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Mus musculus
7 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
NF-κB inhibition rescues cardiac function by remodeling calcium genes in a Duchenne muscular dystrophy model.
Sample Metadata Fields
Age
View Samples- Mus musculus
- 7 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
We found genetic deletion of IKK in mdx cardiomyocytes improved cardiac function and normalized calcium transients. We used microarrays to profile gene expression in hearts of mdx mice with intact IKK signaling and hearts of mdx mice with IKK-deficient cardiomyocytes to identify genes differentially regulated by NF-[kappa]B. signaling in dystrophic hearts.
Publication Title
NF-κB inhibition rescues cardiac function by remodeling calcium genes in a Duchenne muscular dystrophy model.
Sample Metadata Fields
Age
View Samples- Homo sapiens
- 18 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
The main objective of this study is to identify the list of genes differentially expressed between infected with Leishmania braziliensis and non-infected macrophage cultures based on gene expression microarray profiling
Publication Title
Changes in Macrophage Gene Expression Associated with Leishmania (Viannia) braziliensis Infection.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 24 Downloadable Samples
Illumina HiSeq 2500
Description
Oral tolerance prevents pathological inflammatory responses towards innocuous foreign antigens via peripheral regulatory T cells (pTreg cells). However, whether a particular subset of antigen-presenting cells (APCs) is required during dietary antigen exposure to instruct naïve CD4+ T cells to differentiate into pTreg cells has not been defined. Using myeloid lineage-specific APC depletion in mice, we found that monocyte-derived APCs are dispensable, while classical dendritic cells (cDCs) are critical for pTreg cell induction and oral tolerance. CD11b¬– cDCs from the gut-draining lymph nodes efficiently induced pTreg cells, and conversely, loss of IRF8-dependent CD11b– cDCs impaired their polarization, although oral tolerance remained intact. These data reveal the hierarchy of cDC subsets in pTreg cell induction and their redundancy during oral tolerance development. Overall design: Four dendritic cell subpopulations from mouse mesenteric lymphnodes were sorted and compared in their gene expression profile
Publication Title
Classical dendritic cells are required for dietary antigen-mediated induction of peripheral T(reg) cells and tolerance.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 24 Downloadable Samples
- Illumina HiSeq 2500
Description
Oral tolerance prevents pathological inflammatory responses towards innocuous foreign antigens via peripheral regulatory T cells (pTreg cells). However, whether a particular subset of antigen-presenting cells (APCs) is required during dietary antigen exposure to instruct naïve CD4+ T cells to differentiate into pTreg cells has not been defined. Using myeloid lineage-specific APC depletion in mice, we found that monocyte-derived APCs are dispensable, while classical dendritic cells (cDCs) are critical for pTreg cell induction and oral tolerance. CD11b¬– cDCs from the gut-draining lymph nodes efficiently induced pTreg cells, and conversely, loss of IRF8-dependent CD11b– cDCs impaired their polarization, although oral tolerance remained intact. These data reveal the hierarchy of cDC subsets in pTreg cell induction and their redundancy during oral tolerance development. Overall design: Sorted naïve CD45.1 OT-II CD4 T cells were co-cultured with four dendritic cell subpopulations sorted from mouse mesenteric lymphnodes. 24h later OT-II cells were sorted again and compared in their gene expression profile.
