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GSE10082
Mus musculus
17 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Conventional biochemical and molecular techniques identified previously several genes whose expression is regulated by the aryl hydrocarbon receptor (AHR). We sought to map the complete spectrum of AHR-dependent genes in male adult liver using expression arrays to contrast mRNA profiles in Ahr-null mice (Ahr/) with those in mice with wild-type AHR (Ahr+/+). Transcript profiles were determined both in untreated mice and in mice treated 19 h earlier with 1000 g/kg 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Expression of 456 ProbeSets was significantly altered by TCDD in an AHR-dependent manner, including members of the classic AHRE-I gene battery, such as Cyp1a1, Cyp1a2, Cyp1b1, and Nqo1. In the absence of exogenous ligand, AHR status alone affected expression of 392 ProbeSets, suggesting that the AHR has multiple functions in normal physiology. In Ahr/ mice, only 32 ProbeSets exhibited responses to TCDD, indicating that the AHR is required for virtually all transcriptional responses to dioxin exposure in liver. The flavin-containing monooxygenases, Fmo2 and Fmo3, considered previously to be uninducible, were highly induced by TCDD in an AHR-dependent manner. The estrogen receptor alpha as well as two estrogen-receptor-related genes (alpha and gamma) exhibit AHR-dependent expression, thereby extending cross-talk opportunities between the intensively studied AHR and estrogen receptor pathways. p53 binding sites are over-represented in genes down-regulated by TCDD, suggesting that TCDD inhibits p53 transcriptional activity. Overall, our study identifies a wide range of genes that depend on the AHR, either for constitutive expression or for response to TCDD.
Publication Title
Aryl hydrocarbon receptor regulates distinct dioxin-dependent and dioxin-independent gene batteries.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 14 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
Study of gene expression patterns of Drosophila melanogaster Sesb1 mutants compared to wild type
Publication Title
Phenotypic rescue of a Drosophila model of mitochondrial ANT1 disease.
Sample Metadata Fields
Sex
View Samples- Homo sapiens
- 35 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The aim of this dataset was to study in detail the transcription kinetics initiated by cytokines IL-12 and IL-4 in early differentiation of Th1 and Th2 cells, respectively.
Publication Title
An integrative computational systems biology approach identifies differentially regulated dynamic transcriptome signatures which drive the initiation of human T helper cell differentiation.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 18 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Recognition and response to gram-positive bacteria by macrophages and dendritic cells is mediated in part through TLR2. We found that that Streptococcus pneumoniae cell wall fragments, containing primarily peptidoglycan and teichoic acids, induced prodigious secretion of IL-10 from macrophages and dendritic cells and was dependent on TLR2 and NOD2, a cytoplasmic CARD-NACHT-LRR protein encoded by Card15. IL-10 secretion in response to cell walls was also dependent on RICK/RIP2, a kinase associated with NOD2, and MYD88 but independent of the ERK/p38 pathway. The reduction of IL-10 secretion by cell wall-activated NOD2-deficient myeloidderived cells translated into downstream effects on IL-10 target gene expression and elevations in subsets of pro-inflammatory cytokine expression normally restrained by autocrine/paracrine effects of IL-10. Since NOD2 is linked to aberrant immune responses in Crohns Disease patients bearing mutations in CARD15, the temporal and quantitative effects of the TLR2/NOD/RICK pathway on IL-10 secretion may affect homeostatic control of immune responses to gram-positive bacteria.
Publication Title
The TLR2-MyD88-NOD2-RIPK2 signalling axis regulates a balanced pro-inflammatory and IL-10-mediated anti-inflammatory cytokine response to Gram-positive cell walls.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 46 Downloadable Samples
- Sentrix Human-6 Expression BeadChip
Description
Special AT-rich binding protein 1 (SATB1) is a global chromatin organizer and a transcription factor induced by interleukin-4 (IL-4) during the early T helper 2 (Th2) cell differentiation. In this study, we investigated the role of SATB1 in T helper cell differentiation by performing gene expression profiling of human differentiating Th cells in which expression of SATB1 was downregulated by RNA interference (RNAi). Our results indicate that SATB1 is involved in the regulation of more than three hundred genes in primary human CD4+ T cells, including several IL-12 and/or IL-4 regulated factors, suggesting a role in the development or function of Th subtypes.
