Filters
Technology
Platform
GSE54660
Homo sapiens
6 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
It is becoming better understood that radiation resistance in glioblastomas (GBMs) may be secondary to a self-renewing subpopulation of cells in the bulk tumor that form neurospheres in culture. This population has been referred to as Glioma stem cells (GSCs). One of the limitations regarding the use of GSCs is that these studies require fresh tumor biopsy samples obtained from patients, and can be extremely difficult to culture, propagate, and perform treatment-response assays. This report describes the generation of a self-renewing population of GSCs derived from commercially available U87 cells using NOD-SCID mice as carrier. The tumors were dissociated to obtain GSCs that demonstrate stem-like properties and high degree of chemo and radiation resistance. Pathological analysis of tumors obtained using GSCs exhibit all the histological hallmarks of human GBMs which is quite uncommon in GBM rodent models and hence could serve as a better model for pre-clinical study. We have shown that MGH87GSCs have an enhanced tumorogenicity than parental U87 and about 500 cells are sufficient to form tumors. To understand the transcriptome and accompanied proteome better, we explored the gene expression profiles of MGH87GSC and U87. We have shown that these GSCs are plastic like stem cells and can be directed towards a particular progeny within neural lineage by providing suitable growth factor. Our objective was to understand the genetic and biochemical mechanisms that control the self-renewal phenotype, asymmetric subdivision, chemo and radiation resistance and the role of the GSC niche in regulating the biological properties of GSC. Through this model we anticipate to devise therapeutic strategies to target this sub population of GSCs within GBMs to eradicate treatment resistance and tumor recurrence.
Publication Title
Cells isolated from residual intracranial tumors after treatment express iPSC genes and possess neural lineage differentiation plasticity.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Mus musculus
- 15 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
These experiments aim determine the effects of Smo and Ets-2 signaling on fibroblast gene expression.
Publication Title
Genetic ablation of Smoothened in pancreatic fibroblasts increases acinar-ductal metaplasia.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 41 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Effects of Electronic Cigarette Constituents on the Human Lung: A Pilot Clinical Trial.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 112 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
Despite known age-related DNA methylation (aDNAm) changes in breast tumors, little is known about aDNAm in normal breast tissues. Breast tissues from a cross-sectional study of 121 cancer-free women, were assayed for genome-wide DNA methylation. mRNA expression was assayed by microarray technology. Analysis of covariance was used to identify aDNAms. Altered methylation was correlated with expression of the corresponding gene and with DNA methyltransferase protein DNMT3A, assayed by immunohistochemistry. Publically-available TCGA data were used for replication. 1,214 aDNAms were identified; 97% with increased methylation, and all on autosomes. Sites with increased methylation were predominantly in CpG lslands and non-enhancers. aDNAms with decreased methylation were generally located in intergenic regions, non-CpG Islands, and enhancers. Of the aDNAms identified, 650 are known to be involved in cancer, including ESR1 and beta-estradiol responsive genes. Expression of DNMT3A was positively associated with age. Two aDNAms showed significant associations with DNMT3A expression; KRR1 (OR 6.57, 95% CI: 2.51-17.23) and DHRS12 (OR 6.08, 95% CI: 2.33-15.86). A subset of aDNAms co-localized within vulnerable regions for somatic mutations in breast cancer. Expression of C19orf48 was inversely and significantly correlated with its methylation level. In the TCGA dataset, 84% and 64% of the previously identified aDNAms were correlated with age in both normal-adjacent and tumor breast tissues, with differential associations by histological subtype. Given the similarity of findings in the breast tissues of healthy women and breast tumors, and the effects on gene expression, aDNAms may be one pathway for increased breast cancer risk with age.
Publication Title
Landscape of genome-wide age-related DNA methylation in breast tissue.
Sample Metadata Fields
Age, Race
View Samples- Mus musculus
- 101 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Canonical and atypical E2Fs regulate the mammalian endocycle.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
BRD4 Profiling Identifies Critical Chronic Lymphocytic Leukemia Oncogenic Circuits and Reveals Sensitivity to PLX51107, a Novel Structurally Distinct BET Inhibitor.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 41 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
E-cig use is continuing to increase, particularly among youth never-smokers, and is used by some smokers to quit. The acute and chronic toxicity of e-cig use is unclear generally in the context of increasing reports of inflammatory-type pneumonia in some e-cig users. To assess lung effects of e-cigs without nicotine or flavors, we conducted a pilot study with serial bronchoscopies over 4 weeks in 30 never-smokers, randomized either to a four-week intervention with the use of e-cigs containing only 50% propylene glycol (PG) and 50% vegetable glycerine (VG) or to a no-use control group. Compliance to the e-cig intervention was assessed by participants sending daily puff counts and by urinary propylene glycol (PG). Inflammatory cell counts and cytokines were determined in bronchoalveolar lavage (BAL) fluids. Genome-wide expression, microRNA, and mRNA were determined from bronchial epithelial cells. There were no significant differences in changes of BAL inflammatory cell counts or cytokines between baseline and follow-up, comparing the control and e-cig groups. However, in the intervention but not the control group, change in urinary PG as a marker of e-cig use and inhalation, was significantly correlated with change in cell counts (cell concentrations, macrophages, and lymphocytes) and cytokines (IL-8, IL-13, and TNF-α), although the absolute magnitude of changes was small. There were no significant changes in mRNA or microRNA gene expression. Although limited by study size and duration, this is the first experimental demonstration of an impact of e-cig use on inflammation in the human lung among never-smokers.
Publication Title
Effects of Electronic Cigarette Constituents on the Human Lung: A Pilot Clinical Trial.
Sample Metadata Fields
Age, Specimen part
View Samples- Mus musculus
- 48 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Redeployment of Myc and E2f1-3 drives Rb-deficient cell cycles.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 52 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
To understand the underlying cause and mechanisms of embryonic lethality observed in combined loss of E2f7 and E2f8, we compared global gene expression profiles of wild type, germline deleted and sox2-Cre/Cyp19-Cre deleted embryos and placentas.
Publication Title
Atypical E2F repressors and activators coordinate placental development.
Sample Metadata Fields
Specimen part
View Samples- Saccharomyces cerevisiae
- 36 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
tRNAs are transcribed and partially processed in the nucleus before they are exported to the cytoplasm where they have an essential role in protein synthesis. Surprisingly, mature cytoplasmic tRNAs shuttle between nucleus and cytoplasm and its distribution is nutrient-dependent. At least three members of -importin family, Los1, Mtr10, and Msn5, function in tRNA nuclear-cytoplasmic intracellular movement. To test the hypothesis that the tRNA retrograde pathway regulates translation of particular transcripts
Publication Title
Genome-wide investigation of the role of the tRNA nuclear-cytoplasmic trafficking pathway in regulation of the yeast Saccharomyces cerevisiae transcriptome and proteome.
Sample Metadata Fields
Treatment
View Samples