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GSE110446
Homo sapiens
24 Downloadable Samples
Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
In an effort to define unique and common signatures of NK cell activity that is non-detected at the protein level, we studied the entire transcriptome of NK cells.
Publication Title
Transcriptomic signatures of NK cells suggest impaired responsiveness in HIV-1 infection and increased activity post-vaccination.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Bos taurus
- 86 Downloadable Samples
Illumina HiSeq 2000
Description
The transition between pregnancy and lactation is a major physiological change that dairy cows must contend with. Complex systemic and local processes involving gluconeogenesis, energy balance, utilisation of body reserves, insulin resistance and involution of the uterus can have an effect on animal health and farm profitability. Here we used an established Holstein cow model of fertility that displayed genetic and phenotypic divergence in calving interval, a trait used to define reproductive performance using a national breeding index in Ireland. Cows had similar genetic merit for milk production traits, but either very good genetic merit for fertility (‘Fert+’; n = 8) or very poor genetic merit for fertility (‘Fert-‘; n = 8). We investigated three distinct time-points, late pregnancy, early lactation and mid lactation (-18, 1 and 147 days on average with day 0 being birth), using RNA sequencing from both liver and muscle tissue biopsies and conducting a differential expression (DE) analysis. We found 807 and 815 unique genes to be DE in at least one time-point in liver and muscle respectively, of which 79% and 83% were only found in a single time-point; 40 and 41 genes were found DE at every time-point indicating possibly systemic or chronic dysregulation. Functional annotation resulted in evidence for two major physiological processes: immune and inflammation, and metabolic, lipid and carbohydrate-binding. These processes indicate areas of previous interest as well as specific systems that appear differentially regulated, and point towards interesting avenues of further research in a broad and complex field. Overall design: 96 samples total; 8 Fert+ (''high fertility''), 8 Fert- (''low fertility''); no controls; Fert+, Fert- differential gene expression at three timepoints in two tissues
Publication Title
Transcriptomics of liver and muscle in Holstein cows genetically divergent for fertility highlight differences in nutrient partitioning and inflammation processes.
Sample Metadata Fields
Specimen part, Subject, Time
View Samples- Mus musculus
- 11 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
Recent work suggests that imprinted genes may regulate the signalling function of the placenta by modulating the size of the endocrine compartment. Our work provides in vivo evidence that this hypothesis is well founded.
Publication Title
The imprinted Phlda2 gene modulates a major endocrine compartment of the placenta to regulate placental demands for maternal resources.
Sample Metadata Fields
Specimen part
View Samples- Gallus gallus
- 4 Downloadable Samples
- Affymetrix Chicken Genome Array (chicken)
Description
Microarray analysis was performed on retina/RPE/choroid samples taken from the right eyes of male chicks across control and recovery from form deprivation conditions.
Publication Title
Pathway analysis identifies altered mitochondrial metabolism, neurotransmission, structural pathways and complement cascade in retina/RPE/ choroid in chick model of form-deprivation myopia.
Sample Metadata Fields
Sex, Specimen part, Treatment, Time
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Ovarian cancer is one of the most deadly cancers accounting for only 3% of diagnosed cancers, but is the fifth leading cause of cancer deaths among woman; however, the progression of ovarian cancer is poorly understood. To study and further understand the early events that lead to epithelial derived ovarian cancer, we previously developed a cell model of progressive ovarian cancer. Mouse ovarian surface epithelial (MOSE) cells have undergone spontaneous transformation in cell culture and represent pre-neoplastic, non-tumorigenic to an aggressive malignant phenotype.
Publication Title
Changes in gene expression and cellular architecture in an ovarian cancer progression model.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 24 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Beyond the DNA sequence difference between humans and closely related apes, there are large differences in the environments that these species experience. One prominent example for this is diet. The human diet diverges from those of other primates in various aspects, such as having a high calorie and protein content, as well as being cooked. Here, we used a laboratory mouse model to identify gene expression differences related to dietary differences.
Publication Title
Human and chimpanzee gene expression differences replicated in mice fed different diets.
Sample Metadata Fields
Sex, Age
View Samples- Mus musculus
- 24 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Beyond the DNA sequence difference between humans and closely related apes, there are large differences in the environments that these species experience. One prominent example for this is diet. The human diet diverges from those of other primates in various aspects, such as having a high calorie and protein content, as well as being cooked. Here, we used a laboratory mouse model to identify gene expression differences related to dietary differences.
Publication Title
Human and chimpanzee gene expression differences replicated in mice fed different diets.
Sample Metadata Fields
Sex, Age
View Samples- Homo sapiens
- 8 Downloadable Samples
- IlluminaGenomeAnalyzerII
Description
To assess the global effects of HOXC11 in endocrine resistant breast cancer cells we performed RNA-seq on LY2 cells which were transfected with either siRNA targeting HOXC11 (siHOXC11) or a scrambled negative control siRNA (scrHOXC11) in the presence of 4-OH-tamoxifen (10-8M). Knockdown was verified by Taq-man qRT-PCR prior to library preparation. RNA (10µg) was extracted using an Oligotex mRNA kit (Qiagen) as per manufacturer’s instructions (n=4). RNA was reverse transcribed followed by mRNA library preparation and sequencing based on a protocol outlined by Wilhelm et al., 2010. Sequencing was performed on an Illumina Genome Analyzer II (GAII) (54 million reads per sample on average). Overall design: Silencing of HOXC11 in tamoxifen resistant LY2 cells to identify putative HOXC11 target genes.
Publication Title
Prosaposin activates the androgen receptor and potentiates resistance to endocrine treatment in breast cancer.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 23 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
Previous work has suggested that the imprinted gene Phlda2 regulates the signalling function of the placenta by modulating the size of the endocrine compartment. This study investigated the affect that Phlda2 mutant placenta has upon the brains of the wildtype dams carrying different placenta and consequently offspring.
Publication Title
Maternal care boosted by paternal imprinting in mammals.
Sample Metadata Fields
Specimen part
View Samples- Macaca fascicularis
- 23 Downloadable Samples
- Affymetrix Human Genome U95 Version 2 Array (hgu95av2)
Description
Liver gene expression was examined in male cynomolgus monkeys treated with ciprofibrate (PPAR-alpha agonist) for 4 days at 400 mg/kg/day and treated for 15 days at 0, 3, 30, 150 or 400 mg/kg/day. The untreated control group were given only the vehicle (0.5% hydroxypropyl methylcellulose). Two animals per group were used for the 4 day treatment and four animals per group were used for the 15 day treatment (except the 15 day control group, which had three animals). Selection of significantly changed probesets was done using Rosetta Resolver and the fold-change and p values as determined by Resolver are given below. Affymetrix CEL files and MAS5-processed data have been made availabe for convenience. Note that data processing reported in the Toxicological Sciences manuscript was done using Rosetta Resolver and the treated versus control group fold-change and p-value are appended to the Series entry. An article has been published in Toxicological Sciences regarding this dataset; the data interpretation was based on the Rosetta Resolver data.
Publication Title
Gene expression profiling of the PPAR-alpha agonist ciprofibrate in the cynomolgus monkey liver.
Sample Metadata Fields
No sample metadata fields
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