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GSE73592
Mus musculus
10 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
A total number of 1,511 probe sets in the bone marrow showed at least two-fold changes with FDR < 0.05, of which 256 probe sets had over four-fold changes. A group of 63 genes in the bone marrow of NDLD mice had more than a 4-fold change with FDR < 0.0001. From 503 genes encoding proteins with ITIM motif that binds to Ptpn6, 109 were up-regulated and 83 were down-regulated.
Publication Title
A differential gene expression study: Ptpn6 (SHP-1)-insufficiency leads to neutrophilic dermatosis-like disease (NDLD) in mice.
Sample Metadata Fields
Disease, Disease stage
View Samples- Mus musculus
- 46 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
When compared to skin, oral mucosal wounds heal rapidly and with reduced scar formation. This study used an Affymetrix microarray platform to compare the transcriptomes of oral mucosa and skin wounds in order to identify critical differences in the healing response at these two sites.
Publication Title
Positional differences in the wound transcriptome of skin and oral mucosa.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 15 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
analyzed changes in cytokine/chemokine production and gene expression levels in, human peripheral blood mononuclear cells upon teratment with 15M,2,4-benzenetriol
Publication Title
Identification of human cell responses to benzene and benzene metabolites.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
Kaposis sarcoma (KS) is the most frequently occurring malignant tumor in patients infected with the human immunodeficiency virus. Recent studies have revealed that infection of vascular endothelial cells with Kaposi's sarcoma-associated herpes virus in vitro results in a lymphatic re-programming of these cells, with potent induction of the lymphatic marker genes podoplanin and VEGFR-3 which is mediated by upregulation of the transcription factor Prox1. However, the potential effects of Prox1 expression on the biology of KS and, in particular, on the aggressive and invasive behavior of KS tumors in vivo have remained unknown. We stably expressed Prox1 cDNA in the two mouse hemangioendothelioma cell lines EOMA and Py-4-1, well-established murine models for kaposiform hemangioendothelioma. Surprisingly, we found that expression of Prox1 was sufficient to induce a more aggressive behavior of tumors growing in syngenic mice, leading to enhanced local invasion into the muscular layer and to cellular anaplasia. This enhanced malignant phenotype was associated with upregulation of several genes involved in proteolysis, cytoskeletal reorganisation and migration. Together, these results indicate that Prox1 plays an important, previously unanticipated role in mediating the aggressive behavior of vascular neoplasms such as Kaposi's sarcoma.
Publication Title
Prox-1 promotes invasion of kaposiform hemangioendotheliomas.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 8 Downloadable Samples
Illumina HiSeq 2000
Description
APs were isolated from naïve skin and day 5wounds from dorsal skin wound beds of 7-9 weeks old using FACS. This experiment describes changes in AP gene expression associated with injury and subsequent tissue repair. Overall design: APs were isolated by FACS.
Publication Title
Myofibroblast proliferation and heterogeneity are supported by macrophages during skin repair.
Sample Metadata Fields
Sex, Age, Cell line, Subject
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina HiSeq 2000
Description
Cells were isolated from day 5wounds from dorsal skin wound beds of 7-9 weeks old using FACS. This experiment describes the gene expression profile associated with different immune cell subsets during tissue repair. Overall design: Cells were isolated by FACS.
Publication Title
Myofibroblast proliferation and heterogeneity are supported by macrophages during skin repair.
Sample Metadata Fields
Sex, Age, Cell line, Subject
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Phosphorylation of histone H3 at Serine 10 emerges as a mechanism increasing chromatin accessibility of the transcription factor NF-kB for a particular set of immune genes. Here we report that a bacterial pathogen uses this strategy to shape the transcriptional response of infected host cells. We identify the Shigella flexneri type III protein effector OspF as a Dual Specific Phosphatase. OspF dephosphorylates MAP kinases within the nucleus impairing histone H3 phosphorylation at Serine 10 in a gene-specific manner. Therefore, OspF reprograms the transcriptional response for inactivation of a subset of NF-kB responsive genes. This regulation leads to repression of polymorphonuclear leukocytes recruitment in infected tissues. Thus, pathogens have evolved the ability to precisely modulate host cell epigenetic information as a strategy to repress innate immunity.
Publication Title
An injected bacterial effector targets chromatin access for transcription factor NF-kappaB to alter transcription of host genes involved in immune responses.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 35 Downloadable Samples
- NextSeq 500
Description
Here, using genome wide analysis, we demonstrate that canonical mRNA is processed post-transcriptionally through an alternative cleavage and polyadenylation mechanism. As a result of this process, the downstream cleavage fragment of the 3'UTR remains uncapped and stable This finding indicates that different parts of gene mRNA are separate and independent, by re-annotating the human transcriptome using this model, we provide a new overview of the function and impact of microRNA (miRNA) Our results shed new light on the mammalian transcriptome and show that what were considered as 3'UTRs are in fact autonomous RNA fragments. Overall design: Examination of mRNA levels and cleavage across transcripts in U2OS and 293 cell types (3 replicates each)
Publication Title
Post-transcriptional 3´-UTR cleavage of mRNA transcripts generates thousands of stable uncapped autonomous RNA fragments.
Sample Metadata Fields
Treatment, Subject
View Samples- Mus musculus
- 18 Downloadable Samples
- Illumina HiSeq 2500
Description
We have here followed the transcriptional effect of stimulation with the phorbol ester PMA in mouse fibroblasts from HP1gamma null mice recomplemented with either wild-type HP1gamma or an HP1g with an S83A mutation Overall design: Spontaneously immortalized mouse embryonic fibroblasts from HP1gamma null mice were used to stably integrate either an empty expression vector, or expression vectors for either WT or S83A mutant HP1gamma. These cells were then stimulated with PMA for 0 or 60 min. and used for transcriptome analysis by Next Generation sequencing.
Publication Title
Shigella flexneri targets the HP1γ subcode through the phosphothreonine lyase OspF.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 562 Downloadable Samples
- Illumina HiSeq 2500
Description
RNA-seq experiment on five mouse brain regions-- --comparing expression in virgin females to primiparous females three weeks after pup weaning. For each brain region there are 8 replicates, though three samples were not used in the final analysis based on inspection of PCA plots (1 sample from the Hippocampus, Cerebellum and Amygdala data sets; see details below). Overall design: Comparison of gene expression in five brain regions between eight virgin and eight primiparous females three weeks after pup weaning. Pair-wise comparisons were performed using EdgeR transformed data and Limma Voom for statistical analysis.
Publication Title
Maternal Experience Leads to Lasting Gene Expression Changes in Some Regions of the Mouse Brain.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples