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GSE102403
Mus musculus
9 Downloadable Samples
Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
Previous in vitro studies in our lab have shown that CD24, a cell surface receptor, actively regulates lipid accumulation in adipocytes. But how CD24 regulates this process remains unknown. In order to answer this question, we initially tested to determine if CD24 regulates lipid accumulation by regulating glucose uptake in adipocytes in vitro. We observed that instead, CD24 caused the dysregulation of the expression of 134 genes as determined by DNA microarray analysis. We then validated the expression of select four genes, when CD24 is knocked down during the different stages of adipogenesis in 3T3-L1 pre-adipocytes in vitro. To further confirm the role of these genes, we then determined the expression patterns of these four genes in primary cells undergoing adipogenesis that were isolated from the epididymal and inguinal white adipose tissue depots of CD24 knockout mice. Surprisingly, we found that these genes were dysregulated in the inguinal but not the epididymal depot in vitro. Overall, the data presented here suggests that CD24 is necessary for select gene expression, but not glucose uptake, during adipogenesis in vitro.
Publication Title
CD24 is required for regulating gene expression, but not glucose uptake, during adipogenesis.
Sample Metadata Fields
Cell line
View Samples- Glycine max
- 4 Downloadable Samples
Illumina Genome Analyzer II
Description
Sudden death syndrome (SDS) caused by the fungal pathogen, Fusarium virguliforme, is a major threat to soybean production in North America. There are two major components of this disease: (i) root necrosis and (ii) foliar SDS. Root symptoms consist of root necrosis with vascular discoloration that extends upto several nodes and internodes into the stem. Foliar SDS symptom is characterized by interveinal chlorosis and necrosis in leaves which finally curl and fall off, and in severe cases by flower, pod abscission and immature seed formation. A major toxin involved in initiating foliar SDS has been identified. Nothing is known about how root necrosis develops. In order to unravel the mechanisms used by the pathogen to cause root necrosis, the transcriptome of the pathogen in infected soybean root tissues of a susceptible cultivar (Williams 82) was investigated. The transcriptomes of the germinating conidia and mycelia were also examined. Of the 14,845 predicted F. virguliforme genes, we observed that 12,017 (81%) were expressed in germinating conidial spores and 12,208 (82%) in mycelia and 10,626 (72%) in infected soybean roots. Of the 10,626 genes induced in infected roots, 224 were transcribed only following infection. Expression of several infection-induced genes encoding enzymes with oxidation-reduction properties suggests that degradation of antimicrobial compounds such as the phytoalexin, glyceollin could be important in establishing the biotrophic phase. Enzymes with hydrolytic and catalytic activities could play an important role in the transitioning of the pathogen from biotrophic to necrotrophic phase. Expression of a large number of genes encoding enzymes with catalytic and hydrolytic activities during late infection stage suggests cell wall degradation by some of these enzymes could be involved in root necrosis and establishing the necrotrophic phase in this pathogen. Overall design: RNA-seq data for Fusarium virguliforme Mont-1 germinating conidial spores, mycelia and soybean root tissue 3 and 5 days or 10 and 24 days post water incubation or infection with Fusarium virguliforme Mont-1 conidial spores. Raw data for Fusarium virguliforme Mont-1 germinating conidial spores and mycelia are not available due to server failure.
Publication Title
Tanscriptomic Study of the Soybean-Fusarium virguliforme Interaction Revealed a Novel Ankyrin-Repeat Containing Defense Gene, Expression of Whose during Infection Led to Enhanced Resistance to the Fungal Pathogen in Transgenic Soybean Plants.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 8 Downloadable Samples
- IlluminaHiSeq2000
Description
Functional and structural dysfunction of the blood brain barrier (BBB) leads to severe alterations in brain physiology and is believed to trigger neurodegeneration. To investigate the molecular mechanisms driving the BBB dysfunction, very few human BBB cell culture models are available; of which, the human microvascular endothelial cell line (hCMEC/D3) is the most widely used. Thus far, array-based approaches or targeted seqeuncing based approaches have been employed to characterize the gene expression of the hCMEC/D3 model. However,The goal of this study is to perform deep transcriptomic sequencing of the BBB cell line and obtain features like gene expression, expressed single nucleotide variants, alternate splice forms, circular RNAs, long non-coding RNAs and micro RNAs. Overall design: We have developed blood brain barriers transcriptomics landscape using RNA sequencing and micro RNA seqeuncing data obtained from replicates of hCMEC/D3 BBB cell line.
Publication Title
BBBomics-Human Blood Brain Barrier Transcriptomics Hub.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
IL-27 treated DCs were shown to be highly potent inhibitors of cis HIV-1, particularly of CCR5 tropic strains. Microarray studies of IL-27 treated DCs showed no up-regulation of Type I (IFN) gene expression. Neutralization of the Type-I IFN receptor had no impact on the HIV inhibition. Lastly, IL-27 mediated inhibition was shown to act post-viral entry and prior to completion of reverse transcription. These results show for the first time that IL-27 is a potent inhibitor of cis HIV-1 infection in DCs by a Type I IFN independent mechanism.
