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GSE64086
Homo sapiens
11 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Post-transplant molecularly defined Burkitt lymphomas are frequently MYC-negative and characterized by the 11q-gain/loss pattern.
Sample Metadata Fields
Sex, Age, Treatment
View Samples- Homo sapiens
- 11 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We performed genomic and transcriptomic analysis of seven cases of molecular Burkitt lymphoma (mBL) developed in immunosuppressed patients who underwent solid organ transplantation. Interestingly, three cases (43%) were MYC-translocation-negative and revealed the 11q-gain/loss aberration recently identified in 3% of mBL developed in immunocompetent hosts.1 Based on array CGH data, minimal gain and loss regions of 11q (MGR/~4Mb and MLR/~13.5Mb, respectively) were defined and integrative genomic and transcriptomic analysis identified 35 differentially expressed genes, when compared with classic BL. All 16 MGR-dysregulated genes were upregulated, including cancer related USP2, CBL and PAFAH1B2. As expected, all 19 MGL-dysregulated genes were downregulated and two of them, TBRG1 and EI24, are potential tumor suppressor genes. Interestingly, the vast majority of dysregulated 11q23-q25 genes are involved in the MYC and TP53 networks. We hypothesize that the 11q-gain/loss aberration represents a molecular variant of t(8q24/MYC) and affects the same pathological pathways as the MYC oncogene.
Publication Title
Post-transplant molecularly defined Burkitt lymphomas are frequently MYC-negative and characterized by the 11q-gain/loss pattern.
Sample Metadata Fields
Sex, Age, Treatment
View Samples- Homo sapiens
- 15 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Transient expression of two factors, or from Oct4 alone, resulted in efficient generation of human iPSCs. The reprogramming strategy described revealed a potential transcriptional signature for human iPSCs yet retaining the gene expression of donor cells in human reprogrammed cells free of viral and transgene interference.
Publication Title
Transcriptional signature and memory retention of human-induced pluripotent stem cells.
Sample Metadata Fields
Sex, Specimen part
View Samples- Saccharomyces cerevisiae
- 80 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Dynamics of oscillatory phenotypes in Saccharomyces cerevisiae reveal a network of genome-wide transcriptional oscillators.
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 49 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Genetic and environmental factors influence the phenotype of an organism. Time is rarely considered when studying changes in cellular phenotype. Time-resolved microarray data revealed genome-wide transcriptional changes in cells oscillating with ~2 and ~4 h periods. We mapped the global patterns of transcriptional oscillations into a 3-dimensional map to represent different cellular phenotypes of oscillation period. This map shows the dynamic nature of transcripts through time and concentration space, and that they are ordered and coupled to each other. Although cells differed in oscillation periods, transcripts involved in certain processes were conserved in a deterministic way. This ordered timing of biological process may allow cells to grow energetically efficient. Decreased glucose levels in the media were found to increase the redox cycles of yeast strain CEN.PK113-7D. Glucose may have acted as signaling molecules for timing longer catabolic processes in the cell population. As oscillation period lengthened, the peak to trough ratio of transcripts increased and the percent of cells in the unbudded (G0/G1) phase of the cell cycle increased. Gene transcripts appear to be coordinated with metabolic functions and the cell cycle.
Publication Title
Dynamics of oscillatory phenotypes in Saccharomyces cerevisiae reveal a network of genome-wide transcriptional oscillators.
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 31 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Genetic and environmental factors influence the phenotype of an organism. Time is rarely considered when studying changes in cellular phenotype. Time-resolved microarray data revealed genome-wide transcriptional changes in cells oscillating with ~2 and ~4 h periods. We mapped the global patterns of transcriptional oscillations into a 3-dimensional map to represent different cellular phenotypes of oscillation period. This map shows the dynamic nature of transcripts through time and concentration space, and that they are ordered and coupled to each other. Although cells differed in oscillation periods, transcripts involved in certain processes were conserved in a deterministic way. This ordered timing of biological process may allow cells to grow energetically efficient. Decreased glucose levels in the media were found to increase the redox cycles of yeast strain CEN.PK113-7D. Glucose may have acted as signaling molecules for timing longer catabolic processes in the cell population. As oscillation period lengthened, the peak to trough ratio of transcripts increased and the percent of cells in the unbudded (G0/G1) phase of the cell cycle increased. Gene transcripts appear to be coordinated with metabolic functions and the cell cycle.
Publication Title
Dynamics of oscillatory phenotypes in Saccharomyces cerevisiae reveal a network of genome-wide transcriptional oscillators.
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 8 Downloadable Samples
- Affymetrix Rat Expression 230A Array (rae230a)
Description
The goal was to screen for the expressed genes in Semi-Circular Canal Duct (SCCD) that are related to ion transport and its regulation. The objectives was to discover which genes changed expression levels in response to glucocorticoids.
Publication Title
Ion transport regulation by P2Y receptors, protein kinase C and phosphatidylinositol 3-kinase within the semicircular canal duct epithelium.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Gene 1.1 ST Array (hugene11st)
Description
The biological effects of TTR proteins in the vasculature remain unknown.
Publication Title
Transthyretin proteins regulate angiogenesis by conferring different molecular identities to endothelial cells.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 9 Downloadable Samples
Illumina HiSeq 2500
Description
Using a CML mouse model, we identified differences in gene expression between leukemic compared with non-leukemic LTHSC, including increased expression of the thrombopoietin (THPO) receptor MPL. LTHSC expressing high levels of MPL showed enhanced JAK/STAT signaling and proliferation in response to THPO in vitro, and increased leukemogenic capacity in vivo compared to LTHSC with low MPL expression. Although both G0 and S-phase subpopulations were increased in MPL expressing LTHSC, LSC capacity was restricted to quiescent cells. Inhibition of MPL expression in CML LTHSC resulted in reduced THPO-induced JAK/STAT signaling and leukemogenic potential. Similar observations were made with LTHSC from CML patients. MPL expressing LTHSC demonstrated reduced sensitivity to BCR-ABL TKI treatment but demonstrated increased sensitivity to JAK inhibitors. Our studies identify MPL expression levels as a key determinant of heterogeneous leukemia-initiating capacity and drug sensitivity of CML LTHSC, and suggest that MPL-expressing CML stem cells are critical targets for therapy. Overall design: To evaluate heterogeneity in LSC potential, donor LTHSC from SCL-tTA/BCR-ABL mice (200 cells/mouse) were transplanted into a cohort of congenic FVBN mice. Recipient mice were followed for engraftment of donor CML cells and development of CML. LTHSCs were isolated from leukemic and non-leukemic recipient mice and global gene expression was analyzed using RNA-Seq.
Publication Title
Heterogeneity of leukemia-initiating capacity of chronic myelogenous leukemia stem cells.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
Individuals expressing alpha-1-antitrypsin mutant Z protein accumulate misfolded, mutant protein in the liver and are at risk for liver diseases including cirrhosis and hepatocellular carcinoma. Transgenic PiZ mice, a model for this liver disease, display similar pathologies to humans, including inflammation, increases in proliferation, autophagy and apoptosis, accumulation of globules and develop fibrosis and hepatocellular carcinoma with age. Microarrays were used to compare the gene expressions of PiZ mice to wild-type mice in order to identify the pathways that are altered in this disorder.
Publication Title
Oxidative stress contributes to liver damage in a murine model of alpha-1-antitrypsin deficiency.
Sample Metadata Fields
Sex, Specimen part
View Samples