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GSE22986
Homo sapiens
18 Downloadable Samples
Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
The outcome of infections with Toxoplasma gondii in humans is dependent in part on the genetic makeup of the infecting organism. Recent studies have indicated that most infecting Toxoplasma organisms fall into 1 of 3 canonical lineages. Previous studies have investigated the effects of Toxoplasma on its host cell transcriptome. Little is known, however, about the effects of three canonical lineages on brain cells, the principal site of parasite lifelong persistence. In this study, we examined the transcriptional profile of human neuroepithelioma cells in response to T. gondii infection using microarray analysis to characterize the strain-specific host cell response to 3 canonical T. gondii strains. We found that the extent of the expression changes varied considerably among the three strains. Neuroepithelial cells infected with type I exhibited the most differential gene expression, whereas type II infected cells had a substantially smaller number of genes which were differentially expressed. Cells infected with type III exhibited intermediate effects on gene expression. The three strains also differed in the individual genes and gene pathways which were altered following cellular infection. For example, gene ontology (GO) analysis indicated that type I infection largely affects genes related to central nervous system while type III infection largely alters genes which affect nucleotide metabolism; type II infection does not alter expression of a clearly defined set of genes. Moreover, Ingenuity pathway analysis (IPA) revealed the sophistication of different strain in its interactions with the host. These differences may explain some of the variation in the neurobiological effects of different strains of Toxoplasma on infected individuals.
Publication Title
Differential effects of three canonical Toxoplasma strains on gene expression in human neuroepithelial cells.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 23 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
Human mucosal surfaces contain a wide range of microorganisms. The biological effects of these organisms are largely unknown. Large-scale metagenomic sequencing is emerging as a method to identify novel microbes. Unexpectedly, we identified DNA sequences homologous to virus ATCV-1, an algal virus not previously known to infect humans, in oropharyngeal samples obtained from healthy adults. The presence of ATCV-1 was associated with a modest but measurable decrease in cognitive functioning. A relationship between ATCV-1 and cognitive functioning was confirmed in a mouse model, which also indicated that exposure to ATCV-1 resulted in changes in gene expression within the brain. Our study indicates that viruses in the environment not thought to infect humans can have biological effects.
Publication Title
Chlorovirus ATCV-1 is part of the human oropharyngeal virome and is associated with changes in cognitive functions in humans and mice.
Sample Metadata Fields
Treatment
View Samples- Rattus norvegicus
- 12 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
To study the molecular mediators of naturally rewarding effects of palatable food we used a model of palatable snacking (Ulrich-Lai et al., 2007) in which rats are given chronic, brief access to a limited amount of sucrose solution (30%). Single housed, male Long-Evans rats (250g) (n=12 per group) from Harlan Labs (Indianapolis, IN) received normal rat chow (Harlan Teklad) and water ad libitum for the duration of the experiment. After a one-week period of acclimation, rats were randomly assigned to drink treatment groups of either 30% sucrose solution or water. Rats received a 14-day regimen of twice daily (9:30 and 15:30) brief (maximum of 30 minutes) limited (up to 4 mL) access of their assigned drink solution. Drink solutions were delivered via a graduated sipper placed onto the cage top in addition to the existing water bottle and sippers were immediately removed when the animal had consumed 4mL or after the 30-minute access period, whichever occurred first. Drink intake, food intake, and body weight were monitored throughout the experiment to verify that the rats learned to drink sucrose, that they adjusted chow intake for calories consumed from sucrose (~10%), and that there was no effect on body weight gain as is normally seen with this model (Ulrich-Lai et al., 2007). Drink treatment terminated on day 14 and at 8:00 on the morning of day 15, the rats were sacrificed by rapid decapitation. BLA tissue was dissected, RNA extracted, and gene expression changes between water and sucrose groups were accessed by microarray.
Publication Title
Pleasurable behaviors reduce stress via brain reward pathways.