Publication Title
SATB1 dictates expression of multiple genes including IL-5 involved in human T helper cell differentiation.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 42 Downloadable Samples
- Illumina MouseWG-6 v2.0 expression beadchip
Description
The 14-week experiment included three groups: 1) the Acute Cpn group, with one C. pneumoniae inoculation at the age of 9 wks; 2) the Chronic Cpn group, with three C. pneumoniae inoculations at the age of 9, 11, and 13 wks; and 3) the control group, with three SPG inoculations at the age of 9, 11, and 13 wks. The mice were sacrificed at the age of 14 wks. The 24-week experiment included four groups: 1) the recurrent A. actinomycetemcomitans infection group, with ten A. actinomycetemcomitans inoculations once a week from the age of 14 to 23 wks; 2) the chronic C. pneumoniae infection group, with three C. pneumoniae inoculations at the age of 9, 11, and 13 wks; 3) the combined chronic C. pneumoniae and recurrent A. actinomycetemcomitans infection group, with three C. pneumoniae inoculations at the age of 9, 11, and 13 wks, and ten A. actinomycetemcomitans inoculations once a week from the age of 14 to 23 wks; and 4) the control group, with three SPG inoculations at the age of 9, 11, and 13 wks, and ten 0.9% NaCl inoculations once a week from the age of 14 to 23 wks. The mice were sacrificed at the age of 24 wks.Epididymal and inguinal AT gene expression was analyzed using an Illumina Mouse WG-6 v2.0 platform.
Publication Title
The effect of proatherogenic pathogens on adipose tissue transcriptome and fatty acid distribution in apolipoprotein E-deficient mice.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
HMG-CoA reductase inhibitors, statins, have beneficial vascular effects beyond their cholesterol-lowering action. These pleiotropic effects include an anti-inflammatory effect on macrophages. Since macrophages play a central role in atherogenesis, we further characterized the effects on peripheral blood monocyte-macrophages (HPBM). Using Affymetrix gene chip analysis of simvastatin-treated HPBM, we found that simvastatin treatment lead to the downregulation of the expression of many proinflammatory genes including several chemokines (e.g. MCP-1, MIP-1 alpha and , RANTES, several other CC and CXC chemokines, IL-2 receptor-, and leukemia inhibitory factor), members of the tumor necrosis factor family (e.g. lymphotoxin beta and TRAIL), VCAM-1, ICAM-3, and tissue factor (TF). Simvastatin also modulated the expression of several transcription factors essential for the inflammatory response: simvastatin downregulated the expression of NF-kappaB relA/p65 subunit and ets-1 transcription factor, and upregulated the expression of a novel atheroprotective transcription factor, Kruppel-like factor 2 (KLF-2). The effects of simvastatin on KLF-2 and its target genes were dependent on protein prenylation, since inhibitors of protein prenylation had a similar inhibitory effect in THP-1 derived macrophages. Additionally, by lentiviral overexpression KLF-2 we showed that the effect of simvastatin on MCP-1 and TF were dependent on KLF-2. We concluded that simvastatin had a strong anti-inflammatory effect on macrophages, which includes upregulation of the atheroprotective transcription factor KLF-2. These findings further explain the beneficial pleiotropic effects of statins on cardiovascular diseases.
Publication Title
Simvastatin has an anti-inflammatory effect on macrophages via upregulation of an atheroprotective transcription factor, Kruppel-like factor 2.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 9 Downloadable Samples
Ion Torrent Proton
Description
Purpose:To understand the change in cellular metabolism and function for the overxepression of GSTZ1 or PCK1 in hepatoma cells. Methods:Total RNAs of AdGFP- , AdGSTZ1-, or AdPCK1-infected Huh7 cells were extracted using TRIzol (Invitrogen), following the manufacturer's instructions. RNA-seq and bioinformatic data analysis were performed by Shanghai Novel Bio Ltd. Briefly, strand-specific RNA-seq libraries were prepared using the Total RNA-seq (H/M/R) Library Prep Kit (Vazyme Biotech, Nanjing, China) and were sequenced on Ion Torrent Proton sequencing platform. Raw reads in FASTQ format were subjected to quality control using FastQC. RNA-seq reads were aligned to the reference genome using Bowtie. Uniquely mapped reads were used for further analysis. Gene expression levels are expressed as RPKM (reads per kilobase per million reads) and differences in gene expression were calculated with rSeq. Results:There were 498 genes differentially expressed in AdPCK1-infected Huh 7 cells, 513 genes differentially expressed in AdGSTZ1-infected Huh 7 cells compare to the GFP control group respectively (fold change >1.5 or < 0.667; FDR < 0.05). Overall design: mRNA profiles of AdGFP1, AdGSTZ1- or AdPCK1-infected Huh 7 cells were generated by deep sequencing in triplicate, using Ion Torrent Proton sequencing platform.
Publication Title
Transcriptomic changes associated with PCK1 overexpression in hepatocellular carcinoma cells detected by RNA-seq.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 50 Downloadable Samples
- Illumina HumanHT-12 V3.0 expression beadchip
Description
The study aims at identifying transcriptional changes induced by in vitro polarization of human cord blood CD4+ cells towards Th17 subtype with combination of IL6, IL1b and TGFb by using timeseries data.
Publication Title
Identification of early gene expression changes during human Th17 cell differentiation.
Sample Metadata Fields
Specimen part, Time
View Samples- Homo sapiens
- 161 Downloadable Samples
Illumina HumanHT-12 V3.0 expression beadchip, Affymetrix Human Genome U219 Array (hgu219)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Gene expression profiling of immune-competent human cells exposed to engineered zinc oxide or titanium dioxide nanoparticles.
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples