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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of rice over the first 24 hours of germination under aerobic conditions

ABSTRACT: Transcript abundance profiles were examined over the first 24 hours of germination in rice grown under aerobic conditions.

ORGANISM(S): Oryza sativa

SUBMITTER: Reena Narsai

PROVIDER: E-MEXP-1766 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Experimental analysis of the rice mitochondrial proteome, its biogenesis, and heterogeneity.

Huang Shaobai S Taylor Nicolas L NL Narsai Reena R Eubel Holger H Whelan James J Millar A Harvey AH

Plant physiology 20081114 2

Mitochondria in rice (Oryza sativa) are vital in expanding our understanding of the cellular response to reoxygenation of tissues after anaerobiosis, the crossroads of carbon and nitrogen metabolism, and the role of respiratory energy generation in cytoplasmic male sterility. We have combined density gradient and surface charge purification techniques with proteomics to provide an in-depth proteome of rice shoot mitochondria covering both soluble and integral membrane proteins. Quantitative comp ...[more]

PMID: 19010998

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Transcription profiling time course of rice germination under anaerobic conditions, aerobic to anaerobic switch and anaerobic to aerobic switch

Project description:Transcript abundance profiles were examined over the first 24 hours of germination in rice grown under anaerobic conditions. Transcript abundance profiles were also examined for rice grown under aerobic conditions for 24 h and then switched to anaerobic conditions and vice versa.

2009-07-24 | E-MEXP-2267 | biostudies-arrayexpress

Transcription profiling by array of an amylolytic yeast

Project description:The amylolytic S. cerevisiae strain WTPB-G and the wild-type strain (control) from a genetic background of FY23 were used to elucidate the effect brought about to a wild-type strain by the presence of an extrachoromosomal self-replicating element in the form of a recombinant multicopy plasmid. Strains were cultivated in YPD medium in fully controlled 2 L B-Braun Biostat B Plus fermenters, with a working volume of 1.5 L under aerated and micro-aerated conditions. Samples for transcriptional profiling were collected at the mid-exponential phase of growth at an OD range of 0.7-0.9, immediately frozen in liquid nitrogen and stored at -80C until RNA isolation. All experiments were carried out in duplicates.

2016-06-08 | E-MTAB-3545 | biostudies-arrayexpress

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2008-09-05 | E-MEXP-1239 | biostudies-arrayexpress

MicroRNA profiling of liver from vitellogenic and non-vitellogenic zebrafish females

Project description:Liver samples were collected from zebrafish females (3 months old). Vitellogenic females were maintained under conditions of 14 h light: 10 h dark. Non-vitellogenic females were obtained by exposing females to 6 h light/18 h dark regime.

2009-10-01 | E-MEXP-1572 | biostudies-arrayexpress

ccr1-1

Project description:Regulation of carotenoid composition and shoot branching in Arabidopsis by a chromatin modifying histone methyltransferase, SDG8<br>Comparison of transcript profiles between wild type Columbia and ccr1 (carotenoid and chloroplast regulatory) mutant, which contains a mutation in At1g77300 (SDG8)

2009-10-01 | E-MEXP-1787 | biostudies-arrayexpress

Overexpression of clock output factor DBP in skeletal muscle of a rat.

Project description:Circadian transcriptional factor was overexpressed in the right muscle of a rat. Differential gene expression was analysed between the test and control muscle at two different timepoints (zT0 and zT12).

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Project description:Histone modifications are associated with meiotic recombination hotspots, discrete sites with augmented recombination frequency. For example, trimethylation of histone H3 lysine4 (H3K4me3) marks most hotspots in budding yeast and mouse. Modified histones are known to regulate meiotic recombination partly by promoting DNA double strand break (DSB) formation, but the role and precise landscape of histone modifications at hotspots remain unclear. Here, we studied hotspot-associated modifications in fission yeast and found general features: acetylation of H3 lysine9 (H3K9ac) is strikingly elevated, and H3K4me3 is not significantly enriched. Remarkably, elimination of H3K9ac reduced binding of the DSB-inducing enzyme Rec12 and DSB at hotspots. We also found that the H3K4 metyltransferase Set1 promotes DSB formation at some loci, but it restricts Rec12 binding to hotspots. These results suggest that H3K9ac rather than H3K4me3 is a hotspot-associated mark involved in meiotic DSB formation in fission yeast. S.pombe cells in a pat1-114 background were induced to enter meiosis by the haploid meiosis system, and harvested one hour after the induction. ChIP were performed using anti-H3Cter, H3K9ac, -H3K14ac and -H3K4me3 antibodies. pat1-114 rad50S rec12+-FLAG cells in a wild type, H3K9A or set1+ deletion background were induced to enter meiosis by the haploid meiosis system, and harvested five hours after the induction. ChIP were performed using anti-FLAG antibodies.

2013-03-07 | E-GEOD-31648 | biostudies-arrayexpress

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Project description:Effect of the germination stimulant GR24 on hy1 mutants

2008-10-21 | E-MEXP-1608 | biostudies-arrayexpress

Transcription profiling by array of Arabidosis seeds after treatment with EL6 and GR24 to investigate the effect on germination

Project description:Effect of the chemical EL6 and GR24 on germination in Arabidopsis.

2008-10-21 | E-MEXP-1607 | biostudies-arrayexpress

Distinguishing innate memory CD8+ T from homeostatically expanded CD8+ T cells

Project description:Innate memory phenotype (IMP) CD8+ T cells are non-conventional αβ T cells exhibiting features of innate immune cells, and are significantly increased in the absence of non-receptor tyrosine kinase ITK. Their developmental path and function are not clear, particularly whether they can contribute to antigen specific responses. We found that WT bone marrow gives rise to IMP CD8+ T cells in irradiated MHCI-/- recipients, resembling those in Itk-/- mice determined by expression of surface markers. However, CD8+ T cells share similar expression of memory markers. We used microarrays to compare the global programme of gene expression to determine whether the CD8+ T cells selected by hematopoietic MHCI are IMP CD8+ T cells as observed in the absence of ITK, or the result of homeostatic expansion of T cell contamination in the donor bone marrow. Through analysis of global gene expression correlation and differential expression, we determined that hematopoietic MHCI dependent IMP CD8+ T cells generated in irradiated MHCI-/- recipients, resemble those in Itk-/- mice, but distinct from CD8+ T cells derived via homeostatic proliferation. Cell sorting was performed using a FACSAria Cell Sorter (BD Biosciences, San Diego, CA). IMP CD8+ T cells (TCRβ+CD8α+CD44hi) were sorted from splenocytes of WT→MHCI-/- chimeras 8 weeks post transplantation and 8-week old Itk-/- mice. To generate HP cells, naïve CD8+ T cells (TCRβ+CD8α+CD44lo) were sorted and injected into Rag1-/- recipients (0.5 million /mouse, retro-orbital injection), followed by sorting of TCRβ+CD8α+ splenocytes 8 weeks post adoptive transfer. We sought to compare cells with the same gender and age, thus all donors were female, and ages (absolute age for Itk null and age post transfer for chimeras and HP model) were 8 weeks.

2013-02-19 | E-GEOD-41482 | biostudies-arrayexpress

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