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GSE1295
Homo sapiens
32 Downloadable Samples
Affymetrix Human Genome U133A Array (hgu133a)
Description
STRRIDE is an exercise intervention study of different doses and intensities in overweight women and men with the metabolic syndrome. We profiled biopsies from 3 female and 3 male STRRIDE subjects in the high exercise group (2,200 kCal/wk). Muscle biopsies were profiled at entry (0h), and after 9 months of aerobic training (24 hrs post-last bout, 96 hrs post last bout, and 336h (14 days) de-training). Included also are pilot expression data from 3 male subjects.
Publication Title
Exercise training increases electron and substrate shuttling proteins in muscle of overweight men and women with the metabolic syndrome.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 10 Downloadable Samples
Illumina HiSeq 1500
Description
The molecular mechanism by which lncRNAs derived from the promoter region where the transcriptional machinery is assembled regulate the expression of neighboring genes during cell differentiation is largely unknown. Myogenesis process has been studied as a model of cell differentiation. Using this model, we found a novel lncRNA, Myoparr, expressed from the promoter region of myogenin gene, one of the regulators of myogenesis. We show that Myoparr regulates the expression of myogenin in vitro and in vivo. In addition, we identified Ddx17 and hnRNPK as Myoparr-binding-proteins. We compared the Transcriptome profiles of C2C12 cells (mouse myoblast cell line) with or without siRNAs against myogenin, Myoparr, Ddx17, and hnRNPK during myogenesis.
Publication Title
Data describing the effects of depletion of <i>M</i><i>yoparr</i>, <i>myogenin</i>, <i>Ddx17</i>, and <i>hnRNPK</i> in differentiating C2C12 cells.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Danio rerio
- 15 Downloadable Samples
- Affymetrix Zebrafish Genome Array (zebrafish)
Description
Investigating neuronal and photoreceptor regeneration in the retina of zebrafish has begun to yield insights into both the cellular and molecular means by which this lower vertebrate is able to repair its central nervous system. However, knowledge about the signaling molecules in the local microenvironment of a retinal injury and the transcriptional events they activate during neuronal death and regeneration is still lacking. To identify genes involved in photoreceptor regeneration, we combined light-induced photoreceptor lesions, laser-capture microdissection (LCM) of the outer nuclear layer (ONL) and analysis of gene expression to characterize transcriptional changes for cells in the ONL as photoreceptors die and are regenerated. Using this approach, we were able to characterize aspects of the molecular signature of injured and dying photoreceptors, cone photoreceptor progenitors and microglia within the ONL. We validated changes in gene expression and characterized the cellular expression for three novel, extracellular signaling molecules that we hypothesize are involved in regulating regenerative events in the retina.
Publication Title
Identification of the molecular signatures integral to regenerating photoreceptors in the retina of the zebra fish.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 2 Downloadable Samples
- Illumina HiSeq 1500
Description
A promoter associated lncRNA Myoparr is involved in the regulation of skeletal muscle atrophy caused by denervation. However, the molecular mechanism by which Myoparr regulates the expression of downstream genes in skeletal muscle tissue is largely unknown. Thus, we compared the Transcriptome profiles of denervated tibialis anterior muscles transfected with control or Myoparr shRNA.
Publication Title
Long Non-Coding RNA <i>Myoparr</i> Regulates GDF5 Expression in Denervated Mouse Skeletal Muscle.
Sample Metadata Fields
Sex, Specimen part, Cell line, Treatment
View Samples- Saccharomyces cerevisiae
- 12 Downloadable Samples
- Illumina HiSeq 2000, Illumina Genome Analyzer II
Description
During translation elongation, the ribosome ratchets along its mRNA template, incorporating each new amino acid and translocating from one codon to the next. The elongation cycle requires dramatic structural rearrangements of the ribosome. We show here that deep sequencing of ribosome-protected mRNA fragments reveals not only the position of each ribosome but also, unexpectedly, its particular stage of the elongation cycle. Sequencing reveals two distinct populations of ribosome footprints, 28-30 nucleotides and 20-22 nucleotides long, representing translating ribosomes in distinct states, differentially stabilized by specific elongation inhibitors. We find that the balance of small and large footprints varies by codon and is correlated with translation speed. The ability to visualize conformational changes in the ribosome during elongation, at single-codon resolution, provides a new way to study the detailed kinetics of translation and a new probe with which to identify the factors that affect each step in the elongation cycle. Overall design: Ribosome profiling, or sequencing of ribosome-protected mRNA fragments, in yeast. We assay ribosome footprint sizes and positions in three conditions: untreated yeast (3 replicates) and yeast treated with translation inhibitors cycloheximide (2 replicates) and anisomycin (2 biological replicates, one technical replicate). We also treat yeast with 3-aminotriazole to measure the effect of limited histidine tRNAs on ribosome footprint size and distribution (two treatment durations).
