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Homo sapiens
6 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Human peripheral blood mononuclear cells were cultured in presence of H37Ra strain at 37oC, 5%CO2. Cellular aggregates were collected at 24h, and RNA extracted and hybridized to Affymetrix microarrays (HG-U133). Raw data from microarray experiments was analyzed with dCHIP and SAM programs to determine the significance of changes at the biological context.
Publication Title
Microarray analysis of the in vitro granulomatous response to Mycobacterium tuberculosis H37Ra.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 4 Downloadable Samples
- Affymetrix Rat Genome U34 Array (rgu34a)
Description
we analyzed the gene expression profiles of Mat-Lylu cell lines (in duplicate) compared to G cell lines (in duplicate) using Affymetrix tools and dChip software. The objective was to find metastasis-associated genes in prostate cancer, using this in vitro model.
Publication Title
DNA microarray analysis reveals metastasis-associated genes in rat prostate cancer cell lines.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 36 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Satellite cells are the primary source of stem cells for skeletal muscle growth and regeneration. Since adult stem cell maintenance involves a fine balance between intrinsic and extrinsic mechanisms, we performed genome-wide chronological expression profiling to identify the transcriptomic changes involved in acquisition of muscle stem cell characteristics.
Publication Title
Gene Expression Profiling of Muscle Stem Cells Identifies Novel Regulators of Postnatal Myogenesis.
Sample Metadata Fields
Age, Specimen part
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GSE64385- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
These experiments were designed as a benchmark tool for deconvolution methods. 5 immune cell populations were sorted from 3 healthy donors' peripheral bloods. Peripheral Blood Mononuclear Cells (PBCMs) and PolymorphoNuclear Cells (PMN) were separated using gradient centrifugation. T cells (DAPI-/CD3+/CD14-/CD19-/CD56-), monocytes (DAPI-/CD3-/CD14+/CD19-/CD56-), B cells (DAPI-/CD3-/CD14-/CD19+/CD56-) and NK cells (DAPI-/CD3-/CD14-/CD19-/CD56+) were FACS-sorted from PBMCs and neutrophils (DAPI-/CD66b+/CD19-/CD3-/CD56-/CD14-) were sorted from PMNs. RNA was extracted from the purified cell population, as well as from the HCT116 colon cancer cell line. RNAs from pure populations were then mixed in various proportions.
Publication Title
Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 72 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
The therapy-induced PML/RARA catabolism elicits the loss of APL-initiating cell self-renewal through PML NB reformation and P53 activation. These results explain the curative activity of the RA/arsenic combination, the resistance to RA of PLZF/RARA-driven APLs and they raise the prospect that activation of this PML/P53 checkpoint might have therapeutic values in other malignancies.
Publication Title
Activation of a promyelocytic leukemia-tumor protein 53 axis underlies acute promyelocytic leukemia cure.
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples- Homo sapiens
- 3 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
A ""Cartes d'Identite des Tumeurs"" (CIT) project from the french Ligue Nationale Contre le Cancer (<a href="http://cit.ligue-cancer.net" target="_blank">http://cit.ligue-cancer.net</a>). 73 samples (60 tumoral, 6 normal kidneys (NK), 3 fetal kidneys (FK) and 4 cell lines (L)), hybridized on Affymetrix HG-U133A GeneChips.Tumor classification based on a characterization of WT1 and Betacatenin. Identification of major differences between two categories of Wilms' Tumors defined according to WT1 and CTNNB1 genomic and expression features. First large scale study based on post-chemotherapy resected tumors, according to the SIOP protocoles.
Publication Title
WNT/beta-catenin pathway activation in Wilms tumors: a unifying mechanism with multiple entries?
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Disease stage, Subject
View Samples- Homo sapiens
- 299 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
An unexplored consequence of epigenetic alterations associated with cancer is the ectopic expression of tissue-restricted genes. Here, a new strategy was developed to decipher genome-wide expression data in search for these off-context gene activations, which consisted first, in identifying a large number of tissue-specific genes normally epigenetically silenced in most somatic cells and second, in using them as cancer biomarkers on an on/off basis. Applying this concept to analyze whole-genome transcriptome data in lung cancer, we discovered a specific group of 26 genes whose expression was a strong and independent predictor of poor prognosis in our cohort of 293 lung tumours, as well as in two independent external populations. In addition, these 26 classifying genes enabled us to isolate a homogenous group of metastatic-prone highly aggressive tumours, whose characteristic gene expression profile revealed a high proliferative potential combined to a significant decrease in immune and signaling functions. This work illustrates a new approach for a personalized management of cancer, with applications to any cancer type.
Publication Title
Ectopic activation of germline and placental genes identifies aggressive metastasis-prone lung cancers.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 585 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Gene expression classification of colon cancer into molecular subtypes: characterization, validation, and prognostic value.
Sample Metadata Fields
Sex
View Samples- Homo sapiens
- 585 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
From a clinical and molecular perspective, colon cancer (CC) is a heterogeneous disease but to date no classification based on high-density transcriptome data has been established. The aim of this study was to build up a robust molecular classification ofmRNA expression profiles (Affymetrix U133Plus2) ofa large series of 443 CC and 19 non-tumoral colorectal mucosas, and to validate it on an independent serie of 123 CC and 906 public dataset.We identified and validated six molecular subtypes in this large cohort as a combination of multiple molecular processes that complement current disease stratification based on clinicopathological variables and molecular markers. The biological relevance of these subtypes was consolidated by significant differences in survival. These insights open new perspectives for improving prognostic models and targeted therapies.
Publication Title
Gene expression classification of colon cancer into molecular subtypes: characterization, validation, and prognostic value.
Sample Metadata Fields
Sex
View Samples- Homo sapiens
- 69 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Sporadic early onset colorectal carcinoma (EOCRC) is a growing problem that remains poorly understood. Clinical specificities and mechanisms of tumorigenesis might be relevant to both diagnosis and treatment. In this prospective study, clinicopathological features, genomic and gene expression profiles of sporadic EOCRC were compared to other well defined groups of CRC.
Publication Title
Sporadic early-onset colorectal cancer is a specific sub-type of cancer: a morphological, molecular and genetics study.
Sample Metadata Fields
Sex, Specimen part
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