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GSE6454
Saccharomyces cerevisiae
10 Downloadable Samples
Affymetrix Yeast Genome S98 Array (ygs98)
Description
In this study, we focused on air-drying stress and analyzed the changes in gene expression of commercial bakers yeast during the air-drying process. Changes in gene expression profiles of commercial bakers yeast during an air-drying process at 37oC that simulated dried yeast production were analyzed using DNA microarrays.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 4 Downloadable Samples
- Affymetrix Yeast Genome S98 Array (ygs98)
Description
Rsp5 is an essential and multi-functional E3 ubiquitin ligase in Saccharomyces cerevisiae. We previously isolated the Ala401Glu rsp5 mutant, which is hypersensitive to various stresses. To understand the function of Rsp5 in stress responses, suppressor genes whose overexpression allows rsp5A401E cells to grow at high temperature were screened. The KIN28 and POG1 genes, encoding a subunit of the transcription factor TFIIH and a putative transcriptional activator, respectively, were identified as multicopy suppressors of not only high temperature but also LiCl stresses. The overexpression of Kin28 and Pog1 in rsp5A401E cells caused an increase in the transcriptional level of some stress proteins when exposed to temperature up-shift. DNA microarray analysis under LiCl stress revealed that the transcriptional level of some proteasome components was increased in rsp5A401E cells overexpressing Kin28 or Pog1. These results suggest that the overexpression of Kin28 and Pog1 enhances the protein refolding and degradation pathways in rsp5A401E cells.
Publication Title
Overexpression of two transcriptional factors, Kin28 and Pog1, suppresses the stress sensitivity caused by the rsp5 mutation in Saccharomyces cerevisiae.
Sample Metadata Fields
No sample metadata fields
View Samples- Gallus gallus
- 30 Downloadable Samples
- Affymetrix Chicken Genome Array (chicken)
Description
The experiment were perfomed as a part of our Vertebrate Evo-Devo project. The aim of the project is to compare transcription profiles of normal (unmanipulated, wild-type, whole embryo) vertebrate embryos. Total RNA was collected from wild type G.gallus whole embryos at 15 different stages (Stages:HH1,2,4,6,8,9,11,14,16,19,24,27,32,34,38), and hybridized to A-AFFY-103 Chicken Genome Array. All the stages contains data from two biological replications. Each staged-samples consists of pooled total RNA from several whole embryos.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
screening of AtMYB44-responsive genes under 250mM NaCl treatment
Publication Title
Overexpression of AtMYB44 enhances stomatal closure to confer abiotic stress tolerance in transgenic Arabidopsis.
Sample Metadata Fields
Compound
View Samples- Arabidopsis thaliana
- 2 Downloadable Samples
- Affymetrix Arabidopsis Genome Array (ag)
Description
Effect of JMT overexpression in global gene expression
Publication Title
Complement analysis of xeroderma pigmentosum variants.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 66 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Background: Breast cancer is a heterogeneous neoplasm. Distinct subtypes of breast cancer have been defined, suggesting the existence of molecular differences contributing to their clinical outcomes. However, the molecular differences between HER2 positive and negative breast cancer tumors remain unclear. Objective: The aim of this study was to identify a gene expression profile for breast tumors based on HER2 status. Material and methods: The HER2 status was determined by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) in 54 breast tumor samples. Using Affymetrix microarray data from these breast tumors, we established the expression profiling of breast cancer based on HER2 IHC and FISH results. To validate microarray experiment data, real-time quantitative reverse transcription-PCR was performed. Results: We found significant differences between the HER2-positive and HER2-negative breast tumor samples, which included overexpression of HER2, as well as other genes located on 17q12, and genes functionally related to migration. Conclusion: Our study shows the potential of integrated genomics profiling to shed light on the molecular knowledge of HER2-positive breast tumors.
Publication Title
No associated publication
Sample Metadata Fields
Age, Disease, Disease stage
View Samples- Homo sapiens
- 5 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
To better understand the molecular basis of the anticancer effects of acyclic retinoid (ACR), a genome-wide screening was applied to identify novel targets of ACR in human hepatocellular carcinoma (HCC) cells JHH7. Gene expression profiles of JHH7 were measured at 0h, 1h and 4 hours after treatment with1 M All-trans retinoic acid (AtRA) or 10 M ACR. Hierarchical clustering with Wards method of 44,907 genes demonstrated diverse expression changes in HCC cells treated with ACR for 4h. A total of 973 differentially expressed genes in response to ACR by comparing with AtRA for 4h treatments were identified with a fold change more than 2. Then, network analysis was performed on the altered gene expression profiles using Ingenuity Pathways Analysis (IPA) program. The most highly populated networks were associated with the regulation of cell cycle and DNA replication, as ACR is well known to induce apoptosis and suppress cell proliferation in HCC cells. Moreover, networks related with amino acid metabolism, protein synthesis and lipid metabolism, such as the biological network entitled Lipid Metabolism, Small Molecular Biochemistry, Vitamin and Mineral Metabolism were also observed. Of interest, this network contains genes that play critical roles in controlling the development of tissues and organs such as the nuclear orphan receptor nuclear receptor subfamily 2, group F, member 2 (NR2F2), suggesting potential drug targets to prevent/treat HCC.
Publication Title
Metabolome Analyses Uncovered a Novel Inhibitory Effect of Acyclic Retinoid on Aberrant Lipogenesis in a Mouse Diethylnitrosamine-Induced Hepatic Tumorigenesis Model.
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
To identify the molecular targets of orosomucoid (Orm1) during liver regeneration, GeneChip analysis was performed at 48 h after partial hepatectomy (PH) in regenerating mouse liver treated with siControl or siOrm. A total of 180 differentially expressed genes in Orm1 konckdown mouse liver by comparing with siControl were identified with a fold change more than 2. Then, pathway analysis performed on the altered gene expression profiles using Ingenuity Pathways Analysis (IPA) program revealed that cell cycle, Toll-like receptor and TGF-beta receptor signaling pathways were under control of Orm1 in regenerating mouse livers.
Publication Title
Transcriptome Analysis Uncovers a Growth-Promoting Activity of Orosomucoid-1 on Hepatocytes.
Sample Metadata Fields
Sex, Specimen part
View Samples- Arabidopsis thaliana
- 16 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
to identify regulated genes in response to cytokinin in wild-type and 35S:ARR7 plants using the Affymetrix ATH1 full genome array.
Publication Title
Genome-wide expression profiling of ARABIDOPSIS RESPONSE REGULATOR 7(ARR7) overexpression in cytokinin response.
Sample Metadata Fields
Disease, Disease stage, Compound, Time
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
The Columbia (Col-0) ecotype of Arabidopsis thaliana was used as wild type. lbd16, lbd18 single and lbd16 lbd18 double mutants were used as mutants.
Publication Title
No associated publication
Sample Metadata Fields
Time
View Samples