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GSE19846
Homo sapiens
4 Downloadable Samples
Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Demethyl fructiculin A is a diterpenoid quinone component of the exudates from Salvia corrugata (SCO-1) leafes. SCO-1 was recently reported to induce anoikis in mammalian cell lines via a molecular mechanism involving the presence of the membrane scavenging receptor CD36. However, experiments performed with cells lacking CD36, showed that SCO-1 was able to induce apoptosis also via alternate pathways. To contribute to a better characterization of the molecular mechanisms underlining the cytotoxic activity of SCO-1, we decided to pursue an unbiased pharmacogenomic approach by generating the gene expression profile of GBM TICs subjected to the administration of SCO-1 and comparing it with that of control cells exposed to the solvent. With this strategy we hypothesized to highlight those pathways and biological processes unlashed by SCO-1.
Publication Title
Demethyl fruticulin A (SCO-1) causes apoptosis by inducing reactive oxygen species in mitochondria.
Sample Metadata Fields
Time
View Samples- Homo sapiens
- 389 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
The study consist of patients who presented at Memorial Sloan-Kettering Cancer Center with a colonic neoplasm between 1992 and 2004. Biological specimens used in this study include primary colon adenocarcinomas, adenomas, metastasis and corresponding normal mucosae.
Publication Title
Association of survival and disease progression with chromosomal instability: a genomic exploration of colorectal cancer.
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 221 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
RNA expression data was generated as part of a colon cancer study. Samples were obtained from patients, including primary colon cancer, polyps, metastases, and matched normal mucosa (obtained from the margins of the resection). The RNA was extracted from tissue samples obtained from resections and hybridized to Affymetrix HG-U133 arrays. RNA expression data was also obtained for a few cell lines.
Publication Title
Association of survival and disease progression with chromosomal instability: a genomic exploration of colorectal cancer.
Sample Metadata Fields
Specimen part, Disease, Disease stage, Cell line
View Samples- Mus musculus
- 12 Downloadable Samples
Illumina Genome Analyzer IIx, Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Functions of BET proteins in erythroid gene expression.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 12 Downloadable Samples
Affymetrix Mouse Gene 2.0 ST Array (mogene20st), Illumina Genome Analyzer IIx
Description
Role of bromodomain and extra-terminal motif (BET) proteins in GATA1-null erythrolbasts (G1E) and in differentiation induced by activation of conditional GATA1 tested by addition of BET inhibitor JQ1 (250nM)
Publication Title
Functions of BET proteins in erythroid gene expression.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 7 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Increased CREB levels and upregulation of its target genes expression resulted in increased myelopoiesis and colony formation.
Publication Title
MicroRNA-34b promoter hypermethylation induces CREB overexpression and contributes to myeloid transformation.
Sample Metadata Fields
Specimen part, Disease, Disease stage, Subject
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We studied the KRAS and NRAS mutational status in pediatric MLL-AF4+ leukemia patients by means of ultra deep amplicon sequencing. The gene expression profiles of RAS wild type and RAS mutated patients were investigated by gene expression analysis. We showed that mutated patients were characterized by a RAS related expression signature.
Publication Title
Deciphering KRAS and NRAS mutated clone dynamics in MLL-AF4 paediatric leukaemia by ultra deep sequencing analysis.
Sample Metadata Fields
Specimen part, Disease, Disease stage, Subject
View Samples- Homo sapiens
- 30 Downloadable Samples
- Illumina HumanHT-12 V3.0 expression beadchip
Description
The advent of human induced pluripotent stem (iPS) cells enables for the first time the derivation of unlimited numbers of patient-specific stem cells and holds great promise for regenerative medicine. However, realizing the full potential of iPS cells requires robust, precise and safe strategies for their genetic modification. Safe human iPS cell engineering is especially needed for therapeutic applications, as stem cell-based therapies that rely on randomly integrated transgenes pose oncogenic risks. Here we describe a strategy to genetically modify iPS cells from patients with beta-thalassemia in a potentially clinically relevant manner. Our approach is based on the identification and selection of safe harbor sites for transgene expression in the human genome. We show that thalassemia patient iPS cell clones harboring a transgene can be isolated and screened according to chromosomal position. We next demonstrate that iPS cell clones that meet our safe harbor criteria resist silencing and allow for therapeutic levels of beta-globin expression upon erythroid differentiation without perturbation of neighboring gene expression. Combined bioinformatics and functional analyses thus provide a robust and dependable approach for achieving desirable levels of transgene expression from selected chromosomal loci. This approach may be broadly applicable to introducing therapeutic or suicide genes into patient specific iPS cells for use in cell therapy.
Publication Title
Genomic safe harbors permit high β-globin transgene expression in thalassemia induced pluripotent stem cells.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 163 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
High expression of miR-125b-2 and SNORD116 noncoding RNA clusters characterize ERG-related B cell precursor acute lymphoblastic leukemia.
Sample Metadata Fields
Specimen part, Disease, Disease stage
View Samples- Homo sapiens
- 139 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
ERG-related B cell precursor acute lymphoblastic leukemia (BCP ALL) is a recently described childhood ALL subtype characterized by aberrant ERG protein expression and highly recurrent ERG intragenic deletions. Several studies reported a remarkably favourable outcome for ERG-related BCP-ALL despite a high incidence of apparently inauspicious IKZF1 aberrations. In this study we investigated by integrative genomic analysis the main features of the ERG-related group in a cohort of B-others BCP ALL patients enrolled in the AIEOP ALL 2000 therapeutic protocol. We report a specific microRNA and snoRNA signature that characterizes ERG-related patients with up-regulation of the miR-125b-2 cluster on chromosome 21 and several snoRNAs in the Prader-Willi locus at 15q11.2, including the orphan SNORD116 cluster. Given the current lack of parameters for a comprehensive classification we suggest toexploit the noncoding RNAs signature for differential diagnosis of ERG-related patients.
Publication Title
High expression of miR-125b-2 and SNORD116 noncoding RNA clusters characterize ERG-related B cell precursor acute lymphoblastic leukemia.
Sample Metadata Fields
Specimen part, Disease, Disease stage
View Samples