Filters
Organism
Technology
Platform
Arabidopsis thaliana
9 Downloadable Samples
Arabidopsis Gene 1.0 ST Array (aragene10st)
Description
For establishing the photosynthetic apparatus plant cells must orchestrate the expression of genes encoded in both nucleus and chloroplast. Therefore a crosstalk between the two compartments is necessary.
Publication Title
No associated publication
Alternate Accession IDs
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Mus musculus
- 48 Downloadable Samples
- Affymetrix Mouse Gene 2.1 ST Array (mogene21st)
Description
Our mouse model of BE in which overexpression of IL-1b in the squamous esophagus induces chronic inflammation leads to metaplasia and dysplasia at the squamo-columnar junction (SCJ) in the mouse gastro-esophageal junction resembles the human disease. Adult L2-IL1b mice were employed to investigate changes to the transcriptional landscape at the SCJ during disease progression from BE to EAC following pharmaceutical or genetic perturbations of interest to BE biology.
Publication Title
Notch Signaling Mediates Differentiation in Barrett's Esophagus and Promotes Progression to Adenocarcinoma.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Hordeum vulgare
- 36 Downloadable Samples
- Affymetrix Barley Genome Array (barley1)
Description
Colonization of barley roots with the basidiomycete fungus Piriformospora indica enhances resistance against the leaf pathogen Blumeria graminis f.sp. hordei (Bgh). To identify genes involved in this mycorrhiza-induced systemic resistance, we used the Affymetrix Barley1 22K gene chip for leaf transcriptome analysis of P. indica-colonized and non-colonized barley plants 12, 24 and 96 hours post inoculation (hpi) with a compatible Bgh strain.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Age, Specimen part, Disease, Disease stage
View Samples- Mus musculus
- 60 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Background: Information on the carcinogenic potential of chemicals is only availably for High Production Volume products. There is however, a pressing need for alternative methods allowing for the chronic toxicity of substances, including carcinogenicity, to be detected earlier and more reliably. Here we applied advanced genomics to a cellular transformation assay to identify gene signatures useful for the prediction of risk for carcinogenicity. Methods: Genome wide gene expression analysis and qRT-PCR were applied to untransformed and transformed Balb/c 3T3 cells that exposed to 2, 4-diaminotoluene (DAT), benzo(a)pyrene (BaP), 2-Acetylaminoflourene (AAF) and 3-methycholanthrene (MCA) for 24h and 120h, at different concentrations, respectively. Furthermore, various bioinformatics tools were used to identify gene signatures predicting for the carcinogenic risk. Results: Bioinformatics analysis revealed distinct datasets for the individual chemicals tested while the number of significantly regulated genes increased with ascending treatment concentration of the cell cultures. Filtering of the data revealed a common gene signature that comprised of 13 genes whose regulation in cancer tissue has already been established. Strikingly, this gene signature was already identified prior to cell transformation therefore confirming the predictive power of this gene signature in identifying carcinogenic risks of chemicals. Comparison of fold changes determined by microarray analysis and qRT-PCR were in good agreement. Conclusion: Our data describes selective and commonly regulated carcinogenic pathways observed in an easy to use in vitro carcinogenicity assay. Here we defined a set of genes which can serve as a simply assay to predict the risk for carcinogenicity by use of an alternative in vitro testing strategy.
Publication Title
Toxicogenomics applied to in vitro carcinogenicity testing with Balb/c 3T3 cells revealed a gene signature predictive of chemical carcinogens.
Alternate Accession IDs
Sample Metadata Fields
Cell line, Treatment, Time
View Samples- Homo sapiens
- 57 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Background
Publication Title
Adapted Boolean network models for extracellular matrix formation.
Alternate Accession IDs
Sample Metadata Fields
Sex, Age
View Samples- Homo sapiens
- 57 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Background: We got interested whether genes of airway basal cells are enriched in COPD.
Publication Title
BAL Cell Gene Expression Is Indicative of Outcome and Airway Basal Cell Involvement in Idiopathic Pulmonary Fibrosis.
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Disease
View Samples- Homo sapiens
- 57 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Background. Rheumatoid arthritis (RA) is a chronic inflammatory and destructive joint disease, characterized by overexpression of pro-inflammatory/-destructive genes and other activating genes (e.g., proto-oncogenes) in the synovial membrane (SM). The gene expression in disease is often characterized by significant inter-individual variances via specific synchronization/ desynchronization of gene expression. To elucidate the contribution of the variance to the pathogenesis of disease, expression variances were tested in SM samples of RA patients, osteoarthritis (OA) patients, and normal controls (NC).
Publication Title
Identification of intra-group, inter-individual, and gene-specific variances in mRNA expression profiles in the rheumatoid arthritis synovial membrane.
Alternate Accession IDs
Sample Metadata Fields
Sex, Age, Disease
View Samples- Homo sapiens
- 46 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Background: We got interested whether genes of airway basal cells are enriched in sarcoidosis.
Publication Title
BAL Cell Gene Expression Is Indicative of Outcome and Airway Basal Cell Involvement in Idiopathic Pulmonary Fibrosis.
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Disease
View Samples
GSE13637- Homo sapiens
- 29 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
To delineate specific patterns of signaling networks activated by H5N1 we used a comparative systems biology approach analyzing gene expression in endothelial cells infected with three different human and avian influenza strains of high and low pathogenicity.
Publication Title
Essential impact of NF-kappaB signaling on the H5N1 influenza A virus-induced transcriptome.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 24 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
We recently reported isolation of various cancer progenitor cells of transgenic c-Myc and c-Raf mouse lung tumors [Reamon-Buettner SM and Borlak J, 2008]. As lung tumors can arise following dysregulation of signalling pathways normally activated during lung development we were particularly interested in investigating the genetic heterogeneity of these cancer cell lines. By whole genome expression analysis we identified two cell lines (A2C12, cRAF_cMYC) to be very different from the remaining tumor cells. Specifically the A2C12 and cRAF_cMYC cell lines expressed various stem cell markers, most notably CD34, CD44, Pdpn and Dlg7. Likewise, the A2C12 and cRAF_cMYC expressed the ATP-binding cassette (ABC) transporters Abcc1 and Abcg2 at different level when compared to other established cell lines. Furthermore, a genome wide expression profiling displayed differential gene expression pattern between and within progenitor cell lines. That provided important clues on heterogeneity in the signalling pathways amongst the cancer cell lines. We also knock down CD44 using a retroviral delivery system and observed an increased G1 peak and apoptosis as determined by flow cytometry. Finally, we analyzed promoters of regulated genes and identified overrepresented 18 transcription factor binding sites (TFBS) in common regulated genes, 10 unique TFBS in A2C12 and 9 unique TFBS in cRaf_cMyc. These data indicates that our tumor cell lines are suitable models to study the biology of lung cancer progenitor cell. Most importantly, we show that our tumor cell lines do not represent a homogeneous population of tumor-initiating cells. Understanding heterogeneity in tumors will lead to new diagnostic and therapeutic approaches.
Publication Title
No associated publication
Alternate Accession IDs
Sample Metadata Fields
Disease, Disease stage, Cell line
View Samples