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GSE34811
Rattus norvegicus
10 Downloadable Samples
Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Multiple sclerosis is a chronic, inflammatory, demyelinating disease of the central nervous system in which macrophages and microglia play a central role. During active multiple sclerosis foamy macrophages and microglia, containing degenerated myelin, are abundantly found in demyelinated areas. Recent studies have described an altered macrophage phenotype after myelin internalization. However, by which mechanisms myelin affects the phenotype of macrophages and how this phenotype can influence lesion progression is unclear.
Publication Title
Myelin-derived lipids modulate macrophage activity by liver X receptor activation.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Drosophila melanogaster
- 72 Downloadable Samples
Illumina HiSeq 2000
Description
Genome control is operated by transcription factors (TF) controlling their target genes by binding to promoters and enhancers. Conceptually, the interactions between TFs, their binding sites, and their functional targets are represented by gene regulatory networks (GRN). Deciphering in vivo GRNs underlying organ development in an unbiased genome-wide setting involves identifying both functional TF-gene interactions and physical TF-DNA interactions. To reverse-engineer the GRN of eye development in Drosophila, we performed RNA-seq across 72 genetic perturbations and sorted cell types, and inferred a co-expression network. Next, we derived direct TF-DNA interactions using computational motif inference, ultimately connecting 241 TFs to 5632 direct target genes through 24926 enhancers. Using this network we found network motifs, cis-regulatory codes, and new regulators of eye development. We validate the predicted target regions of Grainyhead by ChIP-seq and identify this factor as a general co-factor in the eye network, being bound to thousands of nucleosome-free regions. Overall design: RNA-seq gene expression profiling across Drosophila 3rd instar larval wild type tissues (brain, eye-antennal and wing discs), specific cell types from the eye-antennal disc, sorted by FACS, and genetic perturbations (TF mutants, TF over-expression, and TF RNAi knockdown).
Publication Title
Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Reduced oxygen availability during embryogenesis leads to intra-uterine growth restriction (IUGR), increasing the risk for hypertension, cardiovascular and chronic kidney disease (CKD) in adults. Although this association has long been recognized, underlying mechanisms still require extensive research.
Publication Title
Fetuin-A is a HIF target that safeguards tissue integrity during hypoxic stress.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 24 Downloadable Samples
- IlluminaHiSeq2000
Description
This experiment aims to identify the biological pathways and diseases associated with the cytokine Interleukin 13 (IL-13) using gene expression measured in peripheral blood mononuclear cells (PBMCs). Overall design: The experiment comprised of samples obtained from 3 healthy donors. The expression profiles of in vitro IL-13 stimulation were generated using RNA-seq technology for 3 PBMC samples at 24 hours. The transcriptional profiles of PBMCs without IL-13 stimulation were also generated to be used as controls. An IL-13R-alpha antagonist (Redpath et al. Biochemical Journal, 2013) was introduced into IL-13 stimulated PBMCs and the gene expression levels after 24h were profiled to examine the neutralization of IL-13 signaling by the antagonist.
Publication Title
Combining multiple tools outperforms individual methods in gene set enrichment analyses.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 1 Downloadable Sample
- Illumina HiSeq 2500
Description
Analysis of gene expression in the distal forelimbs Overall design: RNA-Seq polyA on transcripts extracted from the dissection of three pairs of embryonnic forelimbs at E12.5
Publication Title
Nanoscale spatial organization of the HoxD gene cluster in distinct transcriptional states.
Sample Metadata Fields
Cell line, Subject
View Samples- Homo sapiens
- 32 Downloadable Samples
- IlluminaHiSeq2000
Description
Background: Transcription control of mitochondrial metabolism is essential for cellular function. A better understanding of this process will aid the elucidation of mitochondrial disorders, in particular of the many genetically unsolved cases of oxidative phosphorylation (OXPHOS) deficiency. Yet, to date only few studies have investigated nuclear gene regulation in the context of OXPHOS deficiency. In this study, we combined RNA sequencing of human complex I-deficient patient cells across 32 conditions of perturbed mitochondrial metabolism, with a comprehensive analysis of gene expression patterns, co-expression calculations and transcription factor binding sites. Results: Our analysis shows that OXPHOS genes have a significantly higher co-expression with each other than with other genes, including mitochondrial genes. We found no evidence for complex-specific mRNA expression regulation in the tested cell types and conditions: subunits of different OXPHOS complexes are similarly (co-)expressed and regulated by a common set of transcription factors. However, we did observe significant differences between the expression of OXPHOS complex subunits compared to assembly factors, suggesting divergent transcription programs. Furthermore, complex I co-expression calculations identified 684 genes with a likely role in OXPHOS biogenesis and function. Analysis of evolutionarily conserved transcription factor binding sites in the promoters of these genes revealed almost all known OXPHOS regulators (including GABP, NRF1/2, SP1, YY1, E-box factors) and a set of six yet uncharacterized candidate transcription factors (ELK1, KLF7, SP4, EHF, ZNF143, and EL2). Conclusions: OXPHOS genes share an expression program distinct from other mitochondrial genes, indicative of targeted regulation of this mitochondrial sub-process. Within the subset of OXPHOS genes we established a difference in expression between subunits and assembly factors. Most transcription regulators of genes that co-express with complex I are well-established factors for OXPHOS biogenesis. For the remaining six factors we here suggest for the first time a link with transcription regulation in OXPHOS deficiency. Overall design: RNA-SEQ of whole cell RNA in 2 control and 2 complex I deficient patient fibroblast cell lines treated with 4 compounds in duplicate, resulting in a total of 2x2x4x2=32 samples
Publication Title
Transcriptome analysis of complex I-deficient patients reveals distinct expression programs for subunits and assembly factors of the oxidative phosphorylation system.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 18 Downloadable Samples
- Affymetrix Mouse Expression 430B Array (moe430b)
Description
BRCA1 nestin CRE conditional knockout cortrices of P7 animals were compared to wildtype littermates to characterize the mutant phenotype.
Publication Title
BRCA1 tumour suppression occurs via heterochromatin-mediated silencing.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 14 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
SUMMARY
Publication Title
Loss of patched and disruption of granule cell development in a pre-neoplastic stage of medulloblastoma.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 11 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Little is known about the early transcriptional events in innate immune signaling in immature and tolerogenic monocyte-derived dendritic cells (DCs), the professional antigen-presenting cells of our immune system. TLR ligands usually induce a proinflammatory transcriptional response, whereas IL10 and/or dexamethasone induce a more tolerogenic phenotype.
Publication Title
MicroRNA genes preferentially expressed in dendritic cells contain sites for conserved transcription factor binding motifs in their promoters.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 32 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
We used microarrays to detail the global programme of gene expression in lung SCC cells treated with belinostat, a pan-HDAC inhibitor. The primary focus of this work is to investigate the efficacy of belinostat on lung SCC cells. Our phosphoproteomic profiling analyses revealed the downregulation of MAPK signaling pathway upon drug treatment, together with the induction of apoptosis. While HDAC inhibition generally affects transcription, the mechanism of SOS/MAPK downregulation was therefore proposed to be affected at the transcriptomic level. However, genes related to MAPK pathway were not significantly regulated upon belinostat treatment, whereas ubiquitin-proteasome gene signature was affected. This supports an indirect mechanism of epigenetic regulation on MAPK signaling that should be explored further.
Publication Title
Belinostat exerts antitumor cytotoxicity through the ubiquitin-proteasome pathway in lung squamous cell carcinoma.
Sample Metadata Fields
Cell line, Treatment
View Samples