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Gallus gallus
18 Downloadable Samples
Affymetrix Chicken Genome Array (chicken)
Description
Sex determination is still poorly understood in birds and no key determinants have so far been identified. In contrast to most other species, dosage compensation of bird sex chromosomal genes appears rather ineffective. By comparing microarrays of microdissected primitive streak from single chicken embryos, we identified a large number of genes differentially expressed between male and female embryos at a very early stage (Hamburger and Hamilton stage 4), long before any sexual differentiation occurs. Most of these genes are located on the Z chromosome, which indicates that dosage compensation is ineffective in early chicken embryos. Gene ontology analyses using an enhanced annotation tool for Affymetrix probesets of the chicken genome shows that among the male-biased genes found on the Z chromosome, more than 20 genes have a role in sex differentiation.
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
We have previously shown that during lactation, osteocytes directly remodel their perilacunar and pericanalicular matrix, thereby mobilizing calcium and contributing to maternal bone loss. To identify genes potentially responsible for perilacunar remodeling, microarray analysis was performed on osteocytes from CD-1 virgin and lactating mice and mice sacrificed on day 7 post weaning.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Bos taurus
- 159 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
Infertility in lactating dairy cows is explained partially by the metabolic state associated with high milk production. The hypothesis was that lactating and non-lactating cows would differ in endometrial and placental transcriptomes during early pregnancy (day 28 to 42) and this difference would explain the predisposition for lactating cows to have embryonic loss at that time. Cows were either milked or not milked after calving. Reproductive [endometrium (caruncular and intercarunclar) and placenta] and liver tissues were collected on day 28, 35, and 42 of pregnancy. The primary hypothesis was rejected because no effect of lactation on mRNA abundance within reproductive tissues was found. Large differences within liver demonstrated the utility of the model to test an effect of lactation on tissue gene expression. Major changes in gene expression in reproductive tissues across time were found. Greater activation of the transcriptome for the recruitment and activation of macrophages was found in the endometrium and placenta. Changes in glucose metabolism between day 28 and 42 included greater mRNA abundance of rate-limiting genes for gluconeogenesis in intercaruncular endometrium and evidence for the establishment of aerobic glycolysis (Warburg effect) in the placenta. Temporal changes were predicted to be controlled by CSF1, PDGFB, and JUN. Production of nitric oxide and reactive oxygen species by macrophages was a mechanism to promote angiogenesis in the endometrium. Reported differences in pregnancy development for lactating versus non-lactating cows could be explained by systemic glucose availability to the conceptus and appear to be independent of the endometrial and placental transcriptomes.
Publication Title
The transcriptome of the endometrium and placenta is associated with pregnancy development but not lactation status in dairy cows.
Sample Metadata Fields
Specimen part
View Samples- Glycine max
- 41 Downloadable Samples
- Affymetrix Soybean Genome Array (soybean)
Description
Soybean root hair transcriptional response to their inoculation by the symbiotic bacteria B. japonicum involved in soybean nodulation. We used the first generation of an Affymetrix microarray to quantify the abundance of the transcripts from soybean root hair cells inoculated and mock-inoculated by B. japonicum. This experiment was performed on a time-course from 6 to 48 hours after inoculation.
Publication Title
Complete transcriptome of the soybean root hair cell, a single-cell model, and its alteration in response to Bradyrhizobium japonicum infection.
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples- Sus scrofa
- 31 Downloadable Samples
- Affymetrix Porcine Genome Array (porcine)
Description
We adopted a transcriptome-wide microarray analysis approach to determine the extent to which vascular gene expression is altered as a result of juvenile obesity and identify obesity-responsive mRNAs. We examined transcriptional profiles in the left anterior descending coronary artery (LAD), perivascular fat adjacent to the LAD, and descending thoracic aorta between obese (n=5) and lean (n=6) juvenile Ossabaw pigs (age=22 weeks). Obesity was experimentally induced by feeding the animals a high-fat/high fructose corn syrup/high-cholesterol diet for 16 weeks. We found that expression of 189 vascular cell genes in the LAD and expression of 165 genes in the thoracic aorta were altered with juvenile obesity (FDR10%) with an overlap of only 28 genes between both arteries. Notably, a number of genes found to be markedly up-regulated in the LAD of obese pigs are implicated in atherosclerosis, including ACP5, LYZ, CXCL14, APOE, PLA2G7, LGALS3, SPP1, ITGB2, CYBB, and P2RY12. Furthermore, pathway analysis revealed the induction of pro-inflammatory and pro-oxidant pathways with obesity primarily in the LAD. Gene expression in the LAD perivascular fat was minimally altered with juvenile obesity. Together, we provide new evidence that obesity produces artery-specific changes in pre-translational regulation with a clear up-regulation of pro-atherogenic genes in the LAD. Our data may offer potential viable drug targets and mechanistic insights regarding the molecular precursors involved in the origins of over-nutrition and obesity-associated vascular disease. In particular, our results suggest that the oxLDL-LOX-1-NFB signaling axis may be involved in the early initiation of a juvenile obesity-induced pro-atherogenic coronary artery phenotype.
