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Hordeum vulgare
18 Downloadable Samples
Affymetrix Barley Genome Array (barley1)
Description
The wheat gene Lr34 (Yr18/Pm38/Sr57/Ltn1) encodes a putative ABCG-type of transporter and is a unique source of disease resistance providing durable and partial resistance against multiple fungal pathogens. Lr34 has been found to be functional as a transgene in barley.
Publication Title
The wheat resistance gene Lr34 results in the constitutive induction of multiple defense pathways in transgenic barley.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Gallus gallus
- 12 Downloadable Samples
- Affymetrix Chicken Genome Array (chicken)
Description
The mycotoxin deoxynivalenol (DON) is a secondary metabolite from Fusarium species and is frequently present on wheat and other cereals. The main effects of DON are a reduction of the feed intake and reduced weight gain of broilers. At the molecular level DON binds to the 60S ribosomal subunit and inhibits subsequently protein synthesis at the translational level. It has been suggested that cells and tissues with high protein turnover rate, like the liver and small intestine, are most affected by DON. However, little is known about other effects of DON e.g. at the transcriptional level. Therefore we decided to perform a microarray analysis, which allows us the investigation of thousands of transcripts in one experiment.
Publication Title
Fusarium mycotoxin-contaminated wheat containing deoxynivalenol alters the gene expression in the liver and the jejunum of broilers.
Alternate Accession IDs
Sample Metadata Fields
Age, Specimen part, Treatment
View Samples- Mus musculus
- 5 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Ptf1a was identified as the essential transcription factor which controls pancreatic exocrine enzyme expression. With lineage tracing eperiments Ptf1a was recognized as an important pancreatic progenitor transcription factor and Ptf1a null mice do not develop a pancreas.
Publication Title
RNA profiling and chromatin immunoprecipitation-sequencing reveal that PTF1a stabilizes pancreas progenitor identity via the control of MNX1/HLXB9 and a network of other transcription factors.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
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GSE972- Mus musculus
- 19 Downloadable Samples
- Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)
Description
Time course of early development of peripheral nerve, from embryonic day 9.5 to postnatal day 0.
Publication Title
Efficient isolation and gene expression profiling of small numbers of neural crest stem cells and developing Schwann cells.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 5 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Regulation of mRNA stability by RNA-protein interactions contributes significantly to quantitative aspects of gene expression. We have identified potential mRNA targets of the AU-rich element binding protein AUF1. Myc-tagged AUF1 p42 was induced in mouse NIH-3T3 cells and RNA-protein complexes isolated using anti-myc tag antibody beads. Bound mRNAs were analyzed with Affymetrix microarrays. We have identified 508 potential target mRNAs that were at least 3-fold enriched compared to control cells without myc-AUF1. 22.3% of the enriched mRNAs had an AU-rich cluster in the ARED Organism database, against 16.3% of non-enriched control mRNAs. The enrichment towards AU-rich elements was also visible by AREScore with an average value of 5.2 in the enriched mRNAs versus 4.2 in the control group. Yet, many mRNAs were enriched without a high ARE score suggesting that AUF1 has a broader binding spectrum than standard AUUUA repeats. AUF1 did not preferentially bind to unstable mRNAs. Still, some enriched mRNAs were highly unstable, as those of TNFSF11 (known as RANKL), KLF10, HES1, CCNT2, SMAD6, and BCL6. We have mapped some of the instability determinants. HES1 mRNA appeared to have a coding region determinant. Detailed analysis of the RANKL and BCL6 3UTR revealed for both that full instability required two elements, which are conserved in evolution. In RANKL mRNA both elements are AU-rich and separated by 30 bases, while in BCL6 mRNA one is AU-rich and 60 bases from a non AU-rich element that potentially forms a stem-loop structure.
Publication Title
Short-lived AUF1 p42-binding mRNAs of RANKL and BCL6 have two distinct instability elements each.