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples- Rattus norvegicus
- 20 Downloadable Samples
- Affymetrix Rat Clariom S Assay (clariomsrat)
Description
Vocal cord healing is a dynamic process, and many genes and proteins are involved, which play varying roles at different regeneration stages after injury. Previous studies have shown that inflammatory responses occur at the early stage of vocal cord injury, where the fibroblasts proliferate exuberantly with intensive secretion and deposition of ECM. These activities reach the peak at 3-7 days and their intensity begins to decline 15 days later. A study based on the dermal system has shown that ECM remodeling during the repair of injury can last for several months. However, few studies have been conducted as to the dynamic changes of gene expressions and signaling pathway during the healing process of vocal cord injury. Plotting these changes will facilitate the understanding about the physiological changes during healing and the identification of key time points and target genes in fibrosis formation.
Publication Title
Prolactin may serve as a regulator to promote vocal fold wound healing.
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples- Mus musculus
- 29 Downloadable Samples
Illumina HiSeq 2500
Description
Genetically engineered mouse models (GEMM) of cancer are powerful tools to study multiple aspects of caner biology. We developed a novel GEMM for lung squamous cell carcinoma (LSCC) by genetically combining overexpression of Sox2 with loss of Lkb1: Rosa26LSL-Sox2-IRES-GFP;Lkb1fl/fl (SL). We compared gene expression profiles of SL lung tumors with normal mouse lung tissue, mouse lung adenocarcinoma (LADC) tumors from KrasLSL-G12D/+;Trp53fl/fl (KP), mouse LSCC tumors from Lkb1fl/fl;Ptenfl/fl (LP) model as well as Lenti-Sox2-Cre Lkb1fl/fl. Overall design: Tumors were isolated from formalin-fixed paraffin-embedded (FFPE) tissue samples by microdissection and nucleic acid isolation was performed followed by single-read or paired-end RNA sequencing.
Publication Title
The Lineage-Defining Transcription Factors SOX2 and NKX2-1 Determine Lung Cancer Cell Fate and Shape the Tumor Immune Microenvironment.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 2 Downloadable Samples
- Illumina HiSeq 2500
Description
Tumor-associated neutrophils (TANs) can be conditioned to become “N2” pro-tumorigenic neutrophils in the tumor microenvironment. TANs have been shown to acquire N2 features and promote multiple aspects of tumor growth in mouse models of many cancers, including non-small cell lung cancer. We developed a novel mouse model for lung squamous cell carcinoma (LSCC): Rosa26LSL-Sox2-IRES-GFP;Nkx2-1fl/fl;Lkb1fl/fl (SNL). SNL mice develop tumors with short latency of ~3 months and SNL tumors have high neutrophil infiltration similar to other LSCC mouse models. We employed this novel model and single-cell RNA-sequencing to profile TANs in SNL lung tumors in comparison to peripheral blood neutrophils (PBNs) from tumor-bearing SNL mice. Overall design: Flow cytometry sorted neutrophils (CD45+CD11B+LY6G+) from freshly isolated SNL lung tumors or peripheral blood from tumor-bearing mice were single-cell RNA sequenced with 10X Genomics.
Publication Title
The Lineage-Defining Transcription Factors SOX2 and NKX2-1 Determine Lung Cancer Cell Fate and Shape the Tumor Immune Microenvironment.
Sample Metadata Fields
Specimen part, Subject
View Samples- Drosophila melanogaster, Drosophila santomea, Drosophila yakuba, Drosophila sechellia, Drosophila simulans, Drosophila teissieri, Drosophila mauritiana
- 3 Downloadable Samples
- Affymetrix Drosophila Genome Array (drosgenome1)
Description
Co-expression of genes that physically cluster together is a common characteristic of eukaryotic transcriptomes. Identifying these groups of co-expressed genes is important to the functional annotation of genomes and understanding the evolutionary fates of the clustered genes.
