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GSE34002
Mus musculus
9 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Tumor formation constitutes a major obstacle to the clinical application of embryonic stem cells (ESCs). As P-RPCs could successfully integrate into host eyes without development of teratomas or NOG, we sought to identify differentially expressed genes between P-RPCs and ESC-RPCs through genome-wide transcript profiling. Inhibition of Wnt signaling by DKK1 promotes the commitment of ESC-RPCs to more mature retinal cells and reduces the occurrence of NOG to 3%. DKK1-treated ESC-RPCs efficiently integrate to the host retina, form synaptic connections and restore visual function.
Publication Title
WNT signaling determines tumorigenicity and function of ESC-derived retinal progenitors.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 134 Downloadable Samples
Illumina HiSeq 2000
Description
NA
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Cell line
View Samples- Homo sapiens
- 96 Downloadable Samples
- Illumina HiSeq 2000
Description
Single-cell RNA-seq reveals dynamic estrogen-stimulated metabolic reprogramming in breast cancer cell lines
Publication Title
No associated publication
Sample Metadata Fields
Sex, Specimen part, Cell line
View Samples- Homo sapiens
- 93 Downloadable Samples
- Illumina HiSeq 2000
Description
Single-cell RNA-seq reveals dynamic estrogen-stimulated metabolic reprogramming in breast cancer cell lines
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Cell line
View Samples- Homo sapiens
- 50 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Background & Aims: Genome-wide gene expression (GWGE) profiles of mucosal colonic biopsies have suggested the existence of a continuous inflammatory state in quiescent ulcerative colitis (UC). The aim of this study was to use DNA microarray-based GWGE profiling of mucosal colonic biopsies and isolated colonocytes from UC patients and controls in order to identify the cell types responsible for the continuous inflammatory state. Methods: Adjacent mucosal colonic biopsies were obtained endoscopically from the descending colon in patients with active UC (n=8), quiescent UC (n=9), and with irritable bowel syndrome (controls, n=10). After isolation of colonocytes and subsequent extraction of total RNA, GWGE data were acquired using Human Genome U133 Plus 2.0 GeneChip Array (Affymetrix, Santa Clara, CA). Data analysis was carried out by principal component analysis and projection to latent structure-discriminant analysis using the SIMCA-P11 software (Umetrics, Ume, Sweden). Results: A clear separation between active UC, quiescent UC and control biopsies were found, whereas the model for the colonocytes was unable to distinguish between quiescent UC and controls. The differentiation between quiescent UC and control biopsies was governed by unique profiles containing gene expressions with significant fold changes. These primarily belonged to the family of homeostatic chemokines revealing a plausible explanation to the abnormal regulated innate immune response seen in patients with UC. Conclusion: This study has demonstrated the presence of a continuous inflammatory state in quiescent UC, which seems to reflect an altered gene expression profile of lamina propria cells.
Publication Title
Genome-wide gene expression analysis of mucosal colonic biopsies and isolated colonocytes suggests a continuous inflammatory state in the lamina propria of patients with quiescent ulcerative colitis.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 30 Downloadable Samples
- Illumina HiSeq 2000
Description
NA
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Cell line
View Samples- Homo sapiens
- 18 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Klinefelters Syndrome (KS) is one of the common chromosome aneuploidy diseases in males with unexplained physiological mechanism. iPSCs, are similar to ESCs in terms of indefinitive self-renewal and pluripotency, provided an alternative choice for modeling disease to facilitate the disease research in vitro.
Publication Title
Aberrant gene expression profiles in pluripotent stem cells induced from fibroblasts of a Klinefelter syndrome patient.
Sample Metadata Fields
Specimen part, Disease, Disease stage
View Samples- Homo sapiens
- 13 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Background and aim: Analysis of data obtained from genome wide gene expression experiments is challenging, due to the huge amount of variables, management of the data and the need for multivariate analysis. We here present the R package: pcaGoPromoter that facilitates the interpretation of genome wide expression data to overcome these problems. In a first step principal component analysis is applied to overview any differences between the observations and possible groupings. The next step is interpretation of the principal components with respect to both biological function and involvement of predicted transcription factor binding sites. The robustness of the results is evaluated using cross validation. Illustrative plots of PCA score plots and Gene Ontology terms are available. To illustrate the functionality of the R package, we designed a serum stimulation experiment, where the main biological outcome is well documented. Results: Samples from the serum stimulation experiment were analyzed using the Affymetrix Human Genome U133 Plus 2.0 chip. The array data were analyzed by the tools of the pcaGoPromoter package, which resulted in a clear separation of the observations into the three experimental groups - controls, serum only and serum with inhibitor. The functional annotation of the axes in the PCA score plot showed the expected serum promoted biological processes such as cell cycle progression and the predicted involvement of the expected transcription factors including E2F. In addition unexpected results, e.g. the cholesterol synthesis in serum depleted cells and NF-B activation in inhibitor treated cells were uncovered. Conclusion: The pcaGoPromoter R package provides a collection of tools for analyzing gene expression data. It works with any platform using gene symbols or Entrez Ids as probe identifiers. In addition support for several popular Affymetrix GeneChip platforms is provided. The tools give an overview of the data via principal component analysis, functional interpretation by Gene Ontology terms (biological processes), and indication of involvement of possible transcription factors. Thus, pcaGoPromoter structures the high-dimensional data of gene expression experiments and can be applied to generate hypotheses for further exploration.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Cell line
View Samples- Danio rerio
- 12 Downloadable Samples
- Illumina HiSeq 4000
Description
Explore the function of figla gene in zebrafish gonadal development
Publication Title
No associated publication
Sample Metadata Fields
Sex, Age, Specimen part, Cell line
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The identification and characterization of subpopulations of cancer stem cells (CSCs) provide new understandings and possible therapeutic implications in cancer biology. We found the ovarian cancer sphere cells possessed CSCs properties maintained self renewal, drug resistance, and tumorigenesis. Using high-throughput microarray system, we identified common GO terms and pathway signatures significantly enriched in ovarian and breast cancer stem cells.
Publication Title
Ovarian and breast cancer spheres are similar in transcriptomic features and sensitive to fenretinide.
Sample Metadata Fields
Specimen part
View Samples