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GSE4847
Arabidopsis thaliana
18 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Tocopherols (Vitamin E) are lipophilic antioxidants that are synthesized by all plants and are particularly abundant in seeds. Two tocopherol deficient mutant loci were used to examine how tocopherol deficiency impacts global gene expression during the critical peroid of germination and early seedling development when tocopherols are essential. vte1 lacks all tocopherols, but accumulates the tocopherol pathway intermediate DMPBQ,. vte2 which lacks all tocopherols and pathway intermediates.
Publication Title
Nonenzymatic lipid peroxidation reprograms gene expression and activates defense markers in Arabidopsis tocopherol-deficient mutants.
Sample Metadata Fields
Age
View Samples- Arabidopsis thaliana
- 24 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
General detoxification and stress responses are mediated by oxidized lipids through TGA transcription factors in Arabidopsis.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 18 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
12-oxo-phytodienoic acid (OPDA) and phytoprostane A1 (PPA1) are cyclopentenone oxylipins that are formed via the enzymatic
Publication Title
General detoxification and stress responses are mediated by oxidized lipids through TGA transcription factors in Arabidopsis.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
12-Oxo-phytodienoic acid (OPDA) and several phytoprostanes are structurally related cyclopentenone oxylipins that can be formed via the enzymatic jasmonate pathway and a non-enzymatic, free radical-catalyzed pathway, respectively. To elucidate the biological activities of phytoprostanes in comparison to OPDA as well as the metabolism we performed genome-wide expression analysis.
Publication Title
General detoxification and stress responses are mediated by oxidized lipids through TGA transcription factors in Arabidopsis.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 3 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
Osteoarthritis (OA) of the hand is a common disease resulting in pain and impaired function. The pathogenesis of hand OA (HOA) is elusive and models to study it have not been described so far. Culture of chondrocytes is a model to study the development of cartilage degeneration, which is a hallmark of OA and well established in OA of the knee and hip. In the current study we investigated the feasibility human chondrocyte culture derived from proximal interphalangeal (PIP) finger joints of dissecting room cadavers. Index and middle fingers without signs of osteoarthritis were obtained from 30 cadavers using two different protocols. Hyaline cartilage from both articulating surfaces of the proximal interphalangeal (PIP) joint was harvested and digested in collagenase. Cultured chondrocytes were monitored for contamination, viability, and expression of chondrocyte specific genes. Chondrocytes derived from knee joints of the cadavers were cultured under identical conditions. Gene expression comparing chondrocytes from PIP and knee joints was carried out using Affymetrix GeneChip Human 2.0 ST arrays. The resulting differentially expressed genes were validated by real-time PCR and immunohistochemistry.Chondrocytes harvested up to 101 hours after death of the donors were viable. mRNA expression of collagen 2A1, aggrecan and Sox9 was significantly higher in chondrocytes as compared to cultured fibroblasts. Comparison of gene expression by chondrocytes from PIP and knee joints yielded 528 differentially expressed genes. Chondrocytes from the same joint region had a higher grade of similarity than chondrocytes of the same individual. These results were validated using real-time PCR and immunohistochemistry.We demonstrate for the first time a reliable method for culture of chondrocytes derived from PIP joints. PIP chondrocytes show a specific gene expression pattern and could be used as tool to study cartilage degeneration in HOA.
Publication Title
Chondrocyte cultures from human proximal interphalangeal finger joints.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 275 Downloadable Samples
- Affymetrix Human Gene 2.1 ST Array (hugene21st)
Description
This SuperSeries is composed of the SubSeries listed below. A subset of samples profiled in this analysis were also profiled in Series GSE68127, and GSE104066. Corresponding glomerular transcriptome data can be found under GEO ID: GSE108109.
Publication Title
Metabolic pathways and immunometabolism in rare kidney diseases.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 196 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
summary : Glomerular Transcriptome from European Renal cDNA Bank subjects and living donors. Samples included in this analysis have been previously analyzed using older CDF definitions and are included under previous GEO submissions - GSE47183 (chronic kidney disease samples), and GSE32591 (IgA nephropathy samples).
Publication Title
Metabolic pathways and immunometabolism in rare kidney diseases.
Sample Metadata Fields
Specimen part, Disease
View Samples- Homo sapiens
- 194 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
summary : Tubulointerstitial transcriptome from ERCB subjects with chronic kidney disease and living donor biopsies. Samples included in this analysis have been previously analyzed using older CDF definitions and are included under previous GEO submissions - GSE47184 (chronic kidney disease samples), and GSE32591 (IgA nephropathy samples).
Publication Title
Metabolic pathways and immunometabolism in rare kidney diseases.
Sample Metadata Fields
Specimen part, Disease
View Samples- Homo sapiens
- 169 Downloadable Samples
- Affymetrix Human Gene 2.1 ST Array (hugene21st)
Description
Tubulointerstitial transcriptome from human kidney biopsies in Neptune and ERCB. A number of samples profiled in this analysis were also profiled in Series GSE68127.
Publication Title
Metabolic pathways and immunometabolism in rare kidney diseases.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 106 Downloadable Samples
- Affymetrix Human Gene 2.1 ST Array (hugene21st)
Description
Glomerular transcriptome from human kidney biopsies in Neptune and ERCB. A subset of samples profiled in this analysis were also profiled in Series GSE68127, and in GSE104066. Corresponding tubulointerstitial transcriptome data is submitted under GEO ID: GSE108113.
Publication Title
Metabolic pathways and immunometabolism in rare kidney diseases.
Sample Metadata Fields
Specimen part
View Samples