publication_authors:Simonato F Results

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Microarray (444)

Rna-seq (16)

Platform

Affymetrix Mouse Genome 430 2.0 Array (mouse4302) (444)

IlluminaNovaSeq6000 (16)

Includes Publication (16)

GSE39807

Gene and microRNA expression data from tumor induced CD11b+ MDSC

Mus musculus
17 Downloadable Samples

Description

Tumor growth is associated with a profound alteration of myelopoiesis, leading to recruitment of immunosuppressive cells known as myeloid-derived suppressor cells (MDSCs). Immuno-regulatory activity of both tumor-induced and BM-derived MDSCs (by GM-CSF and IL-6 treatment) was entirely dependent on C/EBP transcription factor (TF), a key component of the emergency myelopoiesis triggered by stress and inflammation. We used miR expression analysis to identify miRs which could drive MDSC recruitment/generation/activity by modulating specific TFs and pathway. In particular, we identified a miR signature of 79 miR differentially expressed between not suppressive CD11b+ cells and CD11b+ isolated from tumor mass and spleen of tumor-bearing mice. Moreover on the same samples we profiled gene expression with Affymetrix microarrays to perform an integrated analysis of mirna and gene expression.

Publication Title

miR-142-3p prevents macrophage differentiation during cancer-induced myelopoiesis.

Sample Metadata Fields

Specimen part, Disease, Disease stage, Cell line

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GSE36688

Expression data from sorted interfollicular basal cells (alpha6 integrin-high/CD34-neg) from K14CREER and InvCREER/RosaYFP induced mice

Mus musculus
4 Downloadable Samples

Description

The skin interfollicular epidermis (IFE) is the first barrier against the external environment and its maintenance is critical for survival. Two seemingly opposite theories have been proposed to explain IFE homeostasis. One posits that IFE is maintained by a long-lived slow-cycling stem cell (SC) population that give rise to short-lived transit-amplifying (TA) cell progeny, while the other suggests that homeostasis is achieved by a single committed progenitor (CP) that balances stochastic fate. Here, we probed the cellular heterogeneity within the IFE using two different inducible CREER targeting IFE progenitors. Quantitative analysis of clonal fate data and proliferation dynamics demonstrate the existence of two distinct proliferative cell compartments composed of slow-cycling SC and CP, both of which undergo population asymmetric self-renewal. However, following wounding, only SCs contribute substantially to the repair and long-term regeneration of the tissue, while CP cells make a minimal and transient contribution.

Publication Title

Distinct contribution of stem and progenitor cells to epidermal maintenance.

Sample Metadata Fields

Specimen part

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GSE32529

Mouse ischemic tolerance genomic analysis of the brain and blood.

Mus musculus
218 Downloadable Samples

Description

Ischemic tolerance can be induced by numerous preconditioning stimuli, including various Toll-like receptor (TLR) ligands. We have shown previously that systemic administration of the TLR4 ligand, lipopolysaccharide (LPS) or the TLR9 ligand, unmethylated CpG ODNs prior to transient brain ischemia in mice confers substantial protection against ischemic damage. To elucidate the molecular mechanisms of preconditioning, we compared brain and blood genomic profiles in response to preconditioning with these TLR ligands and to preconditioning via exposure to brief ischemia.

Publication Title

Multiple preconditioning paradigms converge on interferon regulatory factor-dependent signaling to promote tolerance to ischemic brain injury.

Sample Metadata Fields

Specimen part, Treatment

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GSE15452

Expression data from lung of mice bearing mutations of FGFR3 and FGFR4

Mus musculus
26 Downloadable Samples

Description

Gene expression profiling of newborn lung tissue revealed few changes in compound FGFR3/FGFR4 deficient mice, consistent with their normal lung morphology at birth, suggesting the sequence of events leading to the phenotype initiates after birth in this model.

Publication Title

Fibroblast growth factor receptors control epithelial-mesenchymal interactions necessary for alveolar elastogenesis.

