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Xenopus laevis
3 Downloadable Samples
Affymetrix Xenopus laevis Genome Array (xenopuslaevis)
Description
We implemented a functional genomics approach as a means to undertake a large-scale analysis of the Xenopus laevis inner ear transcriptome through microarray analysis.
Publication Title
Probing the Xenopus laevis inner ear transcriptome for biological function.
Sample Metadata Fields
Specimen part
View Samples- Gossypium hirsutum
- 2 Downloadable Samples
- Affymetrix Cotton Genome Array (cotton)
Description
Cotton productivity is affected by water deficit and little is known about the molecular basis of drought tolerance in cotton. In this study, microarray analysis was carried out to identify drought responsive genes in functional leaves of the field-grown drought stressed cotton (Gossypium hirsutum L.) Acala 1517-99. The water stress was imposed after withholding irrigation for 9 days in the early squaring stage, which resulted in 10-15% reduction in plant growth compared to the well watered plants. A total of 110 drought responsive genes (0.5% of the total genes represented in the microarray) were identified, 79% (88 genes) of which were down-regulated and 21% (22 genes) were up-regulated by water stress. The responsiveness of 19 selected drought responsive genes was validated by real time PCR. The drought inducible genes were grouped into six functional categories only including stress related (10 genes, 9 of which are heat shock proteins), metabolism (3) and one each for transcription factor, proline biosynthesis and cellular transport. The down-regulated genes were classified into 14 functional categories including metabolism (20 genes), cellular transport (12), stress related (12), and regulation of gene expression (9) and transcription factor (4), signal transduction (7) and 2 genes each for biosynthesis of secondary compounds, cell wall, fatty acids/lipids and chlorophyll, and protein degradation. Most of the genes have been reported in other plants as drought tolerant/responsive and only 21 drought responsive genes (19%) were functionally unknown. The genes identified provides the first glimpse into the molecular basis of drought response in cotton.
Publication Title
No associated publication
Sample Metadata Fields
Age, Specimen part
View Samples
GSE77741- Homo sapiens
- 100 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
MLL rearrangements impact outcome in HOXA-deregulated T-lineage acute lymphoblastic leukemia: a Children's Oncology Group Study.
Sample Metadata Fields
Specimen part, Disease
View Samples- Homo sapiens
- 100 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The clinical and cytogenetic features associated with T-cell acute lymphoblastic leukemia (T-ALL) are not predictive of early treatment failure or relapse. We used the Affymetrix U133 Plus 2.0 chip to profile 100 newly diagnosed patients who were treated in the Children's Oncology Group (COG) T-ALL AALL0434. We performed unsupervised hierarchical clustering of 25 HOXA probe sets within the cohort of 100 T-ALL cases. We identified a cluster of 20 cases (20%) characterized by increased expression of HOXA3, 5, 7, 9, and 10. In samples with HOXA9/10 deregulation, the presence of specific molecular lesions were confirmed through a systematic review of cytogenetic databases, FISH and PCR testing, and by RNA sequence analysis. Because MLL and AF10 genes rearrangements (MLL-R, AF10-R) are hallmarks of HOXA-deregulated leukemias, we sought to identify specific genes that are enriched with these genomic abnormalities.
Publication Title
MLL rearrangements impact outcome in HOXA-deregulated T-lineage acute lymphoblastic leukemia: a Children's Oncology Group Study.
Sample Metadata Fields
Specimen part, Disease
View Samples- Homo sapiens
- 34 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Primary xenografts were made from a variety of different high-risk childhood BCP-ALL leukemia samples.
Publication Title
Evaluation of the in vitro and in vivo efficacy of the JAK inhibitor AZD1480 against JAK-mutated acute lymphoblastic leukemia.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 20 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
Pregnant C57Bl6N mice were treated with 0 (corn oil), 1.5, 3.0, or 6.0 ug/kg TCDD on gd14.5. Fetal hearts were collected on gd17.5. Hearts from each litter were pooled onto one chip. 4 replicates of each condition were run on affymetrix MG_U74Av2 chips, using standard affymetrix protocols and controls.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
Despite widespread knowledge that bone marrow-resident breast cancer cells (BMRCs) affect tumor progression, signaling mechanisms of BMRCs implicated in maintaining long-term dormancy have not been characterized. To overcome these hurdles, we developed a novel experimental model of tumor dormancy employing circulating tumor cells (CTCs) derived from metastatic breast cancer patients (de novo CTCs), transplanted them in immunocompromised mice, and re-isolated these cells from xenografted mice bone marrow (ex vivo BMRCs) and blood (ex vivo CTCs) to perform downstream transcriptomic analyses.
Publication Title
Molecular Interplay between Dormant Bone Marrow-Resident Cells (BMRCs) and CTCs in Breast Cancer.
Sample Metadata Fields
Sex, Specimen part, Disease stage
View Samples- Saccharomyces cerevisiae
- 8 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
A population of Saccharomyces cerevisiae was cultured for approximately 450 generations in the presence of high glucose to select for genetic variants. This experiment allows for a controlled model of adaptive evolution under natural selection. Using the parental strain BY4741 as the starting population, an evolved culture was obtained after continuous aerobic growth in a glucose-high medium for approximately 450 generations. After the evolution period three single colony isolates were selected for analysis. Next-generation Ion Torrent sequencing was used to evaluate genetic changes. Greater than 100 deletion/insertion changes were found with approximately half of these effecting genes. Additionally, over 180 single-nucleotide polymorphisms (SNPs) were identified with more than one quarter of these resulting in a non-synonymous mutation. Affymetrix DNA microarrays and RNseq analysis were used to determine differences in gene expression in the evolved strains compared to the parental strain. It was established that approximately 900 genes demonstrated significantly altered expression in the evolved strains relative to the parental strain. Many of these genes showed similar alterations in their expression in all three evolved strains. Interestingly, genes with altered expression in the three evolved strains included genes with a role in the TCA cycle. Overall these results are consistent with the physiological observations of decreased ethanol production and suggest that the underlying metabolism switched from fermentation to respiration during aerobic growth.
Publication Title
No associated publication
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 7 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
We conducted a preliminary investigation to determine whether ethanol-induced alterations in placental gene expression may have some utility as a diagnostic indicator of maternal drinking during pregnancy as well as a prognostic indicator of risk for adverse neurobehavioral outcomes in affected offspring.
Publication Title
Effects of moderate drinking during pregnancy on placental gene expression.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 6 Downloadable Samples
- Affymetrix Rat Gene 2.0 ST Array (ragene20st)
Description
The goal of the study was to determine the effect of lentiviral- mediated overexpression of miR-495 (LV-miR-495) on the levels of gene expression in the nuclues accumbens of rats relative to control rats injected with the empty vector (LV-GFP).
Publication Title
In silico identification and in vivo validation of miR-495 as a novel regulator of motivation for cocaine that targets multiple addiction-related networks in the nucleus accumbens.
Sample Metadata Fields
No sample metadata fields
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