Publication Title
Classical dendritic cells are required for dietary antigen-mediated induction of peripheral T(reg) cells and tolerance.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 10 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
The molecular mechanisms underlying the great differences in susceptibility to noise-induced hearing loss (NIHL) exhibited by both humans and laboratory animals are unknown. Using microarray technology, the present study demonstrates that the effects of noise overexposure on the expression of molecules likely to be important to the development of NIHL differ among inbred mice that have distinctive susceptibilities to NIHL including B6.CAST, 129X1/SvJ, and 129S1/SvImJ. The noise-exposure protocol produced, on average, a permanent loss of about 40 dB in sensitivity for auditory brainstem responses in susceptible B6.CAST mice, but no threshold elevations for the two resistant 129S1/SvImJ and 129X1/SvJ substrains. Measurements of noise-induced gene expression changes 6 h after the noise exposure revealed significant alterations in the expression levels of 48 genes in the resistant mice, while by these same criteria, there were seven differentially expressed genes in the susceptible B6.CAST mice. Differentially expressed genes in both groups of mice included subsets of transcription factors. However, only in the resistant mice was there a significant induction of proteins involved in cell-survival pathways such as HSP70, HSP40, p21, GADD45beta, Ier3, and Nf-kappaB. Moreover, increased expression of three of these factors after noise was confirmed at the protein level. Drastically enhanced HSP70, GADD45beta, and p21 immunostaining were detected 6 h after the noise exposure in subsets of cells of the lateral wall, spiral limbus, and organ of Corti as well as in cochlear nerve fibers. Upregulation of these proteins after noise exposure likely contributes to the prevalence of survival cellular pathways and thus to the resistance to NIHL that is characteristic of the 129X1/SvJ mice.
Publication Title
Noise-induced changes in gene expression in the cochleae of mice differing in their susceptibility to noise damage.
Sample Metadata Fields
No sample metadata fields
View Samples
GSE5799- Staphylococcus aureus
- 12 Downloadable Samples
- Affymetrix S. aureus Genome Array (saureus)
Description
A triclosan-ciprofloxacin cross-resistant mutant strain of Staphylococcus aureus displays an alteration in the expression of several cell membrane structural and functional genes.
Publication Title
A triclosan-ciprofloxacin cross-resistant mutant strain of Staphylococcus aureus displays an alteration in the expression of several cell membrane structural and functional genes.
Sample Metadata Fields
No sample metadata fields
View Samples- Anas platyrhynchos, Gallus gallus
- 8 Downloadable Samples
- Affymetrix Chicken Genome Array (chicken)
Description
While infection of chickens with highly pathogenic avian influenza (HPAI) H5N1 subtypes often leads to complete mortality within 24 to 48 h, infection of ducks in contrast causes mild or no clinical signs. Rapid onsets of fatal disease in chickens, but with no evidence of severe clinical symptoms in ducks, suggest underlying differences in their innate immune mechanisms. To understand the molecular basis for such difference, chicken and duck primary lung cells, infected with a low-pathogenicity avian influenza (LPAI) and two HPAI H5N1 viruses, were subjected to RNA expression profiling using Affymetrix Chicken GeneChip arrays.
Publication Title
Highly pathogenic avian influenza virus infection in chickens but not ducks is associated with elevated host immune and pro-inflammatory responses.
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Homo sapiens
- 10 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
For the anucleate platelet it has been unclear how well platelet transcriptomes correlate among different donors or across different RNA profiling platforms, and what the transcriptomes relationship is with the platelet proteome. We generated RNA-seq pro-files of the long RNA transcriptomes from the platelets of 10 healthy young males (5 white and 5 black) with median age of 24.5 years, no notable clinical history, and no pre-vious history of thrombosis or bleeding. We also profiled the subjects messenger RNAs using the Affymetrix microarray gene expression system. We found that the abundance of platelet mRNA transcripts was highly correlated across the 10 individuals, inde-pendently of race and of the employed technology. Our RNA-seq data also showed that these high inter-individual correlations extend beyond mRNAs to several categories of non-coding RNAs. Pseudogenes represented a notable exception to this by exhibiting a clear difference in expression by race. Comparison of our mRNA signatures with the only publicly available quantitative platelet proteome data showed that most (87.5%) identified platelet proteins had a detectable corresponding mRNA. However, a high number of mRNAs that were present in the transcriptomes of all 10 individuals had no representa-tion in the proteome. The Spearman correlation of the relative abundances for those platelet genes that were represented by both an mRNA and a protein showed a weak (~0.3) yet statistically significant (P=5.0E-16) connection. Further analysis of the overlap-ping and non-overlapping platelet mRNAs and proteins identified gene groups corre-sponding to distinct cellular processes, a finding that provides novel insights for platelet biology.