Sample Metadata Fields

Age, Specimen part

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SRP348786

Combined intermittent and sustained hypoxia is a novel and deleterious cardio-metabolic phenotype

Mus musculus
16 Downloadable Samples
Illumina NovaSeq 6000

Description

Study objectives: Chronic obstructive pulmonary disease and obstructive sleep apnea overlap syndrome is associated with excess mortality, and outcomes are related to the degree of hypoxemia. People at high altitude are susceptible to periodic breathing, and hypoxia at altitude is associated with cardio-metabolic dysfunction. Hypoxemia in these scenarios may be described as superimposed sustained plus intermittent hypoxia, or overlap hypoxia (OH), the effects of which have not been investigated. We aimed to characterize the cardio-metabolic consequences of OH in mice. Methods: C57BL/6J mice were subjected to either sustained hypoxia (SH, FiO2=0.10), intermittent hypoxia (IH, FiO2=0.21 for 12 hours, and FiO2 oscillating between 0.21 and 0.06, 60 times/hour, for 12 hours), OH (FiO2=0.13 for 12 hours, and FiO2 oscillating between 0.13 and 0.06, 60 times/hour, for 12 hours), or room air (RA), n=8/group. Blood pressure and intraperitoneal glucose tolerance test were measured serially, and right ventricular systolic pressure (RVSP) was assessed. Results: Systolic blood pressure transiently increased in IH and OH relative to SH and RA. RVSP did not increase in IH, but increased in SH and OH by 52% (p<0.001) and 20% (p=0.001). Glucose disposal worsened in IH and improved in SH, with no change in OH. Serum LDL and VLDL increased in OH and SH, but not in IH. Hepatic oxidative stress increased in all hypoxic groups, with the highest increase in OH. Conclusions: Overlap hypoxia may represent a unique and deleterious cardio-metabolic stimulus, causing systemic and pulmonary hypertension, and without protective metabolic effects characteristic of sustained hypoxia. Overall design: Whole liver mRNA profiles of C57BL/6J mice exposed to RA, SH, IH, or OH.

Publication Title

Combined intermittent and sustained hypoxia is a novel and deleterious cardio-metabolic phenotype.

Sample Metadata Fields

Age, Specimen part, Genotype, Treatment, Subject

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GSE19169

Jumonji modulates Polycomb activity and self-renewal versus differentiation of stem cells

Mus musculus
30 Downloadable Samples

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Jumonji modulates polycomb activity and self-renewal versus differentiation of stem cells.

Sample Metadata Fields

Specimen part

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GSE19165

Microarray profiling analysis in Jmj-Fl/Fl and Jmj-null ESCs.

Mus musculus
30 Downloadable Samples

Description

We used microarrays to detail the role of JMJ in ES cell function.

Publication Title

Jumonji modulates polycomb activity and self-renewal versus differentiation of stem cells.

Sample Metadata Fields

Specimen part

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GSE5891

Nuclear organization of active and inactive chromatin domains revealed by 4C technology

Mus musculus
6 Downloadable Samples

Description

The spatial organization of DNA in the cell nucleus is an emerging key contributor to genomic function. We have developed 4C technology, or 3C-on-chip, which allows for an unbiased genome-wide search for DNA loci that contact a given locus in the nuclear space. We demonstrate here that active and inactive genes are engaged in many long-range intrachromosomal interactions and can also form interchromosomal contacts. The active b-globin locus in fetal liver contacts mostly transcribed, but not necessarily tissue-specific, loci elsewhere on chromosome 7, while the inactive locus in fetal brain contacts different, transcriptionally silent, loci. A housekeeping gene in a gene dense region on chromosome 8 forms long-range contacts predominantly with other active gene clusters, both in cis and in trans, and many of these intra- and interchromosomal interactions are conserved between the tissues analyzed. Our data demonstrate that chromosomes fold into areas of active chromatin and areas of inactive chromatin and establish 4C technology as a powerful tool to study nuclear architecture.