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GSE33392
Hordeum vulgare
144 Downloadable Samples
Affymetrix Barley Genome Array (barley1)
Description
A split-split-plot design with 144 experimental units (3 replications x 4 genotypes x 6 time points x 2 treatment types) was used to profile barley plants containing variants of Mla1 and Mla6 powdery mildew resistance genes in response to inoculation with the Blumeria graminis f. sp. hordei (Bgh) isolates 5874 (AvrMla1, AvrMla6). Barley leaves were harvested from inoculated and non-inoculated plants at 6 time points (0,8,16,20,24 and 32 hrs) after Bgh inoculation. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Rico Caldo. The equivalent experiment is BB10 at PLEXdb.]
Publication Title
Blufensin1 negatively impacts basal defense in response to barley powdery mildew.
Sample Metadata Fields
Specimen part, Time
View Samples- Hordeum vulgare
- 60 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
Barley stripe mosaic virus-induced gene silencing (BSMV-VIGS) was used to identify significant new genes in the regulation of host innate immunity. This experiment was designed to uncover significant changes in Bln1 (Contig12219_at)-silenced plants relative to empty vector and buffer treated controls. Five independent biological replications of a split-plot experimental design were conducted with replications as blocks, treatment with Blumeria graminis f. sp. hordei (Bgh) as the whole-plot factor, and all combinations of genotype (Mla13 and Mla9) and VIGS treatment [Buffer control (mock), BSMV:00 (empty vector), and BSMV:Bln1248] as the split-plot factor for a total of 60 GeneChip hybridizations. Ten seedlings were used as a split-plot experimental unit for each combination of replication, Bgh treatment, genotype, and VIGS treatment. Plants were grown in a controlled 20C glasshouse prior to VIGS treatment. Twelve days after VIGS treatment, half of the plants in each replication were challenged with the compatible Bgh isolate 5874. Top halves of 5 of the 10 seedling third leaves (about 10 cm) from each split-plot experimental unit were harvested into liquid N2 at 32 hours after inoculation (HAI) - the timepoint with the highest differential Bln1 transcript accumulation (Meng et al. 2009), and after initial establishment of the perihaustorial interface (Caldo et al. 2004). The remaining 5 leaves were used to record infection phenotype 7 days later. RNA was isolated for GeneChip hybridization from the 32-HAI samples. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Yan Meng. The equivalent experiment is BB101 at PLEXdb.]
Publication Title
Blufensin1 negatively impacts basal defense in response to barley powdery mildew.
Sample Metadata Fields
Age, Specimen part
View Samples- Hordeum vulgare
- 32 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
A parallel expression profiling of wild-type and loss-of-function mutants of Mla6 and Mla1 powdery mildew resistance alleles was conducted using Barley1 GeneChip. Barley plants were inoculated with powdery mildew isolate 5874 and first leaves were harvested at 6 time points after pathogen inoculation. This experiment was conducted in split-split-plot experimental design with 3 replications.
Publication Title
Blufensin1 negatively impacts basal defense in response to barley powdery mildew.
Sample Metadata Fields
Age, Specimen part, Time
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Boron is an essential micronutrient for plants and is taken up in the form of boric acid (BA). Despite this, a high BA concentration is toxic for the plants, inhibiting root growth and is thus a significant problem in semi-arid areas in the world. In this work, we report the molecular basis for the inhibition of root growth caused by boron. We used microarrays to detail the global gene expression underlying boron toxicity in roots.
Publication Title
A molecular framework for the inhibition of Arabidopsis root growth in response to boron toxicity.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
The tumor microenvironment plays a critical role in cancer progression, but the precise mechanisms by which stromal cells influence the tumor epithelium are poorly understood. The signaling adapter p62 has been implicated as a positive regulator of epithelial tumorigenesis; however, its role in the stroma is unknown. We show here that p62 levels are reduced in the stroma of several tumors. Also, orthotopic and organotypic studies demonstrate that the loss of p62 in the tumor microenvironment or stromal fibroblasts resulted in increased tumorigenesis of epithelial prostate cancer cells. The mechanism involves the regulation of cellular redox through an mTORC1/c-Myc pathway of stromal glucose and amino acid metabolism. Inhibition of the pathway by p62 deficiency results in increased stromal IL-6 production, which is required for tumor promotion in the epithelial compartment. Thus, p62 is an anti-inflammatory tumor suppressor that acts through modulation of metabolism in the tumor stroma.
Publication Title
Metabolic reprogramming of stromal fibroblasts through p62-mTORC1 signaling promotes inflammation and tumorigenesis.
Sample Metadata Fields
Specimen part
View Samples- Drosophila melanogaster
- 48 Downloadable Samples
NextSeq 500
Description
A-to-I RNA editing levels differ across tissues and cell types, but regulators of the editing process are largely unknown. We used RNA-seq on whole fly brains with different RNA binding proteins knocked down to test for A-to-I RNA editing level differences between controls and knockdowns. Overall design: To screen for editing regulators in the Drosophila brain, we crossed a pan-neuronal Gal4 driver, C155-Gal4, to different UAS-shRNA lines targeting individual RNA binding proteins, extracted RNA and made RNA-seq libraries. We sequenced four total replicates of shGFP controls and two replicates of all RNA binding protein knockdowns.
Publication Title
Zinc Finger RNA-Binding Protein Zn72D Regulates ADAR-Mediated RNA Editing in Neurons.
Sample Metadata Fields
Sex, Specimen part, Subject
View Samples- Homo sapiens
- 15 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Hypoxia is a low oxygen condition that occurs in the developing tumor mass and that is associated with poor prognosis and resistance to chemo- and radio-therapy. The definition of the hypoxia gene signature is fundamental for the understanding of tumor biology, as in the case of neuroblastoma, the most common pediatric solid tumor. The issue of identifying a significant group of variables in microarray gene expression experiments is particularly difficult due to the typical high dimensional nature of the data and great effort has been spent in the development of feature selection techniques.
Publication Title
The l1-l2 regularization framework unmasks the hypoxia signature hidden in the transcriptome of a set of heterogeneous neuroblastoma cell lines.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
To compare up-regulation of genes following CpG activation, we performed microarray analysis of activated macrophages from B6 and F1(B6xMOLF) mouse strains. Cells were activated for 0, 2 and 4 hrs with 200nM of type B CpG. Levels of mRNA for many genes differened dramatically between the strains
Publication Title
Mannose receptor 1 mediates cellular uptake and endosomal delivery of CpG-motif containing oligodeoxynucleotides.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 17 Downloadable Samples
- Illumina MouseRef-8 v2.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
PGC-1β promotes enterocyte lifespan and tumorigenesis in the intestine.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 12 Downloadable Samples
- Illumina MouseRef-8 v2.0 expression beadchip
Description
Analysis of metabolic pathway gene expression. The hypothesis tested in the present study is to assess mRNA level changes in metabolic genes in intestinal tumors from APCmin mice overexpressing PGC-1 specifically in the intestine.
Publication Title
PGC-1β promotes enterocyte lifespan and tumorigenesis in the intestine.
Sample Metadata Fields
Specimen part
View Samples