologous OsHAK1 gene in TaAOS transgenic rice plants. These results suggested an essential role of JA in K+ deficiency and gave molecular insight into the responses of plant to K+ deficiency.

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Expression data from three rice lines (1-control, 1-transgenic and 1-negative segregant) throughout generations and under salt stress

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DNA microarray data from transgenic rice Huahui 1 (HH1) and its parent Minghui 63 (MH63)

2011-10-26 | GSE33204 | GEO

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2011-04-07 | E-GEOD-28428 | biostudies-arrayexpress

Transcriptomic shifts in rice roots in response to Cr (VI) stress

Project description:Detailed analysis of genome-wide transcriptome profiling in rice root is reported here, following Cr-plant interaction. Such studies are important for the identification of genes responsible for tolerance, accumulation and defense response in plants with respect to Cr stress. Rice root metabolome analysis was also carried out to relate differential transcriptome data to biological processes affected by Cr (VI) stress in rice. The rice variety IR-64 was germinated and allowed to grow for 5 d at 37 C and then transferred to Hewitt solution for growth. After 10 d of growth, seedlings of uniform size and growth were treated with 100 µM of Cr (VI), As (V), Cd, and Pb under standard physiological conditions of 16 h light (115 μmol m−2 s−1) and 8 h dark photoperiod at 25 ± 2 C for 24 h. Total RNA was extracted from the treated rice roots and microarray was performed using one-cycle target labeling and control reagents (Affymetrix platform).

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