Publication Title
Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments.
Sample Metadata Fields
Cell line, Treatment, Subject
View Samples- Danio rerio
- 8 Downloadable Samples
- Affymetrix Zebrafish Genome Array (zebrafish)
Description
In the retina of adult teleosts, stem cells are sustained in two specialized niches: the ciliary marginal zone (CMZ) and the microenvironment surrounding adult Mller glia. Recently, Mller glia were identified as the regenerative stem cells in the teleost retina. Secreted signaling molecules that regulate neuronal regeneration in the retina are largely unknown. In a microarray screen to discover such factors, we identified midkine-b (mdkb). Midkine is a highly conserved heparin-binding growth factor with numerous biological functions. The zebrafish genome encodes two distinct midkine genes: mdka and mdkb. Here, we describe the cellular expression of mdka and mdkb during retinal development and the initial, proliferative phase of photoreceptor regeneration. The results show that in the embryonic and larval retina mdka and mdkb are expressed in stem cells, retinal progenitors and neurons in distinct patterns that suggest different functions for the two molecules. Following the selective death of photoreceptors in the adult, mdka and mdkb are co-expressed in horizontal cells and proliferating Mller glia and their neurogenic progeny. These data reveal that Mdka and Mdkb are signaling factors present in the retinal stem cell niches in both embryonic and mature retinas, and that their cellular expression is actively modulated during retinal development and regeneration.
Publication Title
Cellular expression of midkine-a and midkine-b during retinal development and photoreceptor regeneration in zebrafish.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
Transcriptomes of mouse embryonic autopods were generated detecting expression of approximately 26179 transcripts in the developing forelimb or hindlimb autopods, representing about 58 % of the probe sets on MOE-430 A/B GeneChip. Three biological replicate array experiments were finished for each condition and MAS5.0 signal were used to do data analysis. Forty-four transcripts with expression differences higher than 2-fold were detected(T test, P<0.05), including Tbx4, Tbx5, Hoxc10 and Pitx1 which were previously shown to be differentially expressed in developing forelimb and hindlimb bud by in situ hybridization and SAGE study (Margulies 2001). RTPCR and in situ experiments confirmed several top differentially expressed genes which were newly discovered by our experiments. Vast amount of transcripts and its family members such as Bmp, Fgf, Epha, Wnt, T-box and Hox families detected to be highly expressed or differentially expressed in developing autopods, suggesting that the complexity of transcriptomes of developing autopods and dynamic differential expression and differential combinations of gene expression signals in the developing limb tissue contributes to differences in forelimb versus hindlimb patterning. The differentially expressed genes are the essential factors for morphological diversification of developing limb structures.
Publication Title
Transcriptome analysis of the murine forelimb and hindlimb autopod.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
To explore gene expression profiles of cells sensitive to necrosis (such as L929 cells) and those sensitive to apoptosis (such as NIH3T3 cells), we conducted expression microarray analysis of L929 cells and NIH3T3 cells.
Publication Title
Identification of a molecular signaling network that regulates a cellular necrotic cell death pathway.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 26 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Chronic infection with the bacterial pathogen Helicobacter pylori is a risk factor for the development of gastric cancer, yet remains asymptomatic in a majority of individuals. We report here that the C57Bl6 mouse model of experimental infection with the closely related H. felis recapitulates this wide range in host susceptibility. A majority of infected mice develop premalignant lesions such as gastric atrophy, compensatory epithelial hyperplasia and intestinal metaplasia, whereas a minority is completely protected from preneoplasia. Protection is associated with the failure to mount an IFN-gamma response to the infection and an associated high Helicobacter burden. We demonstrate that IFN-gamma is essential for clearance of Helicobacter, but also mediates the formation of preneoplastic lesions. We further provide evidence that IFN-gamma triggers a specific transcriptional program in murine gastric epithelial cells in vitro and in vivo, and induces their preferential transformation to the hyperplastic phenotype. In summary, our data suggest a dual role for IFN-gamma in Helicobacter pathogenesis that could provide an explanation for the differential susceptibility to H. pylori-induced gastric pathology in the human population.
Publication Title
The CD4+ T cell-mediated IFN-gamma response to Helicobacter infection is essential for clearance and determines gastric cancer risk.
Sample Metadata Fields
Treatment
View Samples- Mus musculus
- 12 Downloadable Samples
Illumina mouseref-8_v2_0_r3 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
PDGF Engages an E2F-USP1 Signaling Pathway to Support ID2-Mediated Survival of Proneural Glioma Cells.
Sample Metadata Fields
Specimen part, Treatment
View Samples