Publication Title
Interleukin-27 is a potent inhibitor of cis HIV-1 replication in monocyte-derived dendritic cells via a type I interferon-independent pathway.
Sample Metadata Fields
Treatment
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Interleukin-27 treated human macrophages induce the expression of novel microRNAs which may mediate anti-viral properties.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
In this study, we hypothesized that IL-27 could induce the expression of novel miRNAs in macrophages which may have functional relevance in terms of anti-viral activity. In this study, primary monocytes were differentiated into macrophages using M-CSF (M-Mac) or with a combination of M-CSF and IL-27 (I-Mac) for seven days. Following this, total RNA was extracted from these cells and deep sequencing was performed, in parallel with gene expression microarrays. Using the novel miRNA discovery software, miRDeep, seven novel miRNAs were discovered in the macrophages, four of which were expressed higher in I-Mac (miRNAs 2.1, 8.1, 9.1 and 14.2) whilst three were detected in both M-Mac and I-Mac (miRNAs 9.3, 13.6 and 15.8). The expression of six of the seven novel miRNAs was highly correlated with qRT-PCR using specific primer/probes designed for the novel miRNAs. Gene expression microarray further demonstrated that a number of genes were potentially targeted by these differentially expressed novel miRNAs.
Publication Title
Interleukin-27 treated human macrophages induce the expression of novel microRNAs which may mediate anti-viral properties.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 4 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
In this study, we hypothesized that IL-27 could induce the expression of novel miRNAs in macrophages which may have functional relevance in terms of anti-viral activity. In this study, primary monocytes were differentiated into macrophages using M-CSF (M-Mac) or with a combination of M-CSF and IL-27 (I-Mac) for seven days. Following this, total RNA was extracted from these cells and deep sequencing was performed, in parallel with gene expression microarrays. Using the novel miRNA discovery software, miRDeep, seven novel miRNAs were discovered in the macrophages, four of which were expressed higher in I-Mac (miRNAs 2.1, 8.1, 9.1 and 14.2) whilst three were detected in both M-Mac and I-Mac (miRNAs 9.3, 13.6 and 15.8). The expression of six of the seven novel miRNAs was highly correlated with qRT-PCR using specific primer/probes designed for the novel miRNAs. Gene expression microarray further demonstrated that a number of genes were potentially targeted by these differentially expressed novel miRNAs. Overall design: screening novel and known miRNAs which may have antiviral properties in 2 different treatments in 2 donors.
Publication Title
Interleukin-27 treated human macrophages induce the expression of novel microRNAs which may mediate anti-viral properties.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
In order to investigate the function of Bach2 in pre-B ALL, we isolated bone marrow cells from wildtype and Bach2 knockout mice of C57Bl6 background and transformed them with BCR-ABL1.
Publication Title
Mechanistic rationale for targeting the unfolded protein response in pre-B acute lymphoblastic leukemia.
Sample Metadata Fields
Age, Specimen part, Disease, Disease stage, Treatment
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Mechanistic rationale for targeting the unfolded protein response in pre-B acute lymphoblastic leukemia.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
The plasma cell transcription factor XBP1 is critical for terminal differentiation of B cells into plasma cells but has no known role at earlier stages of B-cell development. Here we show that XBP1 is not only important during early B-cell development and for survival of pre-B cells but also protects pre-B ALL cells. Among pre-B ALL subset, XBP1 was hypomethylated and highest expressed in the Ph+ ALL subset. Cre-mediated deletion of XBP1 in a mouse model of Ph+ ALL compromised proliferation and viability and prolonged survival of leukemia-bearing mice. Interestingly, XBP1 expression levels were positively transcriptionally regulated by STAT5 and negatively by BACH2 and BCL6. High XBP1 expression in high risk ALL patients at the time of diagnosis predicted poor outcome in two clinical trials. Clinically, small-molecule inhibition of IRE1-dependent XBP1-activation caused cell death of patient-derived pre-B ALL cells and affected leukemia-initiation in transplant recipient mice. Collectively, these studies identify XBP1 as an important survival factor and as a potential therapeutic target to overcome drug-resistance in pre-B ALL. Overall design: Genome-wide profiling of mRNA levels in p210 transduced murine Xbp1 fl/+ pre-B cells with ERT2 (XE.1,2,3) and Cre- ERT2 Â (XC.1,2,3).
Publication Title
Mechanistic rationale for targeting the unfolded protein response in pre-B acute lymphoblastic leukemia.
Sample Metadata Fields
No sample metadata fields
View Samples