Filters
Technology
Platform
Arabidopsis thaliana
12 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
We performed a microarray experiment to assess the global changes in transcription occurring in leaves and roots of the vitamin B6 deficient pdx1.3 knockout mutant in comparison to WT. Vitamin B6 (pyridoxal 5-phosphate) is an essential cofactor of many metabolic enzymes. Plants biosynthesize the vitamin de novo employing two enzymes, pyridoxine synthase1 (PDX1) and PDX2. In Arabidopsis (Arabidopsis thaliana), there are two catalytically active paralogs of PDX1 (PDX1.1 and PDX1.3) producing the vitamin at comparable rates. Since single mutants are viable but the pdx1.1 pdx1.3 double mutant is lethal, the corresponding enzymes seem redundant.
Publication Title
Consequences of a deficit in vitamin B6 biosynthesis de novo for hormone homeostasis and root development in Arabidopsis.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 24 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Arabidopsis fc2-1 mutants fail to properly de-etiolate after a prolonged period in the dark. Our goal was to monitor whole genome expression during the first 2 hours of de-etiolation to determine the cuase of this growth arrest.
Publication Title
Ubiquitin facilitates a quality-control pathway that removes damaged chloroplasts.
Sample Metadata Fields
Specimen part
View Samples- Bos taurus
- 21 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Negative energy balance and hepatic gene expression patterns in high-yielding dairy cows during the early postpartum period: a global approach.
Sample Metadata Fields
No sample metadata fields
View Samples- Bos taurus
- 11 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
Most dairy cows suffer uterine microbial contamination postpartum. Persistent endometritis often develops, associated with reduced fertility. We used a model of differential feeding and milking regimes to produce cows in differing negative energy balance (NEB) status in early lactation.
Publication Title
Negative energy balance alters global gene expression and immune responses in the uterus of postpartum dairy cows.
Sample Metadata Fields
Age, Specimen part
View Samples- Bos taurus
- 11 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
In high yielding dairy cows the liver undergoes extensive physiological and biochemical changes during the early postpartum period in an effort to re-establish metabolic homeostasis and to counteract the adverse effects of negative energy balance (NEB). These adaptations are likely to be mediated by significant alterations in hepatic gene expression. To gain new insights into these events an EB model was created using differential feeding and milking regimes to produce two groups of cows with either a mild (MNEB) (n=5) or severe NEB (SNEB) (n=6) status. Cows were slaughtered and liver tissues collected on days 6-7 of the first follicular wave postpartum. Using an Affymetrix 23k oligonucleotide bovine array to determine global gene expression in hepatic tissue of these cows, a total of 416 genes (189 up- and 227 down-regulated) were found to be altered by SNEB. Network analysis using Ingenuity Pathway Analysis revealed that SNEB was associated with widespread changes in gene expression classified into 36 gene networks including those associated with lipid metabolism, connective tissue development and function, cell signalling, cell cycle and metabolic diseases. Severe NEB cows displayed reduced expression of transcription activators and signal transducers that regulate the expression of genes and gene networks associated with cell signalling and tissue repair. These alterations are linked with increased expression of abnormal cell cycle and cellular proliferation associated pathways. This study provides new information and insights on the effect of SNEB on gene expression in high yielding Holstein Friesian dairy cows in the early postpartum period.
Publication Title
Negative energy balance and hepatic gene expression patterns in high-yielding dairy cows during the early postpartum period: a global approach.
Sample Metadata Fields
No sample metadata fields
View Samples
GSE46199- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Epithelial and stromal microRNA signatures of columnar cell hyperplasia linking Let-7c to precancerous and cancerous breast cancer cell proliferation.
Sample Metadata Fields
Sex, Specimen part, Disease, Disease stage, Treatment
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Columnar cell hyperplasia (CCH) is the first histologically identifiable lesion in the breast with premalignant potential. Altered miRNA expression in the stroma surrounding CCH compared to normal tissue was discovered. The effect of upregulation of one specific miRNA was investigated by gene expression array in human mammary fibroblasts as well as in epithelial CCH cells coculterd with miR-132 oversexpressing human mammary fibroblasts.