Alternate Accession IDs
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 32 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
Clinical symptoms of dengue virus (DENV) infection, the most prevalent arthropod-borne viral disease, range from classical mild dengue fever to severe, life-threatening dengue shock syndrome. However, most DENV infections cause few or no symptoms. Asymptomatic DENV-infected patients provide a unique opportunity to decipher the host immune responses leading to virus elimination without negative impact on an individuals health. We used an integrated approach of transcriptional profiling and immunological analysis to compare a Cambodian population of strictly asymptomatic viremic individuals with clinical dengue patients. Whereas inflammatory pathways and innate immune response pathways were similar between asymptomatic individuals and clinical dengue patients, expression of proteins related to antigen presentation and subsequent T and B cell activation pathways were differentially regulated, independent of viral load and previous DENV infection history. Feedback mechanisms controlled the immune response in asymptomatic viremic individuals, as demonstrated by increased activation of T cell apoptosis-related pathways and FcRIIB signaling associated with decreased anti-DENV specific antibody concentrations. Taken together, our data illustrate that symptom-free DENV infection in children is associated with determined by increased activation of the adaptive immune compartment and proper control mechanisms, leading to elimination of viral infection without excessive immune activation, with implications for novel vaccine development strategies
Publication Title
Increased adaptive immune responses and proper feedback regulation protect against clinical dengue.
Alternate Accession IDs
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Disease stage
View Samples- Homo sapiens
- 51 Downloadable Samples
Illumina HiSeq 2000
Description
RNA-seq profiling was conducted on clinically-annotated human pancreatic adenocarcinoma cancer tissues Overall design: We measured the transcriptome in 51 clinically-annotated human pancreatic adenocarcinoma cancer tissues
Publication Title
RNA sequencing of pancreatic adenocarcinoma tumors yields novel expression patterns associated with long-term survival and reveals a role for ANGPTL4.
Alternate Accession IDs
Sample Metadata Fields
Age, Subject
View Samples- Homo sapiens
- 14 Downloadable Samples
- IlluminaHiSeq2000
Description
Myelodysplastic syndromes and chronic myelomonocytic leukemia (CMML) are characterized by mutations in epigenetic modifiers and aberrant DNA methylation. DNA methyltransferase inhibitors (DMTis) are used to treat these disorders, but response is highly variable with few means to predict which patients will benefit. To develop a molecular means of predicting response at diagnosis, we examined baseline differences in mutations, DNA methylation, and gene expression in 40 CMML patients responsive and resistant to decitabine (DAC). While somatic mutations did not differentiate responders and non-responders, we were able to identify for the first time 158 differentially methylated regions (DMRs) at baseline between responders and non-responders using next-generation sequencing. These DMRs were primarily localized to non-promoter regions and overlapped with distal regulatory enhancers. Using the methylation profiles, we developed an epigenetic classifier that accurately predicted DAC response at the time of diagnosis. We also found 53 differentially expressed genes between responders and non-responders. Genes up-regulated in responders were enriched in the cell cycle, potentially contributing to effective DAC incorporation. Two chemokines overexpressed in non-responders -- CXCL4 and CXCL7 -- were able to block the effect of DAC on normal CD34+ and primary CMML cells in vitro, suggesting their up-regulation contributes to primary DAC resistance. Overall design: mRNA profiling in bone marrow mononuclear cells (BM MNC) from 14 CMML patients (8 decitabine responders vs. 6 non-responders).
Publication Title
Specific molecular signatures predict decitabine response in chronic myelomonocytic leukemia.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- 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.
Alternate Accession IDs
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 24 Downloadable Samples
- Illumina MouseWG-6 v2.0 expression beadchip
Description
Gp130 receptor engagement on neoplastic cells provides a link by which an inflammatory microenvironment facilitates tumour promotion. Although hyperactivation of the gp130-dependent Stat3 signalling node is commonly observed in solid tumours, Stat3 remains a challenging therapeutic target. To mimic excessive Stat3 signalling, we molecularly validate the gp130FF mouse as a preclinical model for inflammation-associated intestinal-type gastric cancer (IGC), with aberrant mammalian target of rapamycin (mTOR) pathway activity as shared feature. Accordingly, administration of the mTorc1 inhibitor RAD001 reversibly reduced IGC burden in gp130FF mice and suppressed colitis-associated cancer in wild-type mice. Since the therapeutic effect of RAD001 occurs independently of Stat3 hyperactivation, which is also dispensable for gp130-dependent engagement of the PI3K/Akt/mTorc1 pathway, we conclude that mTorc1 signalling limits tumour promoting Stat3 activity
Publication Title
mTORC1 inhibition restricts inflammation-associated gastrointestinal tumorigenesis in mice.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
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