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Mus musculus
4 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Microarray Analyses of Newborn Mouse lens lacking HSF4. Hsf4 is essential for lens development.
Publication Title
No associated publication
Alternate Accession IDs
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 18 Downloadable Samples
- Affymetrix Human Gene Expression Array (primeview)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Dynamic changes in global microRNAome and transcriptome reveal complex miRNA-mRNA regulated host response to Japanese Encephalitis Virus in microglial cells.
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Cell line, Treatment, Time
View Samples- Pseudomonas aeruginosa
- 2 Downloadable Samples
NextSeq 500
Description
We undertook to validate the therapeutic use of a polyherbal preparation described in Ayurved as ‘Panchvalkal’, which has been suggested for treatment of microbial infections. We tested this formulation available in market as Pentaphyte P-5®, against Pseudomonas aeruginosa, for its quorum sensing (QS) modulatory potential. Following demonstration of its in vitro QS modulatory potential, we assayed it for in vivo efficacy using the nematode Caenorhabditis elegans as a model host. This polyherbal formulation conferred notable survival benefit when the nematode worm was challenged with the test pathogen. Todecipher the molecular basis of its efficacy, whole transcriptome analysis of P. aeruginosa exposed to ‘Panchvalkal’ was done, its gene expression profile inpresence of ‘Panchvalkal’ was compared with that in its absence. This polyherbal formulation also enhanced the susceptibility of P. aeruginosa to antibiotics like gentamicin, tetracycline, and cephalexin. This study is a good demonstration of the role of bacterial QS machinery as an important target for development of new antimicrobials/ anti-infectives, and also of the effective use of moderngenomics for validation of ayurvedic prescriptions i.e. ayuromics.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Specimen part, Disease
View Samples- Homo sapiens
- 279 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Gene expression analysis was conducted using a GeneChip Human Genome U133(HGU133A & B) array with more than 39,000 transcripts
Publication Title
No associated publication
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 224 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
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.
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Treatment
View Samples
GSE58331- Homo sapiens
- 168 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Diagnosis of inflamed human orbit tissue with standard clinical and histopathology evaluation data is imprecise. A large number of these patients are diagnosed with the catch-all classification of nonspecific orbital inflammation (NSOI).
Publication Title
Orbital pseudotumor can be a localized form of granulomatosis with polyangiitis as revealed by gene expression profiling.
Alternate Accession IDs
Sample Metadata Fields
Sex, Specimen part, Disease
View Samples- Homo sapiens
- 53 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We hypothesized that patients with sarcoidosis have characteristic mRNA profiles. Microarray analysis of gene expression was done on peripheral blood. Comparing peripheral blood from patients with sarcoidosis to controls, 872 transcripts were upregulated and 1039 were downregulated at >1.5-fold change and a significant q value. Several transcripts associated with interferon and STAT1 were upregulated. Lung and lymph node analyses also showed dramatic increases in STAT1 and STAT1-regulated chemokines. Granulomas in lymph nodes of patients with sarcoidosis expressed abundant STAT1 and phosphorylated STAT1. STAT1 might play an important role in sarcoidosis. This novel hypothesis unites seemingly disparate observations with regard to sarcoidosis including implication of a casual role for interferons, a suspected infectious trigger, TH1 predominating lymphocytes in bronchoalveolar lavage, and the association with hypercalcemia.
Publication Title
Insights in to the pathogenesis of axial spondyloarthropathy based on gene expression profiles.
Alternate Accession IDs
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Disease stage
View Samples- Homo sapiens
- 45 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Diagnosis of inflamed human lacrimal gland with standard clinical and histopathology evaluation data is imprecise. A large number of these patients are diagnosed with the catch-all classification of nonspecific orbital inflammation (NSOI).
Publication Title
Gene Expression Profiling and Heterogeneity of Nonspecific Orbital Inflammation Affecting the Lacrimal Gland.
Alternate Accession IDs
Sample Metadata Fields
Sex, Specimen part, Disease
View Samples- Rattus norvegicus
- 46 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Gene expression along the crypt-villus (C-V) axis was analyzed using cryostat sectioning to isolate fractions representing the crypts (bottom) and villus tops (top). These fractions were used for analyzing gene expression in iron replete Wistar rats (++), iron deficient Wistar rats (low iron), and in iron deficient Wistar rats fed iron for 3 and 6 days (iron-fed). Differences were observed between the crypts and villus tops in the expression of genes associated with Wnt and BNP signaling, cell proliferation and apoptosis, lipid and iron transport and metabolism. Gene expression in villus crypts and tops was also compared between Wistar and Belgrade rats (bb) and Belgrade rats fed iron (iron-fed) particularly as related to iron absorption and metabolism to define the affects of the mutation in DMT1 in the Belgrade rat on the expression of genes related to iron absorption and metabolism and the response to iron feeding.
Publication Title
Hypoxia-inducible factor-2α and iron absorptive gene expression in Belgrade rat intestine.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 20 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
C57BL/6J (B6) and DBA/2J (D2) are two of the most commonly used inbred mouse strains in neuroscience research. However, the only currently available mouse genome is based entirely on the B6 strain sequence. Subsequently, oligonucleotide microarray probes are based solely on this B6 reference sequence, making their application for gene expression profiling comparisons across mouse strains dubious due to their allelic sequence differences, including single nucleotide polymorphisms (SNPs). The emergence of next-generation sequencing (NGS) and the RNA-Seq application provides a clear alternative to oligonucleotide arrays for detecting differential gene expression without the problems inherent to hybridization-based technologies. Using RNA-Seq, an average of 22 million short sequencing reads were generated per sample for 21 samples (10 B6 and 11 D2), and these reads were aligned to the mouse reference genome, allowing 16,183 Ensembl genes to be queried in striatum for both strains. To determine differential expression, 'digital mRNA counting' is applied based on reads that map to exons. The current study compares RNA-Seq (Illumina GA IIx) with two microarray platforms (Illumina MouseRef-8 v2.0 and Affymetrix MOE 430 2.0) to detect differential striatal gene expression between the B6 and D2 inbred mouse strains. We show that by using stringent data processing requirements differential expression as determined by RNA-Seq is concordant with both the Affymetrix and Illumina platforms in more instances than it is concordant with only a single platform, and that instances of discordance with respect to direction of fold change were rare. Finally, we show that additional information is gained from RNA-Seq compared to hybridization-based techniques as RNA-Seq detects more genes than either microarray platform. The majority of genes differentially expressed in RNA-Seq were only detected as present in RNA-Seq, which is important for studies with smaller effect sizes where the sensitivity of hybridization-based techniques could bias interpretation.
Publication Title
Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays.
Alternate Accession IDs
Sample Metadata Fields
Sex, Specimen part
View Samples