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GSE17867
Saccharomyces cerevisiae
6 Downloadable Samples
Affymetrix Yeast Genome S98 Array (ygs98)
Description
Excess/residual urea is a pervasion problem in wine and Sake fermentation. We sought to reduce residual urea levels (to reduce ethyl carbamate leves) by engineering the Sake yeast strain K7 to constitutively express either the urea amidolyase (Dur1,2) or urea importer (Dur3). We sought to then compare the gene expression profiles of the metabolically engineered yeast strains to the parental strain during fermentation.
Publication Title
Functional enhancement of Sake yeast strains to minimize the production of ethyl carbamate in Sake wine.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 3 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
Mast cells originate from the bone marrow and develop into c-kit+ FcRI+ cells. As both mast cell progenitors and mature mast cells express these cell surface markers, ways validated to distinguish between the two maturation forms with flow cytometry have been lacking.
Publication Title
Distinguishing Mast Cell Progenitors from Mature Mast Cells in Mice.
Sample Metadata Fields
Specimen part, Disease
View Samples- Saccharomyces cerevisiae
- 57 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
For each strain two time courses for mRNA abundance: Oxidative and MMS and two time courses for decay: reference decay and following oxidative stress
Publication Title
Transcriptome kinetics is governed by a genome-wide coupling of mRNA production and degradation: a role for RNA Pol II.
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 52 Downloadable Samples
- Affymetrix Rat Gene 1.0 ST Array (ragene10st)
Description
Urethra was partially ligated and the urinary bladder was removed 10 days or 6 weeks after obstruction. Sham operated rats were used as controls. An addtitonal group of rats were repoerated 6 weeks after surgery and the obstruction was removed. These rats were then sacrificed 10 days after deobstruction. The bladder (including the urothelium) was frozen and used for RNA extraction.
Publication Title
Mir-29 repression in bladder outlet obstruction contributes to matrix remodeling and altered stiffness.
Sample Metadata Fields
Specimen part, Time
View Samples- Saccharomyces cerevisiae
- 13 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
We created a comprehensive tRNA deletion library in yeast and characterized the phenotypic and further characterized the molecular changes in a subset of deletion strains
Publication Title
A comprehensive tRNA deletion library unravels the genetic architecture of the tRNA pool.
Sample Metadata Fields
No sample metadata fields
View Samples- Triticum aestivum
- 12 Downloadable Samples
- Affymetrix Wheat Genome Array (wheat)
Description
This study compared the photosynthetic performance and the global gene expression of the winter hardy wheat Triticum aestivum cv Norstar grown under non-acclimated (NA) or cold-acclimated (CA) condition at either ambient CO2 or elevated CO2 (EC). CA Norstar maintained comparable light saturated and CO2 saturated rates of photosynthesis but lower quantum requirements for photosystem II and non photochemical quenching relative to NA plants even at EC. Neither NA nor CA plants were sensitive to feedback inhibition of photosynthesis at EC. Global gene expression using microarray combined with bioinformatics analysis revealed that genes affected by EC were 3 times higher in NA (1022 genes) compared to CA (372 genes) Norstar. The most striking effect was the down-regulation of genes involved in the plant defense responses in NA Norstar. In contrast, cold acclimation reversed this down regulation due to the cold induction of genes involved in plant pathogenesis resistance, and cellular and chloroplast protection. These results suggest that EC have less impact on plant performance and productivity in cold adapted winter hardy plants in the northern climates compared to warmer environments. Selection for cereal cultivars with constitutively higher expression of biotic stress defense genes may be necessary under EC during the warm growth period and in warmer climates.
Publication Title
Long-term growth under elevated CO2 suppresses biotic stress genes in non-acclimated, but not cold-acclimated winter wheat.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
Illumina Genome Analyzer IIx
Description
RNA localization is a regulatory mechanism that is conserved from bacteria to mammals. Yet, little is known about the mechanism and the logic that govern the distribution of RNA transcripts within the cell. Here we present a novel organ culture system, which enables the isolation of RNA specifically from NGF dependent re-growing peripheral axons of mouse embryo sensory neurons. In combination with massive parallel sequencing technology, we determine the sub-cellular localization of most transcripts in the transcriptome. We found that the axon is enriched in mRNAs that encode secreted proteins, transcription factors and the translation machinery. In contrast, the axon was largely depleted from mRNAs encoding transmembrane proteins, a particularly interesting finding, since many of these gene products are specifically expressed in the tip of the axon at the protein level. Comparison of the mitochondrial mRNAs encoded in the nucleus with those encoded in the mitochondria, uncovered completely different localization pattern, with the latter much enriched in the axon fraction. This discovery is intriguing since the protein products encoded by the nuclear and mitochondrial genome form large co-complexes. Finally, focusing on alternative splice variants that are specific to axonal fractions, we find short sequence motifs that are enriched in the axonal transcriptome. Together our findings shed light on the extensive role of RNA localization and its characteristics. Overall design: For each RNA sample, Spinal Cords\ DRGs were dissected from 40 E13.5 embryos and cultured for 48H. Total RNA was extracted from whole DRG and Peripheral axons. Poly-A enriched. In duplicates, using GAIIx. Read length - 80nt.
Publication Title
Subcellular transcriptomics-dissection of the mRNA composition in the axonal compartment of sensory neurons.
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 37 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
We subjected yeast to two stresses, oxidative stress, which under current settings induces a fast and transient response in mRNA abundance, and DNA damage, which triggers a slow enduring response. Using microarrays, we performed a transcriptional arrest experiment to measure genome-wide mRNA decay profiles under each condition. Genome-wide decay kinetics in each condition were compared to decay experiments that were performed in a reference condition (only transcription inhibition without an additional stress) to quantify changes in mRNA stability in each condition. We found condition-specific changes in mRNA decay rates and coordination between mRNA production and degradation. In the transient response, most induced genes were surprisingly destabilized, while repressed genes were somewhat stabilized, exhibiting counteraction between production and degradation. This strategy can reconcile high steady-state level with short response time among induced genes. In contrast, the stress that induces the slow response displays the more expected behavior, whereby most induced genes are stabilized, and repressed genes destabilized. Our results show genome-wide interplay between mRNA production and degradation, and that alternative modes of such interplay determine the kinetics of the transcriptome in response to stress.
Publication Title
Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation.
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 40 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
We conducted a set of lab-evolution experiments in yeast and followed the long-term dynamics of aneuploidy under diverse conditions including heat shock and high PH.
Publication Title
Chromosomal duplication is a transient evolutionary solution to stress.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
Hyperglycemia can contribute to the detrimental effects of diabetes in the vasculature.
Publication Title
Elevated Glucose Levels Promote Contractile and Cytoskeletal Gene Expression in Vascular Smooth Muscle via Rho/Protein Kinase C and Actin Polymerization.
Sample Metadata Fields
Specimen part
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