Publication Title
Coordinated evolution of co-expressed gene clusters in the Drosophila transcriptome.
Sample Metadata Fields
No sample metadata fields
View Samples- Macaca mulatta
- 10 Downloadable Samples
- Affymetrix Human Genome U133A Array (hgu133a)
Description
Nuclei of the mammalian thalamus are aggregations of neurons with unique architectures and input-output connections, yet the molecular determinants of their organizational specificity remain unknown. By comparing expression profiles of thalamus and cerebral cortex in adult rhesus monkeys we identified transcripts that are unique to dorsal thalamus or to individual nuclei within it. Real-time quantitative polymerase chain reaction and in situ hybridization analyses confirmed the findings. Expression profiling of individual nuclei microdissected from the dorsal thalamus revealed additional subsets of nucleus-specific genes. Functional annotation using Gene Ontology (GO) vocabulary and Ingenuity Pathway analysis revealed over-representation of GO categories related to development, morphogenesis, cell-cell interactions, and extracellular matrix within the thalamus- and nucleus-specific genes-many involved in the Wnt signaling pathway. Examples included the transcription factor TCF7L2, localized exclusively to excitatory neurons, a calmodulin-binding protein PCP4, the bone extracellular matrix molecules SPP1 and SPARC, and other genes involved in axon outgrowth and cell matrix interactions. Other nucleus-specific genes such as CBLN1 are involved in synaptogenesis. The genes identified likely underlie nuclear specification, cell phenotype and connectivity during development and their maintenance in the adult thalamus.
Publication Title
Nucleus- and cell-specific gene expression in monkey thalamus.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 7 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The skin is a protective barrier against external insults and any lesion must be rapidly and efficiently repaired. Dermal fibroblasts are the major source of extracellular connective tissue matrix and play an important role in wound healing. Vitamin C is an important water-soluble free radical scavenger and an essential cofactor for collagen synthesis by dermal fibroblasts and, consequently, may contribute to the maintenance of healthy skin. Using microarray analysis, we investigated the effects of long-term exposure to a stable vitamin C derivative, ascorbic acid 2-phosphate (AA2P), in contact-inhibited populations of primary human dermal fibroblasts. Compared with "scorbutic" cells, cells exposed to AA2P increased the expression of genes associated with DNA replication and repair and with the G(2)/M phase of the cell cycle. Consistent with the gene expression changes, AA2P increased the mitogenic stimulation of quiescent fibroblasts by serum factors and cell motility in the context of wound healing. Furthermore, AA2P-treated fibroblasts showed faster repair of oxidatively damaged DNA bases. We propose that vitamin C may protect the skin by promoting fibroblast proliferation, migration, and replication-associated base excision repair of potentially mutagenic DNA lesions, and we discuss the putative involvement of hypoxia-inducible transcription factor-1 and collagen receptor-related signaling pathways.
Publication Title
Gene expression profiling reveals new protective roles for vitamin C in human skin cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Glycine max
- 8 Downloadable Samples
- Illumina HiSeq 2000, Illumina Genome Analyzer II
Description
In a previous study, seed coat and cotyledon tissues of Williams, Richland and T157 soybean lines were investigated to show tissue specificity of CHS siRNA expression (Tuteja et al., 2009). Here, we investigated more tissues such as leaf, root and germinating cotyledon to ascertain the tissue specificity of CHS siRNAs in Williams. Data from multiple small RNA libraries were sequenced deeply by the Illumina high-throughput sequencing technology. The total numbers of small RNA reads were from three million to thirty million, providing sufficient data to show the tissue specificity of CHS siRNA. Overall design: High-throughput sequencing using Genome Analyzer II and Illumina HiSeq 2000 was performed.
Publication Title
The transition from primary siRNAs to amplified secondary siRNAs that regulate chalcone synthase during development of Glycine max seed coats.
Sample Metadata Fields
Subject
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