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GSE70918
Rattus norvegicus
4 Downloadable Samples
Affymetrix Rat Gene 2.1 ST Array (ragene21st)
Description
Tendon is a hypocellular tissue that contains functional cable-like units of type I collagen responsible for the transmission of force from muscle to bone. In the setting of injury or disease, patients can develop chronic tendinopathies that are characterized by pain, loss of function and persistent inflammatory changes that are often difficult to treat. Platelet-rich plasma (PRP) has shown promise in the treatment of chronic tendinopathy, but little is known about the mechanisms by which PRP can improve tendon healing. PRP contains many different growth factors and cytokines, and since these proteins can both activate and inhibit various signaling pathways it has been challenging to determine precisely which signaling pathways and cellular responses are most important. Using state-of-the-art bioinformatics tools and genome wide-expression profiling, the purpose of this study was to determine the signaling pathways activated within cultured tendon fibroblasts in response to PRP treatment.
Publication Title
Platelet-Rich Plasma Activates Proinflammatory Signaling Pathways and Induces Oxidative Stress in Tendon Fibroblasts.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 131 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Background
Publication Title
Decision tree-based method for integrating gene expression, demographic, and clinical data to determine disease endotypes.
Sample Metadata Fields
Sex, Disease
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
Morbidity and mortality associated with retinoblastoma have decreased drastically in recent decades, in large part due to better prediction of high-risk disease and appropriate treatment stratification. High-risk histopathologic features and severe anaplasia both predict the need for more aggressive treatment; however, not all centers are able to easily assess tumor samples for degree of anaplasia. Instead, identification of genetic signatures able to distinguish among anaplastic grades and thus predict high versus low risk retinoblastoma would facilitate appropriate risk stratification in a wider patient population. A better understanding of genes dysregulated in anaplasia would also yield valuable insights into pathways underlying the development of more severe retinoblastoma. Here, we present the histopathologic and gene expression analysis of 28 retinoblastoma cases using microarray analysis. Tumors of differing anaplastic grade show clear differential gene expression, with significant dysregulation of unique genes and pathways in severe anaplasia. Photoreceptor and nucleoporin expression in particular are identified as highly dysregulated in severe anaplasia and suggest particular cellular processes contributing to the development of increased retinoblastoma severity. A limited set of highly differentially expressed genes are also able to accurately predict severe anaplasia in our dataset. Together, these data contribute to the understanding of the development of anaplasia and facilitate the identification of genetic markers of high-risk retinoblastoma.
Publication Title
Distinct Gene Expression Profiles Define Anaplastic Grade in Retinoblastoma.
Sample Metadata Fields
Specimen part
View Samples- Glycine max
- 38 Downloadable Samples
Illumina HiSeq 2500
Description
Soybean plants that do not produce a sink, such as depodded or male sterile plants, exhibit physiological and morphological changes during the reproductive stages, including increased levels of nitrogen and starch in the leaves and a delayed senescence. To identify transcriptional changes that occur in leaves of sink-limited plants, we used RNAseq to compare gene expression levels in trifoliate leaves from depodded and ms6 male sterile plants and control plants. In sink-limited tissues, we observed a deferral of the expression of senescence-associated genes and a continued high expression of genes associated with the maturity phase of leaf development. We identified GO-terms associated with growth and development and storage protein in sink limited tissues. We also identified that the bHLH. ARFs, and SBP transcription factors were expressed in sink limited tissues while the senescing control leaves expressed WRKY and NAC transcription factors. We identified genes that were not expressed during normal leaf development but highly expressed in sink-limited plants, including the D4 “non-yellowing” gene. These changes highlighted several metabolic pathways that were involved in distinct modes of resource parttioning in the “stay green” leaves. Overall design: Timecourse gene expression analysis of sink-limited soybean leaves. Gene expression was profiled from R2 growth stage (flowering) until the onset of leaf seenscence, and contrasted between mechanically and genetically sink-limited soybeans.
Publication Title
Transcriptional profiling of mechanically and genetically sink-limited soybeans.
Sample Metadata Fields
Specimen part, Subject, Time
View Samples- Glycine max
- 41 Downloadable Samples
- Illumina HiScanSQ, Illumina HiSeq 2500
Description
We use RNA sequencing technology in a time course study to measure transcript abundance from three developmental stages in cotyledons and five stages in the trifoliate leaf of Glycine max to identify genes with distinct temporal patterns of expression during leaf or cotyledon development. We also examine the diffrences between these two photosynthetic tissues. Overall design: Timecourse Expression analysis of Cotyledon Development and Leaf Development using RNAseq on distinct timepoints. 3 stages of the cotyledon were sequenced with 3 biological replicates in each stage. Five stages of the leaf were sequenced with 3 biological replicates for each stage.
