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Mus musculus
8 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Homeobox genes of the Hox class are required for proper patterning of skeletal elements and play a role in cartilage differentiation. In transgenic mice with overexpression of Hoxd4 during cartilage development, we observed severe defects, namely physical instability of cartilage, accumulation of immature chondrocytes, and decreased maturation to hypertrophy. To define the molecular basis underlying these defects, we performed gene expression profiling using the Affymetrix microarray platform.
Publication Title
Microarray Analysis of Defective Cartilage in Hoxc8- and Hoxd4-Transgenic Mice.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Homeobox genes of the Hox class are required for proper patterning of skeletal elements and play a role in cartilage differentiation. In transgenic mice with overexpression of Hoxc8 during cartilage development, we observed severe defects, namely physical instability of cartilage, accumulation of immature chondrocytes, and decreased maturation to hypertrophy. To define the molecular basis underlying these defects, we performed gene expression profiling using the Affymetrix microarray platform.
Publication Title
Microarray Analysis of Defective Cartilage in Hoxc8- and Hoxd4-Transgenic Mice.
Sample Metadata Fields
Specimen part
View Samples- Hordeum vulgare
- 44 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
Barley cv. Morex inoculated with Fusarium graminearum (isolate Butte 86) or water (mock). Sampled at 24, 48, 72, 96 and 144 hours after treatment. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Jayanand Boddu. The equivalent experiment is BB9 at PLEXdb.]
Publication Title
Transcriptome analysis of the barley-Fusarium graminearum interaction.
Sample Metadata Fields
Specimen part, Time
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GSE42214- Triticum aestivum
- 12 Downloadable Samples
- Affymetrix Wheat Genome Array (wheat)
Description
Three wheat genotypes were exposed to water stress and root tissue collected for expression analysis
Publication Title
Introgression of novel traits from a wild wheat relative improves drought adaptation in wheat.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 10 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
AIMS/HYPOTHESIS: Pregnancies complicated by diabetes have a higher risk of adverse outcomes for mothers and children, including predisposition to disease later in life, such as metabolic syndrome and hypertension. We hypothesized that adverse outcomes from diabetic pregnancies may be linked to compromised placental function. Our goal in this study was to identify cellular and molecular abnormalities in diabetic placenta.
Publication Title
Altered gene expression and spongiotrophoblast differentiation in placenta from a mouse model of diabetes in pregnancy.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This study sought to provide a novel ex vivo model for analyzing healing kinetics and gene expression of primary human gingival fibroblasts (hGF) within collagen scaffolds.
Publication Title
Cell population kinetics of collagen scaffolds in ex vivo oral wound repair.
Sample Metadata Fields
Specimen part
View Samples- Zea mays
- 33 Downloadable Samples
Illumina HiSeq 2000
Description
Maize is highly sensitive to short term flooding and submergence. We aimed to discover genetic variation for submergence tolerance in maize and elucidate the genetic basis of submergence tolerance through transcriptional profiling of contrasting genotypes. A diverse set of maize nested association mapping (NAM) founder lines were screened, and two highly tolerant (Mo18W and M162W) and sensitive (B97 and B73) genotypes were identified. Transcriptome analysis was performed on these inbreds to provide genome level insights into the molecular responses to submergence. Overall design: RNA deep sequencing of shoot tissue from four inbreds (B73, B97, Mo18W and M162W) in three conditions 24h control (non-submerged), 24h submerged and 72h submerged.
Publication Title
Genetic and molecular characterization of submergence response identifies Subtol6 as a major submergence tolerance locus in maize.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Saccharomyces cerevisiae
- 8 Downloadable Samples
- Illumina HiSeq 2000
Description
Heritable differences in gene expression between individuals are an important source of phenotypic variation. The question of how closely the effects of genetic variation on protein levels mirror those on mRNA levels remains open. Here, we addressed this question by using ribosomal footprinting to examine how genetic differences between two strains of the yeast S. cerevisiae affect translation. Strain differences in translation were observed for hundreds of genes, more than half as many as showed genetic differences in mRNA levels. Similarly, allele specific measurements in the diploid hybrid between the two strains found roughly half as many cis-acting effects on translation as were observed for mRNA levels. In both the parents and the hybrid, strong effects on translation were rare, such that the direction of an mRNA difference was typically reflected in a concordant footprint difference. The relative importance of cis and trans acting variation on footprint levels was similar to that for mRNA levels. Across all expressed genes, there was a tendency for translation to more often reinforce than buffer mRNA differences, resulting in footprint differences with greater magnitudes than the mRNA differences. Finally, we catalogued instances of premature translation termination in the two yeast strains. Overall, genetic variation clearly influences translation, but primarily does so by subtly modulating differences in mRNA levels. Translation does not appear to create strong discrepancies between genetic influences on mRNA and protein levels. Overall design: Ribsosomal footprinting and RNASeq in the two yeast strains BY and RM as well as their diploid hybrid. We generated one library each for the BY and RM parents, and two libraries (biological replicates) for the hybrid data.
Publication Title
Genetic influences on translation in yeast.
Sample Metadata Fields
Cell line, Subject
View Samples- Sus scrofa
- 9 Downloadable Samples
- Porcine Gene 1.0 ST Array (porgene10st)
Description
Microarray analysis was used to compare the transcriptome of esophageal submucosal gland (ESMG) derived spheroids in culture relative to squamous epithelium and fresh ESMGs.
Publication Title
Porcine Esophageal Submucosal Gland Culture Model Shows Capacity for Proliferation and Differentiation.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 45 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Transcriptional changes were analyzed in two colorectal cancer, two pancreatic cancer, and one small cell lung cancer cell line following treatment with the BET inhibitor GSK525762 and/or the MEK inhibitor trametinib using Affymetrix Human Genome U133 Plus 2.0 Arrays.
Publication Title
MEK inhibitors overcome resistance to BET inhibition across a number of solid and hematologic cancers.
Sample Metadata Fields
Cell line, Treatment, Time
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