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GSE11200
Hordeum vulgare
22 Downloadable Samples
Affymetrix Barley Genome Array (barley1)
Description
Malting is seed germination under strictly controlled environmental conditions. Malting quality is a complex phenotype that combines a large number of interrelated components, each of which shows complex inheritance. Currently, only a few genes involved in determining malting quality have been characterized. This study combined transcript profiling with phenotypic correlations to identify candidate genes for malting quality.
Publication Title
Differentially expressed genes during malting and correlation with malting quality phenotypes in barley (Hordeum vulgare L.).
Sample Metadata Fields
No sample metadata fields
View Samples- Bos taurus
- 15 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
Fetal spleens were collected at days 82 and 97 of gestation following maternal infection with BVDV on day 75 of gestation.
Publication Title
Attenuated lymphocyte activation leads to the development of immunotolerance in bovine fetuses persistently infected with bovine viral diarrhea virus†.
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 11 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Mammalian gonadal sex determination is dependent on proper expression of sex determining genes in fetal gonadal somatic support cells (i.e., pre-granulosa and pre-Sertoli cells in XX and XY gonads, resp.). We used a unique transgenic mouse strain combined with microarray profiling to identify all the differentially expressed transcripts in XX and XY isolated somatic support cells during critical stages of gonadal development and differentiation.
Publication Title
New candidate genes identified for controlling mouse gonadal sex determination and the early stages of granulosa and Sertoli cell differentiation.
Sample Metadata Fields
Sex, Specimen part
View Samples- Ovis aries
- 12 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
Ovine interferon-tau (IFNT) is released from the conceptus by Day 12 of pregnancy and disrupts pulsatile release of endometrial prostaglandin F2 alpha (PGF), thereby protecting the corpus luteum (CL). IFNT may also have endocrine action through inducing interferon stimulated genes (ISGs) in the CL. The hypothesis that gene expression differs in CL collected from pregnant (P) and non-pregnant (NP) ewes by Day 14 due to the lytic action of PGF during the estrous cycle or the presence of a conceptus was tested. RNA was isolated on Days 12 and 14 in NP or P ewes (n = 3 ewes/group) and analyzed using the Affymetrix bovine microarray (24,000 targets). Differential gene expression (>1.5 fold, P < 0.05) was confirmed using semi-quantitative real time PCR (RTPCR). Serum progesterone concentrations decreased (P < 0.05) from 1.7 ng/ml on Day 12 to 1.3 ng/ml by Day 14 in NP ewes suggesting initiation of luteolysis; and remained > 1.7 ng/ml in Day 12 and 14 P ewes indicating that the conceptus protected the CL from luteolysis. Early luteolysis from Day 12 to 14 NP was associated with differential expression of 683 genes, including SERPINE1 and THBS1. Presence of a conceptus from Day 12 to 14 also induced expression of 743 genes, i.e., ISGs (ISG15, MX1), PTX3, and IL-6 and stabilized expression of VEGF and LHR genes. In conclusion, pregnancy circumvents luteolytic pathways, and activates or stabilizes genes associated with interferon, chemokine, cell adhesion, cytoskeletal, angiogenic and epithelial to mesynchymal transition pathways in the CL.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part
View Samples- Danio rerio
- 11 Downloadable Samples
- Affymetrix Zebrafish Genome Array (zebrafish)
Description
Mesoderm differentiation in zebrafish relies on a complex interaction between transcription factors and signaling pathways. Tbx16 is a t-box transcription factor involved in this interaction. Here, we examine downstream targets of tbx16 in the intermediate mesoderm at the 4/5-somite stage and tail mesoderm at the 21-somite stage by comparing wild-type tissues with tissues from the tbx16 mutant, spadetail (spt).
Publication Title
Spatio-temporal regulation of Wnt and retinoic acid signaling by tbx16/spadetail during zebrafish mesoderm differentiation.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Induced pluripotent stem cell-derived human hepatocyte-like cells (iHeps) could provide a powerful tool for studying the mechanisms underlying human liver development and disease, testing the efficacy and safety of pharmaceuticals across different patients (i.e. personalized medicine), and enabling cell-based therapies in the clinic. However, current in vitro protocols that rely upon growth factors and extracellular matrices (ECM) alone yield iHeps with low levels of liver functions relative to adult primary human hepatocytes (PHHs). Moreover, these low hepatic functions in iHeps are difficult to maintain for prolonged times (weeks to months) in culture. Here, we engineered a micropatterned co-culture (iMPCC) platform in a multi-well format that, in contrast to conventional confluent cultures, significantly enhanced the functional maturation and longevity of iHeps in culture for 4 weeks in vitro when benchmarked against multiple donors of PHHs. In particular, iHeps were micropatterned onto collagen-coated domains of empirically optimized dimensions, surrounded by 3T3-J2 murine embryonic fibroblasts, and then sandwiched with a thin layer of ECM gel (Matrigel). We assessed iHep maturity via global gene expression profiles, hepatic polarity, secretion of albumin and urea, basal CYP450 activities, phase-II conjugation, drug-mediated CYP450 induction, and drug-induced hepatotoxicity. Conclusion: Controlling both homotypic interactions between iHeps and heterotypic interactions with stromal fibroblasts significantly matures iHep functions and maintains them for several weeks in culture. In the future, iMPCCs could prove useful for drug screening, studying molecular mechanisms underlying iHep differentiation, modeling liver diseases, and integration into human-on-a-chip systems being designed to assess multi-organ responses to compounds.
