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GSE6814
Macaca mulatta
11 Downloadable Samples
Affymetrix Human Genome U133A Array (hgu133a)
Description
The objective of this study was to elucidate age-related differences in gene expression profiles of rhesus monkey bone marrow-derived mesenchymal stem cells (rhMSC) obtained from fetal, infant, and adult donors relevant to their growth and other properties. Although a high degree of similarity was observed in the rhMSC gene expression profiles when comparing the three age groups, significant differences were found that strongly parallel gene expression profiles of human MSC. The potential functional relevance of differential gene expression was most apparent when comparing fetal and adult rhMSC transcript profiles. Overall, the observed gene expression profiles are consistent with a loss of rhMSC pluripotency and proliferative capacity with advancing donor age. In addition, these data highlight the importance of use of non-human primates as a model system for studying the properties of human stem cells.
Publication Title
Age-related gene expression profiles of rhesus monkey bone marrow-derived mesenchymal stem cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 14 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Interactions between the gene products encoded by the mitochondrial and nuclear genomes play critical roles in normal eukaryotic cellular function. Here, we characterized the metabolic and transcriptional properties of A549 lung cancer cells and their isogenic mitochondrial DNA (mtDNA)-depleted rho zero counterparts grown in cell culture and as tumor xenografts in immune-deficient mice. A manuscript summarizing our conclusions is under review.
Publication Title
mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens, Rattus norvegicus
- 15 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip, Illumina ratRef-12 v1.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Integrated transcriptomic and epigenomic analysis of primary human lung epithelial cell differentiation.
Sample Metadata Fields
Sex, Specimen part, Time
View Samples- Rattus norvegicus
- 15 Downloadable Samples
Illumina ratRef-12 v1.0 expression beadchip
Description
Analysis of gene expression during differentiation of alveolar epithelial type 2 (AT2) cells into AT1 cells. Timepoints taken at Day 0 (AT2 cell), Days 2, 4, and 6 in culture (differentiating) and Day 8 in culture (AT1-like cells).
Publication Title
Integrated transcriptomic and epigenomic analysis of primary human lung epithelial cell differentiation.
Sample Metadata Fields
Sex, Specimen part, Time
View Samples- Homo sapiens
- 22 Downloadable Samples
- Illumina HumanWG-6 v3.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression.
Sample Metadata Fields
Sex, Age, Specimen part, Race, Subject
View Samples- Homo sapiens
- 22 Downloadable Samples
- Illumina HumanWG-6 v3.0 expression beadchip
Description
Gene expression profiling of 60 lung adenocarcinoma tumors and their matched histologically normal adjacent lung tissue samples were analyzed using Illumina HumanWG-6 v3.0 expression beadchip. We integrated these data with DNA methylation profiles of the same samples to identify potential DNA methylation regulated genes.
Publication Title
Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression.
Sample Metadata Fields
Sex, Age, Specimen part, Race, Subject
View Samples- Homo sapiens
- 4 Downloadable Samples
Illumina HiSeq 2000
Description
Diseases involving the distal lung alveolar epithelium include chronic obstructive pulmonary disease (COPD), idiopathic pulmonary fibrosis (IPF) and lung adenocarcinoma. Accurate labeling of specific cell types is critical for determining the contribution of each to pathogenesis of these diseases. The distal lung alveolar epithelium is comprised of two cell types, alveolar epithelial type 1 (AT1) and type 2 (AT2) cells. While cell type-specific markers, most prominently surfactant protein C (SFTPC), have allowed detailed studies of AT2 cell differentiation and their roles in disease, studies of AT1 cells have been hampered by lack of genes with expression unique to AT1 cells. To address this, we performed genome-wide expression profiling of multiple rat organs alongside purified rat AT2, AT1 and in vitro differentiated AT1-like cells, resulting in identification of 54 candidate AT1 cell markers. Cross-referencing with genes upregulated in human in vitro differentiated AT1-like cells narrowed the potential list to 18 candidate genes. Testing the top four candidate genes at RNA and protein levels revealed GRAM domain 2 (GRAMD2), a protein of unknown function, as unique to AT1 cells, while SCNN1G within lung is restricted to AT1 cells. RNAseq confirmed that GRAMD2 is transcriptionally silent in human AT2 cells. Immunofluorescence of mouse alveoli verified that GRAMD2 expression is restricted to the plasma membrane of AT1 cells. These new AT1 cell-specific genes, with GRAMD2 as a leading candidate, will enhance AT1 cell isolation, investigation of alveolar epithelial cell differentiation potential, and contribution of AT1 cells to distal lung diseases. Overall design: RNAseq of purified primary human alveolar epithelial type 2 (AT2) and in vitro differentiated type 1 (AT1-like) cells.
Publication Title
Cross-Species Transcriptome Profiling Identifies New Alveolar Epithelial Type I Cell-Specific Genes.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
We report the gene expression profiles of germinal center B cells obtained by FACS analyses of normal human lymph nodes.
Publication Title
Identification and functional relevance of de novo DNA methylation in cancerous B-cell populations.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
We performed microarray analysis in order to evaluate the combination effect of the mitochondrial matrix chaperone inhibitor gamitrinib-triphenylphosphonium (G-TPP) and Liver X receptor agonist LXR623 on gene expression in stem cell like glioma cells (NCH644).
Publication Title
Activation of LXR Receptors and Inhibition of TRAP1 Causes Synthetic Lethality in Solid Tumors.
Sample Metadata Fields
Specimen part, Cell line, Treatment
View Samples- Mus musculus
- 26 Downloadable Samples
- Illumina HiSeq 2500
Description
Transcriptional profiling shows that Peyer´s patch CD4+ T cells from mice kept on dietary antigens are skewed towards a Tfh cell programme. Continous recognition of dietary antigens does not lead to classical signature of exhaustion. Overall design: Examination of conventional and elemental diet on gene expression of PP T cells
Publication Title
Intestinal development and homeostasis require activation and apoptosis of diet-reactive T cells.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples