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Platform
E-MEXP-750
Homo sapiens
42 Downloadable Samples
Affymetrix Human Genome U133B Array (hgu133b), Affymetrix Human Genome U133A Array (hgu133a)
Description
Comparatative gene expression analysis for CD4 T cell subsets isolated from peripheral blood and palatine tonsils
Publication Title
A methodology for global validation of microarray experiments.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 30 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
DNA microarrays are popular tools for measuring gene expression of biological samples. This ever increasing popularity is ensuring that a large number of microarray studies are conducted, many of which with data publicly available for mining by other investigators. Under most circumstances, validation of differential expression of genes is performed on a gene to gene basis. Thus, it is not possible to generalize validation results to the remaining majority of non-validated genes or to evaluate the overall quality of these studies. <br></br> We have devised an approach for the global validation of DNA microarray experiments that will allow researchers to evaluate the general quality of their experiment and to extrapolate validation results of a subset of genes to the remaining non-validated genes. We applied this method to a microarray experiment validated with quantitative real time polymerase chain reaction. The experiment consists of three biological replicate treatments of mouse 3T3-L1 preadipocytes with the steroid hormone dexamethasone for 3 hours. Total RNA was extracted from each of our three treatment and three control samples, and we labeled and hybridized five aliquots of each sample to Affymetrix MGU74Av2 microarrays, for a total of 30 microarrays.<br></br> We illustrate why the popular strategy of selecting only the most differentially expressed genes for validation generally fails as a global validation strategy and propose random-stratified sampling as a better gene selection method. We also illustrate shortcomings of often-used validation indices such as overlap of significant effects and the correlation coefficient and recommend the concordance correlation coefficient (CCC) as an alternative.
Publication Title
A methodology for global validation of microarray experiments.
Sample Metadata Fields
Cell line, Subject, Compound
View Samples- Homo sapiens
- 61 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
FITFATTWIN study identified from the FinnTwin16 Cohort, which is a population based, longitudinal study of Finnish twins born between October 1974 and December 1979. The participants had no chronic disease affecting the ability to exercise, no acute disease, and no drug or alcohol abuse.
Publication Title
iGEMS: an integrated model for identification of alternative exon usage events.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 39 Downloadable Samples
Illumina HiSeq 2000
Description
Whole blood RNA-Seq was applied to investigate gene expression kinetics in Tanzanian males who underwent controlled malaria infection by intradermal injection with aseptic, purified, cryopreserved Plasmodium falciparum sporozoites. Overall design: 10 volunteers injected intradermally with a total of 25'000 infectious Plasmodium falciparum sporozoites (PfSPZ).
Publication Title
Whole blood transcriptome changes following controlled human malaria infection in malaria pre-exposed volunteers correlate with parasite prepatent period.
Sample Metadata Fields
Subject
View Samples- Homo sapiens
- 3 Downloadable Samples
- NextSeq 500
Description
Acute myeloid leukemia (AML) is a complex, heterogeneous disease with variable outcomes following curative intent chemotherapy. AML with inv(3) is a genetic subgroup characterized by low response rate to induction type chemotherapy and hence is among the worst long term survivorship of the AMLs. Here, we present RNA-Seq transcriptome data from OCI-AML-20, a new AML cell line with inv(3) and deletion of chromosome 7. Overall design: RNA-Seq transcriptome analysis of OCI-AML-20 cell line with three biological replicates.
Publication Title
Characterization of inv(3) cell line OCI-AML-20 with stroma-dependent CD34 expression.
Sample Metadata Fields
Disease, Cell line, Subject
View Samples- Homo sapiens
- 10 Downloadable Samples
- IlluminaHiSeq2000
Description
We report that knockdown of EJC core proteins, eIF4A3, Y14, Magoh, causes a transcript-wide changes in alternative splicing, as well as some transcriptional changes. These changes are specific to EJC core proteins, and KD of UPF1 protein caused different sets of alterantive splicing changes. These changes are linked to the rate of transcription. Overall design: Examination of 4 different knockdown, as well as GFP knockdown in HeLa cells, 2 replicates each condition.
Publication Title
Transcriptome-wide modulation of splicing by the exon junction complex.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 64 Downloadable Samples
- Illumina HiSeq 2000
Description
Chronic obstructive pulmonary disease (COPD) is an independent risk factor for lung cancer, but the underlying molecular mechanisms are unknown. We hypothesized that lung stromal cells activate pathological gene expression programs supporting oncogenesis. To identify molecular mechanisms operating in the lung stroma that support development of lung cancer. Study subjects included patients with- or without- lung cancer across a spectrum of lung function. We conducted multi-omics analysis of non-malignant lung tissue to quantify the transcriptome, translatome and proteome. Cancer-associated gene expression changes predominantly manifested as alterations in the efficiency of mRNA translation modulating protein levels in the absence of corresponding changes in mRNA levels. The molecular mechanisms driving these cancer-associated translation programs differed based on lung function. In subjects with normal to mildly impaired lung-function, the mammalian target of rapamycin (mTOR) pathway served as an upstream driver; whereas in severe airflow obstruction, pathways downstream of pathological extracellular matrix (ECM) emerged. Consistent with a role during cancer initiation, both the mTOR and ECM gene expression programs paralleled activation of previously identified pro-cancer secretomes. Furthermore, in situ examination of lung tissue documented that stromal fibroblasts express cancer-associated proteins from the two pro-cancer secretomes including IL6 in mild or no airflow obstruction and BMP1 in severe airflow obstruction. Two distinct stromal gene expression programs promoting cancer initiation are activated in lung cancer patients depending on lung function. Our work has implications both for screening strategies and personalized approaches to cancer treatment. Overall design: Polysome-profiling of non-cancerous lung stroma tissue samples from patients with or without lung cancer across a range of forced expiratory volume in one second (FEV1)
Publication Title
Distinct Cancer-Promoting Stromal Gene Expression Depending on Lung Function.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 15 Downloadable Samples
- NextSeq 500
Description
Tumors have the capacity to trigger the formation of blood vessels allowing them to spread to other body parts. We examined here the stem cells that form arteries and veins within tumors and propose that their inhibition reduces metastatic spread. Overall design: Examination of dynamics and differentiation of tissue resident endothelial hierarchy in a melanoma setting
Publication Title
Endovascular progenitors infiltrate melanomas and differentiate towards a variety of vascular beds promoting tumor metastasis.
Sample Metadata Fields
Specimen part, Subject
View Samples- Drosophila melanogaster
- 9 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
Chromosomal instability (CIN) is thought to be a source of mutability in human cancer. However, CIN is highly deleterious for the cell, and the resulting aneuploidy induces metabolic stress and compromises cell fitness. Here we utilized the X-chromosome dosage compensation mechanism and changes in X-chromosome number to demonstrate in Drosophila epithelial cells the causal relationship between CIN, aneuploidy, gene dosage imbalance and tumorigenesis. Whereas the harmful effects of CIN can be buffered by resetting the X-chromosome dosage compensation to compensate for changes in X-chromosome number, interfering with the mechanisms of dosage compensation suffices to induce tumorigenesis. In addition, multiple mechanisms buffer the deleterious effects of CIN including DNA-damage repair, activation of the p38 signalling pathway, and induction of cytokine expression to promote compensatory cell proliferation. These data reveal a key role of gene dosage imbalances to CIN-induced programmed cell death and tumorigenesis and the existence of robust compensatory mechanisms.
Publication Title
Gene Dosage Imbalance Contributes to Chromosomal Instability-Induced Tumorigenesis.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Comparison of transcriptional profile of CD8 cytotoxic T lymphocytes terated with the mTORC1 inhibitor rapamycin or the mTOR inhibitor KU-0063794 and comparison with proteomic analysis.
Publication Title
The cytotoxic T cell proteome and its shaping by the kinase mTOR.
Sample Metadata Fields
Specimen part, Treatment
View Samples