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GSE79308
Homo sapiens
6 Downloadable Samples
Illumina HumanHT-12 V4.0 expression beadchip
Description
Expression profile of parental wild type non-small cell lung cancer, NCI-H460, and cancer stem cell-rich (CSC-rich) populations treated with PNAs-A15 for 6 h. Results provide the information that PNAs-A15, a peptide nucleic acid of A-repeats length 15 bp, suppressed up-regulated A-repeats containing genes in both parental wild type and CSC-rich cells.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Mononucleotide A and T repeats are abundant in human genome. Many of A repeats are bound by Argonaute proteins (AGOs). To evaluate the role of AGOs and A repeats in gene regulation, HEK293 cells were treated with 8-amino-3,6-dioxaoctanoic acid added peptide nucleic acid (PNA) AAAAAAAAAAAAAAA oligo (OO-A(15)).
Publication Title
Upstream mononucleotide A-repeats play a cis-regulatory role in mammals through the DICER1 and Ago proteins.
Sample Metadata Fields
Cell line, Treatment
View Samples- Saccharomyces cerevisiae
- 4 Downloadable Samples
Illumina HiSeq 1000
Description
Transcriptome sequencing of wild-type and Rad30 knockout strains under normal conditions and 2 mM H2O2 conditions to study physiological mechanisms of the gene Rad30 response to oxidative stress
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Disease, Cell line
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- Saccharomyces cerevisiae
- 24 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Yeast cells were grown up in SD media containing all required amino acids. Each strain set was performed in triplicate. One set had no changes, the second set had 1mM methionine supplenting the media for the duration of growth and the third set was exposed to 0.5mM hydrogen peroxide for 15 minutes prior to harvesting
Publication Title
Gcn4 is required for the response to peroxide stress in the yeast Saccharomyces cerevisiae.
Sample Metadata Fields
Compound
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