Publication Title
Vascular transcriptional alterations produced by juvenile obesity in Ossabaw swine.
Sample Metadata Fields
Specimen part
View Samples- Sus scrofa
- 28 Downloadable Samples
- Affymetrix Porcine Genome Array (porcine)
Description
While the salutary effects of exercise training on conduit artery endothelial cells have been reported in animals and humans with cardiovascular risk factors or disease, whether a healthy endothelium is alterable with exercise training is less certain. The purpose of this study was to evaluate the impact of exercise training on transcriptional profiles in normal endothelial cells using a genome-wide microarray analysis. Brachial and internal mammary endothelial gene expression was compared between a group of healthy pigs that exercise-trained for 16-20 weeks (n=8) and a group that remained sedentary (n=8). We found that a total of 130 genes were up regulated and 84 genes down regulated in brachial artery endothelial cells with exercise training. In contrast, a total of 113 genes were up regulated and 31 genes down regulated in internal mammary artery endothelial cells (>1.5-fold and false discovery rate<15%). Although there was an overlap of 66 genes (59 up regulated and 7 down regulated with exercise training) between the brachial and internal mammary arteries, the identified endothelial gene networks and biological processes influenced by exercise training were distinctly different between the brachial and internal mammary arteries. These data indicate that a healthy endothelium is indeed responsive to exercise training and support the concept that the influence of physical activity on endothelial gene expression is not homogenously distributed throughout the vasculature.
Publication Title
Impact of exercise training on endothelial transcriptional profiles in healthy swine: a genome-wide microarray analysis.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 20 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Bos taurus
- 14 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
Cows exposed to short day photoperiod (SD, 8L:16D) during the 60-day non-lactating period prior to parturition produce more milk in their subsequent lactation compared to cows exposed to long day photoperiod (LD,16L:8D). Although this response is well-established in dairy cows, the underlying mechanisms are not understood. We hypothesized that differential gene expression in cows exposed to SD or LD photoperiods during the dry period could be used to identify the functional basis for the subsequent increase in milk production during lactation. Pregnant, multiparous cows were maintained on a SD or LD photoperiod for 60-days prior to parturition. Mammary biopsies were obtained on days -24 and -9 relative to parturition and Affymetrix GeneChip Bovine Genome Arrays were used to quantify gene expression. Sixty-four genes were differentially expressed (p 0.05 and fold-change |1.5|) between SD and LD treatments. Many of these genes were associated with cell growth and proliferation, or immune function. Ingenuity Pathway Analysis predicted upstream regulators to include TNF, TGF1, interferon and several interleukins. In addition, expression of 125 genes was significantly different between day -24 and day -9; those genes were associated with milk component metabolism and immune function. The interaction of photoperiod and time affected 32 genes associated with insulin-like growth factor (IGF-I) signaling. Genes differentially expressed in response to photoperiod were associated with mammary development and immune function consistent with the enhancement of milk yield in the ensuing lactation. Our results provide insight into the mechanisms by which photoperiod affects the mammary gland and subsequently lactation.
Publication Title
Responses of the mammary transcriptome of dairy cows to altered photoperiod during late gestation.
Sample Metadata Fields
Specimen part
View Samples- Glycine max
- 11 Downloadable Samples
- Affymetrix Soybean Genome Array (soybean)
Description
Comparison of syncytia gene expression between soybean near-isogenic lines 7923R (NIL-R) and 7923S (NIL-S) infected with the soybean cyst nematode (PA3).
Publication Title
The Soybean Rhg1 locus for resistance to the soybean cyst nematode Heterodera glycines regulates the expression of a large number of stress- and defense-related genes in degenerating feeding cells.
Sample Metadata Fields
Specimen part
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GSE52610- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Extracellular adenosine 5-triphosphate (ATP) is a signaling molecule. To define the global transcriptional response to ATP, we performed DNA microarray analysis using RNA derived from wild-type (Col-0) Arabidopsis and the dorn1-1 mutant, Lectin receptor kinase I.9 (At5g60300) carrying a EMS point mutation, seedlings after 100 M ATP.
Publication Title
Identification of a plant receptor for extracellular ATP.
Sample Metadata Fields
Specimen part
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