Publication Title
Epithelial and stromal microRNA signatures of columnar cell hyperplasia linking Let-7c to precancerous and cancerous breast cancer cell proliferation.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 6 Downloadable Samples
Illumina HiSeq 2500
Description
We examined mRNA level changes in two mouse enteroids clones expressing different levels of PLAGL2 from a constitutive Piggybac transposon vector. Overall design: Expression analysis, PLAGL2 O/E vs. GFP O/E
Publication Title
The Zinc Finger Transcription Factor PLAGL2 Enhances Stem Cell Fate and Activates Expression of ASCL2 in Intestinal Epithelial Cells.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 24 Downloadable Samples
- IlluminaGenomeAnalyzerII
Description
microRNAs (miRNAs) are small noncoding RNAs that post-transcriptionally regulate gene expression by targeting specific mRNAs. Altered expression of circulating miRNAs have been associated with age-related diseases including cancer and cardiovascular disease. Although we and others have found an age-dependent decrease in miRNA expression in peripheral blood mononuclear cells (PBMCs), little is known about the role of circulating miRNAs in human aging. Here, we examined miRNA expression in human serum from young (mean age 30 years) and old (mean age 64 years) individuals using next generation sequencing technology and real-time quantitative PCR. Of the miRNAs that we found to be present in serum, three were significantly decreased in 20 older individuals compared to 20 younger individuals: miR-151a-5p, miR-181a-5p and miR-1248. Consistent with our data in humans, these miRNAs are also present at lower levels in the serum of elderly rhesus monkeys. In humans, miR-1248 was found to regulate the expression of mRNAs involved in inflammatory pathways and miR-181a was found to correlate negatively with the pro-inflammatory cytokines IL-6 and TNFa and to correlate positively with the anti-inflammatory cytokines TGFb and IL-10. These results suggest that circulating miRNAs may be a biological marker of aging and could also be important for regulating longevity. Identification of stable miRNA biomarkers in serum could have great potential as a noninvasive diagnostic tool as well as enhance our understanding of physiological changes that occur with age. Overall design: Examination of microRNAs isolated from human serum from 11 young (mean age 30 yrs) and 11 old (mean age 64 yrs) individuals and from peripheral blood mononuclear cells from one young (30 yr) and one old (64 yr) individual.
Publication Title
Age-related changes in microRNA levels in serum.
Sample Metadata Fields
No sample metadata fields
View Samples- Bos taurus
- 10 Downloadable Samples
- Affymetrix Bovine Genome Array (bovine)
Description
Increased energy demands to support lactation, coupled with lowered feed intake capacity results in negative energy balance (NEB) and is typically characterized by extensive mobilization of body energy reserves in the early postpartum dairy cow. The catabolism of stored lipid leads to an increase in the systemic concentrations of nonesterified fatty acids (NEFA) and -hydroxy butyrate (BHB). Oxidation of NEFA in the liver result in the increased production of reactive oxygen species and the onset of oxidative stress and can lead to disruption of normal metabolism and physiology. The immune system is depressed in the peripartum period and early lactation and dairy cows are therefore more vulnerable to bacterial infections causing mastitis and or endometritis at this time. A bovine Affymetrix oligonucleotide array was used to determine global gene expression in the spleen of dairy cows in the early postpartum period. Spleen tissue was removed post mortem from five severe NEB (SNEB) and five medium NEB (MNEB) cows 15 days postpartum.SNEB increased systemic concentrations of NEFA and BHB, and white blood cell and lymphocyte numbers were decreased in SNEB animals. A total of 545 genes were altered by SNEB. Network analysis using Ingenuity Pathway Analysis revealed that SNEB was associated with NRF2-mediated oxidative stress, mitochondrial dysfunction, endoplasmic reticulum stress, natural killer cell signaling, p53 signaling, downregulation of IL-15, BCL-2, and IFN- ; upregulation of BAX and CHOP and increased apoptosis with a potential negative impact on innate and adaptive immunity.
Publication Title
Pleiotropic effects of negative energy balance in the postpartum dairy cow on splenic gene expression: repercussions for innate and adaptive immunity.
Sample Metadata Fields
No sample metadata fields
View Samples