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GSE2044
Homo sapiens
27 Downloadable Samples
Affymetrix Human Genome U133A Array (hgu133a)
Description
Compatibility between high-density oligonucleotide arrays is significantly affected by probe-level sequence information. With a careful filtering of the probes based on their sequence overlaps, data from different generations of microarrays can be combined more effectively. The dataset of 14 human muscle biopsy samples from patients with inflammatory myopathies that were hybridized on both HG-U95Av2 and HG-U133A human arrays for this purpose. Signal values from GCOS 1.2 with Detection call and p-value are provided here, and CEL files are also available for download.
Publication Title
Combining gene expression data from different generations of oligonucleotide arrays.
Sample Metadata Fields
No sample metadata fields
View Samples- Pseudomonas aeruginosa
- 29 Downloadable Samples
- Affymetrix Pseudomonas aeruginosa Array (paeg1a)
Description
To better understand the role of QscR in P. aeruginosa gene regulation and to better understand the relationship between QscR, LasR and RhlR control of gene expression we used transcription profiling to identify a QscR-dependent regulon. Our analysis revealed that QscR activates some genes and represses others. Some of the repressed genes are not regulated by the LasR-I or RhlR-I systems while others are. The LasI-generated 3-oxododecanoyl-homoserine lactone serves as a signal molecule for QscR. Thus QscR appears to be an integral component of the P. aeruginosa quorum sensing circuitry. QscR uses the LasI-generated acyl-homoserine lactone signal and controls a specific regulon that overlaps with the already overlapping LasR and RhlR-dependent regulons.
Publication Title
A distinct QscR regulon in the Pseudomonas aeruginosa quorum-sensing circuit.
Sample Metadata Fields
No sample metadata fields
View Samples- Staphylococcus aureus
- 4 Downloadable Samples
- Affymetrix S. aureus Genome Array (saureus)
Description
These cultures were grown to examine the differences in Agr-regulated virulence factor gene expression between wild-type S. aureus FRI1169 and a non-hemolytic variant isolated from a biofilm inoculated with FRI1169. The study is described more thoroughly in the paper "Generation of virulence factor variants in Staphylococcus aureus biofilms", Yarwood et al., J. Bacteriol. 2007.
Publication Title
Generation of virulence factor variants in Staphylococcus aureus biofilms.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 31 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Immune cell infiltration in myositis were by examining microarray expression profiles in muscle biopsies from 31 myositis patients and 5 normal controls.
Publication Title
Genomic signatures characterize leukocyte infiltration in myositis muscles.
Sample Metadata Fields
Sex, Specimen part, Disease, Disease stage
View Samples- Homo sapiens
- 26 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [probe set (exon) version (huex10st)
Description
Sub-thalamic deep brain stimulation (DBS) reversibly modulates Parkinsons disease (PD) motor symptoms, providing an unusual opportunity to compare leukocyte transcripts in the same subjects before and after neurosurgery and after disconnecting the stimulus (ON-and OFF-stimulus). Here, we report rapid stimulus-induced and largely reversible changes in PD leukocyte transcripts, which were larger in scope than the disease-induced changes. These transcript changes classified advanced pre- from post-surgery PD patients and discriminated patients from controls. Moreover, the extent of changes correlated with the neurological efficacy of the DBS neurosurgery, and covered both regulatory pathways and individual transcript changes, e.g. SNCA, PARK7 and the splicing factor SFRS1. Following 1 hour OFF-stimulus, these changes were largely reversed. We extracted from these differences a modified transcripts signature which discriminated controls from advanced PD patients, pre- from post-surgery and ON-from OFF-stimulus conditions. A further gene-list independent analysis detected reversed pathways. Our findings suggest future uses of this approach and the discovered molecular signature for early diagnostics of PD and for identifying novel targets for therapeutic intervention in this and other DBS-treatable neurological diseases.
Publication Title
Deep brain stimulation induces rapidly reversible transcript changes in Parkinson's leucocytes.
Sample Metadata Fields
Sex, Specimen part, Disease stage
View Samples- Homo sapiens
- 26 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Multiple Sclerosis (MS) is an immune-mediated chronic inflammatory disease affecting the central nervous system. The cause of MS is not known and the mechanism of IFN-beta, a disease-modifying treatment (DMT) approved for MS, is not well-understood. Oligonucleotide microarrays were used to study gene expression in plasmacytoid denditic cells (pDCs) which are antigen-presenting cells implicated in MS pathogenesis.
Publication Title
Multiple sclerosis-linked and interferon-beta-regulated gene expression in plasmacytoid dendritic cells.
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Disease stage, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
The adaptor protein MERIT40 is a core subunit of deubiquitinating (DUB) complexes that specifically cleave Lysine63-polyubiquitin chains. We found that MERIT40 is an important negative regulator of hematopoietic stem cell (HSC) homeostasis, quiescence and self-renewal. This study aims to investigate the molecular mechanism by which MERIT40 regulates HSC expansion and cell cycle. We performed expression profiling of bone marrow CD150+CD48-LSK LT-HSCs from WT and Merit40-/- mice. Results identify select MERIT40-mediated pathways with potential involvement in HSC cell cycle regulation.
Publication Title
MERIT40 deficiency expands hematopoietic stem cell pools by regulating thrombopoietin receptor signaling.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 33 Downloadable Samples
Affymetrix Mouse Expression 430A Array (moe430a), Affymetrix Mouse Genome 430 2.0 Array (mouse4302), Affymetrix Mouse Expression 430B Array (moe430b)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Activity-dependent regulation of inhibitory synapse development by Npas4.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 24 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
To identify the activity-induced gene expression programs in inhibitory and excitatory neurons, we analyzed RNA extracted from cultured E14 mouse MGE- and CTX-derived neurons (DIV 10) after these cultures were membrane-depolarized for 0, 1 and 6 hrs with 55mM extracellular KCl. To identify the gene programs regulated in these cells by the activity-induced early-response transcription factor Npas4, we repeated the same experiment in the MGE- and CTX-cultures lacking Npas4 (Npas4-KO).
Publication Title
Npas4 regulates excitatory-inhibitory balance within neural circuits through cell-type-specific gene programs.
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples- Mus musculus
- 23 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302), Affymetrix Mouse Expression 430A Array (moe430a)
Description
we performed a DNA microarray experiment to identify activity-regulated genes that are misregulated in the absence of Npas4.
Publication Title
Activity-dependent regulation of inhibitory synapse development by Npas4.
Sample Metadata Fields
No sample metadata fields
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