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Homo sapiens
29 Downloadable Samples
Illumina HiSeq 2500
Description
While acute aerobic and resistance exercise stimulate a number of shared genes, each exercsie mode stimlutes a number of uniquely responsive genes, thus highlighting that different forms of exercise facilitate distinct molecular responses in skeletal muscle. Overall design: Randomized, counter-balanced, cross-over design (n=6) in which subjects performed an acute bout aerobic and resistance exercise separated by ~1 week.
Publication Title
Transcriptome response of human skeletal muscle to divergent exercise stimuli.
Sample Metadata Fields
Sex, Subject, Time
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GSE7852- Mus musculus
- 18 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Comparisons of global gene-expression profiles revealed a greater distinction between CD4+ Treg cells and CD4+ conventional (Tconv) T cells residing in abdominal (epidydimal) fat versus in more standard locations such as the spleen, thymus and LN.
Publication Title
Lean, but not obese, fat is enriched for a unique population of regulatory T cells that affect metabolic parameters.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 12 Downloadable Samples
- Affymetrix Rat Gene 2.0 ST Array (ragene20st)
Description
Regulation of homeostasis and development of cardiac muscle tissues is controlled by a core set of transcription factors. The MEF2 family plays a critical role in these processes.
Publication Title
Antagonistic regulation of cell-cycle and differentiation gene programs in neonatal cardiomyocytes by homologous MEF2 transcription factors.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
In this study, we have identified MEF2A-sensitive genes in atrial and ventricular chambers of the adult heart. MEF2A is a member of the myocyte enhancer factor 2 (MEF2) family of transcription factors. MEF2 proteins are expressed in skeletal and cardiac muscle tissues and are conserved across many mammalian species, but the gene programs regulated by MEF2A in adult cardiac chambers are largely unknown. We compared gene expression profiles between WT and Mef2a knockout atria and ventricles from adult mice, and the results identified distinct and overlapping sets of genes sensitive to the loss of MEF2A in the adult heart.
Publication Title
The transcription factor MEF2A fine-tunes gene expression in the atrial and ventricular chambers of the adult heart.
Sample Metadata Fields
Specimen part
View Samples- Drosophila melanogaster
- 15 Downloadable Samples
- NextSeq 500
Description
The spliceosome is a dynamic RNA-protein complex that executes pre-mRNA splicing and is composed of five core small nuclear ribonucleoprotein particles (U1, U2, U4/5/6 snRNP) and >150 additional proteins specific for each snRNP. We report a circadian role for Pre-mRNA Processing factor 4 (PRP4), a conserved component of the spliceosomal U4/U6.U5 triple small nuclear ribonucleoprotein (tri-snRNP) complex. We broadly hypothesized that downregulation of prp4 led to the aberrant splicing of one or many of the core clock transcripts. To identify these splicing events in an unbiased way, we performed RNA-Sequencing (RNA-Seq) analysis. We reasoned that we could have a more targeted approach if we could zoom in on the overlapping splicing changes that would be driven by the knockdown of at least two different tri-snRNP components. Because the pan-neuronal knockdown of all tri-snRNP components tested in our study led to lethality, we decided to utilize an alternative broad driver. For that purpose, we selected a strong eye-specific Glass Multiple Promoter driver (GMR-Gal4). Because most of the signal from head lysates comes directly from the eye tissue and because the core splicing factors are ubiquitously expressed, GMR-specific downregulation of prp4 and prp8 promised to be a viable alternative to the pan-neuronal knockdown. We examined changes in both the total transcript levels and splicing events upon prp4 knockdown in the eye. The overall gene expression seemed to be dramatically influenced by prp4 downregulation (433 DOWN, 310 UP at FDR < 0.05). Despite the fact that PRP4 is a component of the core spliceosome that is required for constitutive exon splicing, we did not detect dramatic effects on global splicing. Only 45 genes exhibited differential alternate splicing upon prp4 downregulation at FDR < 0.05). Overall design: 3 samples with 5 replicates each were analyzed using Illumina Next-Generation Sequencing (NextSeq 500).
Publication Title
Spliceosome factors target timeless (<i>tim</i>) mRNA to control clock protein accumulation and circadian behavior in Drosophila.
Sample Metadata Fields
Specimen part, Subject
View Samples- Oryza sativa
- 6 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
RNAi mediated suppression of MADS29 severely affects seed set; the surviving seeds are smaller in size with reduced grain filling, abnormal starch grains and aberrant embryo development. To identify the affected pathways due to suppression of this transcription factor in the transgenic seeds, transcriptome analysis using microarray was carried out.
Publication Title
Functional delineation of rice MADS29 reveals its role in embryo and endosperm development by affecting hormone homeostasis.
Sample Metadata Fields
Specimen part
View Samples- Oryza sativa
- 5 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
Overexpression of MADS29 results in severely dwarfed phenotype, resulting from a shift in auxin-cytokinin ratio in favor of cytokinins. To see the extent of change in gene expression in the leaves of the transgenic plants, whole genome transcript analysis was carried out using microarray.
Publication Title
Functional delineation of rice MADS29 reveals its role in embryo and endosperm development by affecting hormone homeostasis.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 285 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
We used microarrays to examine gene expression levels from 95 unrelated CEPH-Utah individuals 0, 2 or 6 hours after treatment with 10Gy of ionizing radiation.
Publication Title
Stress-induced changes in gene interactions in human cells.
Sample Metadata Fields
Cell line, Treatment, Time
View Samples- Homo sapiens
- 258 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We used microarrays to examine gene expression levels from 131 unrelated CEPH-Utah grandparents with either DMSO or tunicamycin.
Publication Title
Stress-induced changes in gene interactions in human cells.
Sample Metadata Fields
Cell line, Treatment, Time
View Samples- Vitis vinifera
- 32 Downloadable Samples
- Affymetrix Vitis vinifera (Grape) Genome Array (vitisvinifera)
Description
We used Affymetrix microarray analyses of thirty-two individual Vitis vinifera cv. Cabernet Sauvignon berries sampled from two clusters at fifty-percent ripening initiation. By delineating four developmental stages of ripening initiation, we demonstrate that color is a statistically significant indicator of transcriptional state during ripening initiation. We report on clustered gene expression patterns which were mined for genes annotated with signal transduction functions in order to advance regulatory network modeling of ripening initiation in grape berries.
Publication Title
Gene expression analyses in individual grape (Vitis vinifera L.) berries during ripening initiation reveal that pigmentation intensity is a valid indicator of developmental staging within the cluster.
Sample Metadata Fields
No sample metadata fields
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