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Mus musculus
2 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
ETV4 and ETV5 are FGF-activated transcription factor genes. Inactivation of Etv4 and Etv5 in the lung epithelium led to prolonged branch tip growth and delayed new branch formation.
Publication Title
FGF-Regulated ETV Transcription Factors Control FGF-SHH Feedback Loop in Lung Branching.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
Analysis of whole heart samples from Hdac3-Isl1KO embryos at embryonic day E9.5. Results provide insights into the role of Hdac3 in second heart field-derived cardiac cells.
Publication Title
Histone Deacetylase 3 Coordinates Deacetylase-independent Epigenetic Silencing of Transforming Growth Factor-β1 (TGF-β1) to Orchestrate Second Heart Field Development.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 2 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Analysis of KLS cells purified from bone marrow of mice conditionally inactivated for TIF1 gene. TIF1 deletion results in multiple defects in adult hematopoiesis. Results provide insight into the role of TIF1 in hematopoietic stem cells functions.
Publication Title
Adult hematopoiesis is regulated by TIF1γ, a repressor of TAL1 and PU.1 transcriptional activity.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 21 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
The full complement of molecular pathways contributing to Parkinsons disease (PD) pathogenesis remains unknown. Here, to address this issue, we began by using a high-resolution variant of functional magnetic resonance imaging (fMRI) to pinpoint brainstem regions differentially affected by, and resistant to, the disease. Then, relying on the imaging information as a guide, we profiled gene expression levels of postmortem brain samples and used a factorial statistical model to identify a disease related decrease in the expression of the polyamine enzyme spermidine/spermine N1-acetyltransferase 1 (SAT1). Next, a series of studies were performed to confirm the pathogenic relevance of this finding. First, to test for a causal link between polyamines and -synuclein toxicity, we investigated a yeast model expressing -synuclein. Polyamines were found to enhance the toxicity of -synuclein, and an unbiased genome-wide screen for modifiers of -synuclein toxicity identified Tpo4, a member of a family of proteins responsible for polyamine transport. Second, to test for a causal link between SAT1 activity and PD histopathology we investigated a mouse model expressing -synuclein. DENSPM (N1, N11-diethylnorspermine), a polyamine analog that increases SAT1 activity, was found to reduce PD histopathology, while Berenil (diminazene aceturate), a pharmacological agent that reduces SAT1 activity, worsened the histopathology. Third, we genotyped PD patients and controls and isolated a rare but novel variant in the SAT1 gene, although the functional significance of this genetic variant was not identified. Taken together, the results suggest that the polyamine pathway contributes to PD pathogenesis.
Publication Title
Polyamine pathway contributes to the pathogenesis of Parkinson disease.
Sample Metadata Fields
Sex, Age, Subject
View Samples- Arabidopsis thaliana
- 29 Downloadable Samples
Illumina HiSeq 1000
Description
RNAseq profiling of 10 time points during germination in Arabidopsis, from freshly harvested seed, through mature seed, stratification, germination and to post-germination. Overall design: Total RNA was extracted from Arabidopsis seeds at 10 time points during germination in triplicate. The time points were: freshly harvested seed (H), seeds following 15 days of ripening (0 h), seeds after; 1 h of stratification (1 h S), 12 h of stratification (12 h S), 48 h of stratification (48 h S), followed by seed collected 1 hour into the light (1 h SL), 6 hours into the light (6 h SL), 12 hours into the light (12 h SL), 24 hours into the light (24 h SL) and 48 hours into the light (48 h SL).
Publication Title
Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination.
Sample Metadata Fields
Specimen part, Subject, Time
View Samples- Mus musculus
- 20 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
The amygdala is a prominent region of the brain processing stress-related emotion and vigilance. Additionally it is known that the serotonergic system is strongly involved in stress response and adaptation. The serotonin transporter (5-HTT) as key regulator of serotonergic activity in the brain is associated with stress-related neuropsychiatric disorders as well as heightened trait anxiety/dysphoria and exaggerated response to fear and environmental stress in humans. Also 5-HTT knockout mice display increased anxiety- and depression-related behaviors, altered stress reactivity and stress-coping abilities, gene expression differences and altered dendritic morphology.
Publication Title
Effect of acute stressor and serotonin transporter genotype on amygdala first wave transcriptome in mice.
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples- Rattus norvegicus
- 44 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Many heavy metals, including nickel (Ni), cadmium (Cd), and chromium (Cr) are toxic industrial chemicals with an exposure risk in both occupational and environmental settings that may cause harmful outcomes. While these substances are known to produce adverse health effects leading to disease or health problems, the detailed mechanisms remain unclear. To elucidate the processes involved in the of toxicity of nickel, cadmium, and chromium at the molecular level and to perform a comparative analysis, H4-II-E-C3 rat liver-derived cell lines were treated with soluble salts of each metal using concentrations derived from viability assays, and gene expression patterns were determined with DNA microarrays.
Publication Title
Exposure to nickel, chromium, or cadmium causes distinct changes in the gene expression patterns of a rat liver derived cell line.
Sample Metadata Fields
No sample metadata fields
View Samples- Danio rerio
- 15 Downloadable Samples
- Affymetrix Zebrafish Genome Array (zebrafish)
Description
In this report, we describe a successful protocol for isolating and expression-profiling live fluorescent- protein-labelled neurons from zebrafish embryos. As a proof-of-principle for this method, we FAC-sorted and RNA-profiled GFP-labelled spinal CiA interneurons and compared the expression profile of these cells to those of post-mitotic spinal neurons in general and to all trunk cells. We show that RNA of sufficient quality and quantity to uncover both expected and novel transcription profiles via Affymetrix microarray analysis can be extracted from 5,700 to 20,000 FAC-sorted cells. As part of this study, we also further confirm the genetic homology of mammalian and zebrafish V1 interneurons, by demonstrating that zebrafish V1 cells (CiAs) express genes that encode for the transcription factors Lhx1a and Lhx5. This protocol for dissociating, sorting and RNA-profiling neurons from organogenesis-stage zebrafish embryos should also be applicable to other developing organs and tissues and potentially other model organisms.
Publication Title
RNA profiling of FAC-sorted neurons from the developing zebrafish spinal cord.
Sample Metadata Fields
Age, Specimen part
View Samples
GSE3142- Mus musculus
- 10 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
Hair follicle matrix, outer root sheath, dermal papilla cells and melanocytes and a dermal fraction enriched in fibroblasts were FACS isolated from 4d backskins. Targets from two biological replicates of each were generated and the expression profiles were determined using Affymetrix Mouse Genechip 430A arrays. Comparisons between the sample groups allow the identification of cell-type specific genes.
Publication Title
Molecular dissection of mesenchymal-epithelial interactions in the hair follicle.
Sample Metadata Fields
No sample metadata fields
View Samples- Caenorhabditis elegans
- 146 Downloadable Samples
- Affymetrix C. elegans Genome Array (celegans)
Description
The principal toxicity of acute organophosphate (OP) pesticides poisoning is the disruption of neurotransmission through inhibition of acetylcholinesterase (AChE). However, other mechanisms leading to persistent effects and neurodegeneration remain controversial and difficult to detect. Because Caenorhabditis elegans is relatively resistant to OP lethalityparticularly through the inhibition of AChEstudies in this nematode provide an opportunity to observe alterations in global gene expression following OP exposure that cannot be readily observed in less resistant organisms.
Publication Title
Alterations in gene expression in Caenorhabditis elegans associated with organophosphate pesticide intoxication and recovery.
Sample Metadata Fields
No sample metadata fields
View Samples