Publication Title
The human platelet: strong transcriptome correlations among individuals associate weakly with the platelet proteome.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 190 Downloadable Samples
- Illumina HiSeq 2500
Description
Airway epithelial cells and macrophages differ markedly in their responses to influenza A virus (IAV) infection. To investigate transcriptional responses underlying these differences, purified subsets of type II airway epithelial cells (ATII) and alveolar macrophages (AM) recovered from the lungs of mock- or IAV-infected mice were subjected to RNA sequencing. In the absence of infection, AM predominantly expressed genes related to immunity whereas ATII expressed genes consistent with their physiological roles in the lung. Following IAV infection, AM almost exclusively activated cell-intrinsic antiviral pathways that were dependent on interferon regulatory factor (IRF)3/7 and/or type I interferon (IFN) signaling. In contrast, IAV-infected ATII activated a broader range of physiological responses, including cell-intrinsic antiviral pathways, which were both independent and dependent on IRF3/7 and/or type I IFN. These data suggest that transcriptional profiles hardwired during development could be a major determinant underlying the different responses of ATII and AM to IAV infection. Overall design: 96 samples were analyzed: (A) 4 replicates of HA+ Alveolar Macrophage (AM) and 4 replicates of CD103+ Dendritic cells (DC) isolated from the lung lobes of C57/BL6 mice on 9 h p.i. with PR8. 4 replicates of mock-infected (HA-) AM and 4 replicates of mock-infected (HA-) CD103+ DC isolated from the lung lobes of mock-infected C57/BL6 mice on 9 h p.i. with allantoic fluid of equal dilution as PR8. 4 replicates of HA+ Airway epithelial cell Type II (ATII) and 4 replicates of HA+ Ciliated Cell (CC) isolated from the lung lobes of C57/BL6 mice on 9 h p.i. with PR8. 4 replicates of mock-infected (HA-) ATII and 4 replicates of mock-infected (HA-) CC isolated from the lung lobes of mock-infected C57/BL6 mice on 9 h p.i. with allantoic fluid of equal dilution as PR8. (B) 4 replicates of HA+ AM and 4 replicates of CD103+ DC isolated from the lung lobes of IFNAR2-/- mice on 9 h p.i. with PR8. 4 replicates of mock-infected (HA-) AM and 4 replicates of mock-infected (HA-) CD103+ DC isolated from the lung lobes of mock-infected IFNAR2-/- mice on 9 h p.i. with allantoic fluid of equal dilution as PR8. 4 replicates of HA+ ATII and 4 replicates of HA+ CC isolated from the lung lobes of IFNAR2-/- mice on 9 h p.i. with PR8. 4 replicates of mock-infected (HA-) ATII and 4 replicates of mock-infected (HA-) CC isolated from the lung lobes of mock-infected IFNAR2-/- mice on 9 h p.i. with allantoic fluid of equal dilution as PR8. (C) 4 replicates of HA+ AM and 4 replicates of CD103+ DC isolated from the lung lobes of IRF3/7-/- mice on 9 h p.i. with PR8. 4 replicates of mock-infected (HA-) AM and 4 replicates of mock-infected (HA-) CD103+ DC isolated from the lung lobes of mock-infected IRF3/7-/- mice on 9 h p.i. with allantoic fluid of equal dilution as PR8. 4 replicates of HA+ ATII and 4 replicates of HA+ CC isolated from the lung lobes of IRF3/7-/- mice on 9 h p.i. with PR8. 4 replicates of mock-infected (HA-) ATII and 4 replicates of mock-infected (HA-) CC isolated from the lung lobes of mock-infected IRF3/7-/- mice on 9 h p.i. with allantoic fluid of equal dilution as PR8.
Publication Title
Unique Transcriptional Architecture in Airway Epithelial Cells and Macrophages Shapes Distinct Responses following Influenza Virus Infection <i>Ex Vivo</i>.
Sample Metadata Fields
Specimen part, Subject
View Samples