Publication Title
Enhancing the functional maturity of induced pluripotent stem cell-derived human hepatocytes by controlled presentation of cell-cell interactions in vitro.
Sample Metadata Fields
Specimen part, Subject
View Samples- Arabidopsis thaliana
- 8 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Selenate is chemically similar to sulfate and can be taken up and assimilated by plants via the same transporters and enzymes. In contrast to many other organisms, selenium (Se) has not been shown to be essential for higher plants. In excess, Se is toxic and restricts development. Both Se deficiency and toxicity pose problems worldwide. To obtain better insight into the effects of Se on plant metabolism and into plant mechanisms involved in Se tolerance, the transcriptome of Arabidopsis plants grown with or without selenate was studied, and Se-responsive genes identified. Roots and shoots exhibited different Se-related changes in gene regulation and metabolism. Many genes involved in sulfur (S) uptake and assimilation were upregulated. Accordingly, Se treatment enhanced sulfate levels in plants, but the quantity of organic S metabolites decreased. Transcripts regulating the synthesis and signaling of ethylene and jasmonic acid were also upregulated by Se. Selenate appeared to repress plant development, as suggested by the down-regulation of genes involved in cell wall synthesis and auxin-regulated proteins. The Se-responsive genes discovered in this study may help create plants that can better tolerate and accumulate Se, which may enhance the effectiveness of Se phytoremediation or serve as Se-fortified food.
Publication Title
Transcriptome analyses give insights into selenium-stress responses and selenium tolerance mechanisms in Arabidopsis.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Proline rich 15 (PRR15) is a small nuclear protein required for normal conceptus development in the sheep.
Publication Title
No associated publication
Sample Metadata Fields
Cell line, Treatment
View Samples- Rattus norvegicus
- 6 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
LV hypertrophy is associated with Western diet consumption, while intake of n-3 polyunsaturated fatty acids is associated with anti-hypertrophic effects. We treated rats for 12 weeks with either a Control diet, a Western diet or a Western + DHA diet. For each of the 3 dietary treatments there were 2 pooled samples of heart tissue (with each pooled sample representing 5 rats) for a total of 6 arrays. Microarray analysis identified 66 differentially expressed transcripts. Pathways were identified using Ingenuity and DAVID software.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Pseudomonas aeruginosa pao1
- 6 Downloadable Samples
- Affymetrix Pseudomonas aeruginosa Array (paeg1a)
Description
Although Pseudomonas aeruginosa is an opportunistic pathogen that does not often naturally infect alternate hosts such as plants, the plant-P. aeruginosa model has become a widely recognized system for identifying new virulence determinants and studying pathogenesis of this organism. Here we examine how both host factors and P. aeruginosa PAO1 gene expression are affected in planta after infiltration into incompatible and compatible cultivars of tobacco (Nicotiana tabacum L.) Nicotiana tabacum has a resistance gene (N) against tobacco mosaic virus; and although resistance to PAO1 infection correlated to the presence of a dominant N-gene, our data suggests that it is not a factor in resistance against Pseudomonas. We did observe that the resistant tobacco cultivar had higher basal levels of salicylic acid, and a stronger salicylic acid response upon infiltration of PAO1. Salicylic acid acts as a signal to activate defense responses in plants, limiting the spread of the pathogen and preventng access to nutrients. It has also been shown to have direct virulence modulating effects on P. aeruginosa. We also examined host effects on the pathogen by analyzing global gene expression profiles of bacteria removed from the intracellular fluid of the two plant hosts. We discovered that the availability of micronutrients, particularly sulfate and Pi, are important factors in in planta pathogenesis, and that the amounts of these nutrients made available to the bacteria may in turn have an effect on virulence gene expression. Indeed, there are several reports suggesting that P. aeruginosa virulence is influenced in mammalian hosts by the availability of iron and by levels of O2.
Publication Title
Global gene expression profiles suggest an important role for nutrient acquisition in early pathogenesis in a plant model of Pseudomonas aeruginosa infection.
Sample Metadata Fields
No sample metadata fields
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