Publication Title
Developmental profiling of gene expression in soybean trifoliate leaves and cotyledons.
Sample Metadata Fields
Specimen part, Subject
View Samples- Saccharomyces cerevisiae
- 10 Downloadable Samples
- Affymetrix Yeast Genome S98 Array (ygs98)
Description
Transcriptome analyses using a wild-type strain of Saccharomyces cerevisiae were performed to assess the overall pattern of gene expression during the transition from glucose-based fermentative to glycerol-based respiratory growth. These experiments revealed a complex suite of metabolic and structural changes associated with the adaptation process. Alterations in gene expression leading to remodeling of various membrane transport systems and the cortical actin cytoskeleton were observed. Transition to respiratory growth was accompanied by alterations in transcript patterns demonstrating not only a general stress response, as seen in earlier studies, but also the oxidative and osmotic stress responses. In some contrast to earlier studies, these experiments identified modulation of expression for many genes specifying transcription factors during the transition to glycerol-based growth. Importantly and unexpectedly, an ordered series of changes was seen in transcript levels from genes encoding components of the TFIID, SAGA (Spt-Ada-Gcn5-Acetyltransferase), and SLIK (Saga LIKe) complexes and all three RNA polymerases, suggesting a modulation of structure for the basal transcriptional machinery during adaptation to respiratory growth. In concert with data given in earlier studies, the results presented here highlight important aspects of metabolic and other adaptations to respiratory growth in yeast that are common to utilization of multiple carbon sources. Importantly, they also identify aspects specific to adaptation of this organism to growth on glycerol as sole carbon source.
Publication Title
Transcriptome profiling of Saccharomyces cerevisiae during a transition from fermentative to glycerol-based respiratory growth reveals extensive metabolic and structural remodeling.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 9 Downloadable Samples
- Illumina HiSeq 2500
Description
We report a gene expression changes during development and maturation of the murine utricle Overall design: Using RNA-sequencing, we examined the gene expression in the murine utricle at E17.5, p0, and p9
Publication Title
SoxC transcription factors are essential for the development of the inner ear.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Saccharomyces cerevisiae
- 22 Downloadable Samples
- Affymetrix Yeast Genome S98 Array (ygs98)
Description
Rsf1p is a putative transcription factor required for efficient growth using glycerol as sole carbon source but not for growth on the alternative respiratory carbon source ethanol.
Publication Title
Rsf1p is required for an efficient metabolic shift from fermentative to glycerol-based respiratory growth in S. cerevisiae.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Studied gene regulation in bronchial smooth muscle cells following vitamin D stimulation.
Publication Title
1alpha,25-dihydroxy-vitamin D3 stimulation of bronchial smooth muscle cells induces autocrine, contractility, and remodeling processes.
Sample Metadata Fields
Sex, Age, Specimen part, Race
View Samples- Saccharomyces cerevisiae
- 5 Downloadable Samples
- Affymetrix Yeast Genome S98 Array (ygs98)
Description
A putative yeast mitochondrial upstream activating sequence (UAS) was used in a one-hybrid screening procedure that identified the YJR127C ORF on chromosome X. This gene was previously designated ZMS1 and is listed as a transcription factor on the SGD website. Real time RT-PCR assays showed that expression of YJR127C/ZMS1 was glucose-repressible, and a deletion mutant for the gene showed a growth defect on glycerol-based but not on glucose- or ethanol-based medium. Real time RT-PCR analyses identified severely attenuated transcript levels from GUT1 and GUT2 to be the source of that growth defect, the products of GUT1 and GUT2 are required for glycerol utilization. mRNA levels from a large group of mitochondria- and respiration-related nuclear genes also were shown to be attenuated in the deletion mutant. Importantly, transcript levels from the mitochondrial OLI1 gene, which has an associated organellar UAS, were attenuated in the DeltaYJR127C mutant during glycerol-based growth, but those from COX3 (OXI2), which lacks an associated mitochondrial UAS, were not. Transcriptome analysis of the glycerol-grown deletion mutant showed that genes in several metabolic and other categories are affected by loss of this gene product, including protein transport, signal transduction, and others. Thus, the product of YJR127C/ZMS1 is involved in transcriptional control for genes in both cellular genetic compartments, many of which specify products required for glycerol-based growth, respiration, and other functions.
Publication Title
The YJR127C/ZMS1 gene product is involved in glycerol-based respiratory growth of the yeast Saccharomyces cerevisiae.
Sample Metadata Fields
No sample metadata fields
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