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GSE115660
Saccharomyces cerevisiae
12 Downloadable Samples
Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Non-steroidal anti-inflammatory drugs, principally aspirin (acetylsalicylic acid, ASA), have anti-neoplastic properties, as shown by epidemiological studies on colorectal cancer and many other types of tumours. The chemopreventive and anti-proliferative properties of aspirin towards tumour cells have been shown to be due to the induction of programmed cell death such as apoptosis. Yeast cells are among the experimental models used extensively for the study of oxidative stress and apoptosis in living organisms because yeast, such as S. cerevisiae, retains many of the core eukaryotic cellular processes, including the hallmarks of eukaryotic apoptosis. An important contribution of our previous work has been the clarification of the critical defensive role of the antioxidant mitochondrial enzyme manganese superoxide dismutase (MnSOD) against apoptosis, confirmed to be the attenuation of aspirin-induced superoxide radical accumulation in the yeast mitochondria (Farrugia et al. (2013) FEMS Yeast Res 13, 755-768). To study the possible differential expression of gene transcripts in relation to the induction of apoptosis by aspirin, we used gene expression profiling by means of GeneChip Microarray Technology (Affymetrix). The yeast strains considered for this study included (1) the wild type strain S. cerevisiae EG103, which contains both MnSOD and cytosolic copper, zinc superoxide dismutase (CuZnSOD) and (2) the redox-compromised MnSOD-deficient S. cerevisiae EG110 strain. [This work was financed by the Malta Council for Science and Technology through the R&I Technology Development Programme (Project R&I-2015-001)].
Publication Title
Aspirin impairs acetyl-coenzyme A metabolism in redox-compromised yeast cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 34 Downloadable Samples
Illumina HiSeq 4000
Description
RNA-seq libraries were generated on thymic epithelial cell (TEC) subsets from thymic samples (11 days to 3 months of age). Cells were sorted to isolate cortical TEC (cTEC), MHC low medullary TEC (mTEClo) and MHC high medullary TEC (mTEChi). Between 7,575 and 50,000 cells were isolated for each sample. TEC were isolated using CD45 MACS depletion followed by the sorting protocol described in Stoeckler et al. J Vis Exp 2013 (PMID 24084687; doi: 10.3791/50951). The study has been granted ethical approval and is publicly listed (IRAS ID 156910, CPMS 19587). Overall design: 1 sample for each of cTEC, mTEClo and mTEChi were generated on a total of 3 individuals (~50,000 cells per sample) and 3 replicates for each of cTEC, mTEClo and mTEChi were generated on 1 individual (7,575 cells per sample)
Publication Title
Keratinocyte growth factor impairs human thymic recovery from lymphopenia.
Sample Metadata Fields
Specimen part, Subject
View Samples- Saccharomyces cerevisiae
- 25 Downloadable Samples
- Affymetrix Yeast Genome S98 Array (ygs98)
Description
These Affymetrix data were used to determine the role of each non-essential subunit of the conserved Ccr4-Not complex in the control of gene expression in the yeast S. cerevisiae. The study was performed with cells growing exponentially in high glucose and with cells grown to glucose depletion. Specific patterns of gene de-regulation were observed upon deletion of any given subunit, revealing the specificity of each subunits function. Consistently, the purification of the Ccr4-Not complex through Caf40p by tandem affinity purification from wild-type cells or cells lacking individual subunits of the Ccr4-Not complex revealed that each subunit had a particular impact on complex integrity. Furthermore, the micro-arrays revealed that the role of each subunit was specific to the growth conditions. From the study of only two different growth conditions, revealing an impact of the Ccr4-Not complex on more than 85% of all studied genes, we can infer that the Ccr4-Not complex is important for expression of most of the yeast genome.
Publication Title
Specific roles for the Ccr4-Not complex subunits in expression of the genome.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
Mouse ES cells were differentiated for 6 days. Undifferentiated cells (d0) were compared to cells harvested at 24 hour timepoints (d1-d6).
Publication Title
Transcriptional profiling of mouse and human ES cells identifies SLAIN1, a novel stem cell gene.
Sample Metadata Fields
Age, Specimen part, Cell line, Time
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U133B Array (hgu133b), Affymetrix Human Genome U133A Array (hgu133a)
Description
Undifferentiated cells of different passage numbers (p19 and p128) were compared to cells differentiated in hanging drops for 5 days (d5 embryoid bodies) or expanded on gelatin coated dishes for a further 9 days (d14 embryoid bodies).
Publication Title
Transcriptional profiling of mouse and human ES cells identifies SLAIN1, a novel stem cell gene.
Sample Metadata Fields
Age, Specimen part, Cell line, Time
View Samples- Homo sapiens
- 36 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Role of TAZ as mediator of Wnt signaling.
Sample Metadata Fields
Cell line, Treatment
View Samples- Homo sapiens
- 20 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
To investigate the role of TAZ downstream of APC and beta-catenin in mammary epithelial cells cells, we compared the expression profiles of MCF10-T1k (MII) cells transfected with siControl, siAPC, siAPC+siTAZ, sibeta-catenin, or sibeta-catenin+siTAZ.
Publication Title
Role of TAZ as mediator of Wnt signaling.
Sample Metadata Fields
Cell line, Treatment
View Samples- Homo sapiens
- 16 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
To investigate the role of TAZ downstream of the abberrant Wnt signaling in CRC cells, we compared the expression profiles of parental SW480 cells (empty vector) transfected with siControl, siTAZ, sibeta-catenin or reconstituted with wild type APC and transfected with siControl
Publication Title
Role of TAZ as mediator of Wnt signaling.
Sample Metadata Fields
Cell line, Treatment
View Samples- Rattus norvegicus
- 6 Downloadable Samples
- Affymetrix Rat Gene 1.0 ST Array (ragene10st)
Description
High-protein diets are known to reduce adiposity in the context of high carbohydrate and Western diets. However, few studies have investigated the specific high-protein effect on lipogenesis induced by a high-sucrose (HS) diet or fat deposition induced by high-fat feeding. We aimed to determine the effects of high protein intake on the development of fat deposition and partitioning in response to high-fat and/or HS feeding. A total of thirty adult male Wistar rats were assigned to one of the six dietary regimens with low and high protein, sucrose and fat contents for 5 weeks. Body weight (BW) and food intake were measured weekly. Oral glucose tolerance tests and meal tolerance tests were performed after 4th and 5th weeks of the regimen, respectively. At the end of the study, the rats were killed 2 h after ingestion of a calibrated meal. Blood, tissues and organs were collected for analysis of circulating metabolites and hormones, body composition and mRNA expression in the liver and adipose tissues. No changes were observed in cumulative energy intake and BW gain after 5 weeks of dietary treatment. However, high-protein diets reduced by 20 % the adiposity gain induced by HS and high-sucrose high-fat (HS-HF) diets. Gene expression and transcriptomic analysis suggested that high protein intake reduced liver capacity for lipogenesis by reducing mRNA expressions of fatty acid synthase (fasn), acetyl-CoA carboxylase a and b (Acaca and Acacb) and sterol regulatory element binding transcription factor 1c (Srebf-1c). Moreover, ketogenesis, as indicated by plasma -hydroxybutyrate levels, was higher in HS-HF-fed mice that were also fed high protein levels. Taken together, these results suggest that high-protein diets may reduce adiposity by inhibiting lipogenesis and stimulating ketogenesis in the liver.
Publication Title
High dietary protein decreases fat deposition induced by high-fat and high-sucrose diet in rats.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2), Illumina HiSeq 2500
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Genome-wide association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth.
Sample Metadata Fields
Specimen part, Cell line
View Samples