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Homo sapiens
4 Downloadable Samples
Illumina Genome Analyzer IIx
Description
Acute myeloid leukemia (AML) continues to have the lowest survival rates of all leukemias. Therefore, new therapeutic strategies are urgently needed to improve clinical outcomes for AML patients. Here, we report a novel role for Wilms’ tumor 1-associated protein (WTAP) in pathogenesis of AML. We have performed RNA-Seq in K562 cells with knockdown of WTAP to ascertain which genes it regulates. Overall design: We have 2 replicates of total RNA for K562 cells and 2 replicates with WTAP knocked down
Publication Title
WTAP is a novel oncogenic protein in acute myeloid leukemia.
Sample Metadata Fields
Subject
View Samples- Homo sapiens
- 59 Downloadable Samples
Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
Parkinson's disease (PD) is a chronic progressive neurodegenerative disorder that is clinically defined in terms of motor symptoms. These are preceded by prodromal non-motor manifestations that prove the systemic nature of the disease. Identifying genes and pathways altered in living patients provide new information on the diagnosis and pathogenesis of sporadic PD. We study changes in gene expression in the blood of 40 sporadic PD patients and 20 healthy controls (Discovery set) by taking advantage of the Affymetrix platform. Patients were at the onset of motor symptoms and before initiating any pharmacological treatment. By applying Ranking-Principal Component Analysis, PUMA and Significance Analysis of Microarrays, gene expression profiling discriminates patients from healthy controls and identifies differentially expressed genes in blood. The majority of these are also present in dopaminergic neurons of the Substantia Nigra, the key site of neurodegeneration. Together with neuronal apoptosis, lymphocyte activation and mitochondrial dysfunction, already found in previous analysis of PD blood and post-mortem brains, we unveiled transcriptome changes enriched in biological terms related to epigenetic modifications including chromatin remodeling and methylation. Candidate transcripts were validated by RT-qPCR in an independent cohort of 12 patients and controls (Validation set). Our data support the use of blood transcriptomics to study neurodegenerative diseases. It identifies changes in crucial components of chromatin remodeling and methylation machineries as early events in sporadic PD suggesting epigenetics as target for therapeutic intervention.
Publication Title
Blood transcriptomics of drug-naïve sporadic Parkinson's disease patients.
Sample Metadata Fields
Specimen part, Disease
View Samples- Mus musculus
- 22 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
The transcriptional regulator Aire binds to and activates super-enhancers.
Sample Metadata Fields
Sex, Age, Specimen part, Treatment
View Samples- Homo sapiens
- 27 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Poorly differentiated thyroid carcinomas (PDTC) represent a heterogeneous, aggressive entity, presenting features that suggest a progression from well-differentiated carcinomas.
Publication Title
Gene expression profiling associated with the progression to poorly differentiated thyroid carcinomas.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 22 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Microarray profiles of MECs from mice treated with topoisomerase inhibitors
Publication Title
The transcriptional regulator Aire binds to and activates super-enhancers.
Sample Metadata Fields
Sex, Age, Treatment
View Samples- Oryza sativa indica group
- 12 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
High quality RNA was extracted from the whole seedlings (Combined root and leaf samples) using TRI Reagent (Ambion, Inc. USA) and pooled from 12 independent stressed and non-stressed plant samples separately, and treated with DNase-I (QIAGEN GmbH, Germany). Subsequently, RNA cleanup was carried out using RNeasy Plant Mini Kit (QIAGEN GmbH, Germany) and 5 ug of total RNA from each sample in triplicates were reverse-transcribed to double stranded cDNA using the GeneChipﾮ One-Cycle cDNA Synthesis Kit. The biotin-labelled cRNA was made using the GeneChipﾮ IVT Labelling Kit (Affymetrix, CA, USA). Twenty microgram of cRNA samples was fragmented and out of which which 7.5 ug cRNA were hybridized for 16 hours at 45C to the Affymetrix GeneChipﾮ Rice Genome Array (Santa Clara, CA, USA). After washing and staining with R-phycoerythrin streptavidin in a Fluidics Station, using the Genechipﾮ Fluidics Station 450, the arrays were scanned by the Genechipﾮ 3000 Scanner. The chip images were scanned and extracted using default settings and the CEL files were produced with the Affymetrix GeneChip Operating Software (GCOS 1.2). The resulting .CEL files were imported into the GeneSpring GX 10 (Agilent Technologies Inc, Santa Clara CA) and normalized with the PLIER16 algorithm. The resulting expression values were log2-transformed. Average log signal intensity values of three technical replicates for each sample were used for advance analysis.
Publication Title
Comparative analysis of drought-responsive transcriptome in Indica rice genotypes with contrasting drought tolerance.
Sample Metadata Fields
Specimen part
View Samples- Escherichia coli
- 8 Downloadable Samples
- Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
VS94 gene expression at different time-points in SAPI medium in absence and presence of AI-2 was studied.
Publication Title
Temporal regulation of enterohemorrhagic Escherichia coli virulence mediated by autoinducer-2.
Sample Metadata Fields
No sample metadata fields
View Samples- Schizosaccharomyces pombe
- 6 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Mitotic entry is accompanyed by the expression of a cluster of so called mitotic genes, whose activation is critical for mitosis in human and yeast cells. We found a link between the transcription machinery and cell cycle control network at mitosis in fission yeast, involving the Cdk8 kinase dependent phosphorylation of the fork head transcription factor Fkh2. We have generated a non-phosphorylatable fkh2 mutant (fkh2-S2A) also.
Publication Title
Cyclin-dependent kinase 8 regulates mitotic commitment in fission yeast.
Sample Metadata Fields
No sample metadata fields
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GSE6195- Escherichia coli
- 4 Downloadable Samples
- Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
For the microarray experiments, 10 g glass wool (Corning Glass Works, Corning, N.Y.) were used to form biofilms (30) in 250 mL in 1 L Erlenmeyer shake flasks which were inoculated with overnight cultures diluted that were 1:100. For EHEC with 7-hydroxyindole and isatin, 1000 mM 7-hydroxyindole in 250 mL DMF, 250 mM isatin in 250 mL DMF, or 250 mL DMF alone were added to cells grown in LB. The cells were shaken at 250 rpm and 30C for 7 hours to form biofilms on the glass wool, and RNA was isolated from the suspension cells and the biofilm.
Publication Title
Enterohemorrhagic Escherichia coli biofilms are inhibited by 7-hydroxyindole and stimulated by isatin.
Sample Metadata Fields
No sample metadata fields
View Samples- Escherichia coli
- 4 Downloadable Samples
- Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
E coli O157H7 (EHEC) wildtype 7 hour biofilm cells studied in LB glucose medium with and without chemicals - Epinephrine, Norepinephrine and Indole. Biofilm cells were cultured from glass wool.
Publication Title
Differential effects of epinephrine, norepinephrine, and indole on Escherichia coli O157:H7 chemotaxis, colonization, and gene expression.
Sample Metadata Fields
No sample metadata fields
View Samples