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Platform
E-MEXP-2298
Escherichia coli
18 Downloadable Samples
Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
Gene expression profiling of two different E. coli CAUTI strains during biofilm growth in human urine.<br></br>
Publication Title
Escherichia coli isolates causing asymptomatic bacteriuria in catheterized and noncatheterized individuals possess similar virulence properties.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 42 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The specialisation of mammalian cells in time and space requires genes associated with specific pathways and functions to be co-ordinately expressed. Here we have combined a large number of publically available microarray datasets (745 samples, from over 100 separate studies) derived from human primary cells and analysed on the Affymetrix U133plus2.0 array. Using the network analysis tool BioLayout Express3D we have constructed and clustered large correlation graphs of these data in order to identify robust co-associations of genes expressed in a wide variety of cell lineages. We discuss the biological significance of a number of these associations, in particular the coexpression of key transcription factors with the genes that they are likely to control. We consider the regulation of genes in human primary cells and specifically in the human mononuclear phagocyte system. Of particular note is the fact that these data do not support the identity of putative markers of antigen-presenting dendritic cells, nor classification of M1 and M2 activation states, a current subject of debate within immunological field. We have provided this data resource on the BioGPS web site (www.biogps.org) and on macrophages.com (www.macrophages.com).
Publication Title
An expression atlas of human primary cells: inference of gene function from coexpression networks.
Sample Metadata Fields
Specimen part
View Samples- Sus scrofa
- 9 Downloadable Samples
- Porcine Gene 1.1 ST Array (porgene11st)
Description
The expression was designed to determine whether exposure to CSF1-Fc has any effect on liver-specific gene expression in pigs.
Publication Title
Macrophage colony-stimulating factor (CSF1) controls monocyte production and maturation and the steady-state size of the liver in pigs.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus, Homo sapiens
- 48 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Topoisomerases facilitate transcription of long genes linked to autism.
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Mus musculus
- 48 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Topoisomerases are necessary for the expression of neurodevelopmental genes, and are mutated in some patients with autism spectrum disorder (ASD). We have studied the effects of inhibitors of Topoisomerase 1 (Top1) and Topoisomerase 2 (Top2) enzymes on mouse cortical neurons. We find that topoisomerases selectively inhibit long genes (>100kb), with little effect on all other gene expression. Using ChIPseq against RNA Polymerase II (Pol2) we show that the Top1 inhibitor topotecan blocks transcriptional elongation of long genes specifically. Many of the genes inhibited by topotecan are candidate ASD genes, leading us to propose that topoisomerase inhibition might contribute to ASD pathology.
Publication Title
Topoisomerases facilitate transcription of long genes linked to autism.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 10 Downloadable Samples
Description
Topoisomerases are necessary for the expression of neurodevelopmental genes, and are mutated in some patients with autism spectrum disorder (ASD). We have studied the effects of inhibitors of Topoisomerase 1 (Top1) and Topoisomerase 2 (Top2) enzymes on mouse cortical neurons. We find that topoisomerases selectively inhibit long genes (>100kb), with little effect on all other gene expression. Using ChIPseq against RNA Polymerase II (Pol2) we show that the Top1 inhibitor topotecan blocks transcriptional elongation of long genes specifically. Many of the genes inhibited by topotecan are candidate ASD genes, leading us to propose that topoisomerase inhibition might contribute to ASD pathology. Overall design: [Mouse] 5 biological replicates of transcriptome sequencing (RNAseq) from topotecan treated neurons and vehicle treated controls; Pol2 ChIPseq of topotecan and vehicle treated neurons [Human] Transcriptome sequencing (RNAseq) from topotecan treated neurons and vehicle treated control.
Publication Title
Topoisomerases facilitate transcription of long genes linked to autism.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 1 Downloadable Sample
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
We observed that follicular dendritic cell line induced a new type of CD11b+ myeloid cells (FDMCs) when cultured with a lineage-negative c-kit+ population from mouse spleen cells.
Publication Title
CSF-1 receptor-mediated differentiation of a new type of monocytic cell with B cell-stimulating activity: its selective dependence on IL-34.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 30 Downloadable Samples
- NextSeq 500
Description
We have previously demonstrated older skin exhibits increased sterile inflammation 6 hours after saline-injection. In this work, we examined whether p38MAPK inhibitor in vivo would attenuate this non-specific inflammatory response towards saline in elder individuals (=65 years). Overall design: Skin mRNA profiles 6 hours after saline injection were studied before and after losmapimod treatment.
Publication Title
Enhancement of cutaneous immunity during aging by blocking p38 mitogen-activated protein (MAP) kinase-induced inflammation.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Sus scrofa
- 12 Downloadable Samples
- Porcine Gene 1.0 ST Array (porgene10st)
Description
Expression data from valvular interstitial cells cultured in 2D or 3D PEG hydrogel systems compared to culture on tissue culture polystyrene and freshly isolated cells
Publication Title
Transcriptional profiles of valvular interstitial cells cultured on tissue culture polystyrene, on 2D hydrogels, or within 3D hydrogels.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 32 Downloadable Samples
- Affymetrix Rat Gene 2.1 ST Array (ragene21st)
Description
We used microarray to examine changes in gene expression in the absence of Csf1r in the brain and spleen.
Publication Title
Pleiotropic Impacts of Macrophage and Microglial Deficiency on Development in Rats with Targeted Mutation of the <i>Csf1r</i> Locus.
Sample Metadata Fields
Sex
View Samples