Project description:In order to explore the potential mechanism of HNF4α in ICC, RNA-seq was performed to obtain differentially expressed genes (DEGs) between HuCCT-1 cells infected with AdGFP or AdHNF4α
Project description:We compared the proteomic profile of blood plasma in healthy and white-nose syndrome affected Myotis lucifugus in order to identify patho-physiological changes associated with the disease. Using two-dimensional gel electrophoresis and liquid chromatography-mass spectrometry we identified differentially expressed proteins for acute phase response, constitutive and adaptive immunity, oxidative stress defense, metabolism and structural proteins of exosomes and desmosomes, suggesting a systemic response against Pseudogymnoascus destructans infection in a North American bat species.
Project description:Transcriptome analysis of tomato fruits under heat stress revealed that most SlCRK genes were downregulated upon heat treatment. GO enrichment analysis of genes that were co-expressed with SlCRK members have identified various stress response related and proteasoma protein catabolic process related genes, which may be involved in heat stress signaling Overall, our results provide valuable information for further research on the roles of SlCRKs in response to abiotic stress, especially heat stress.
Project description:Phytophthora parasitica is one of the most widespread Phytophthora species, which is known to cause root rot, foot rot/gummosis and brown rot of fruits in citrus. In this study, we have analyzed the transcriptome of a commonly used citrus rootstock Carrizo citrange in response to P. parasitica infection using the RNA-seq technology. In total, we have identified 6692 differentially expressed transcripts (DETs) among P. parasitica-inoculated and mock-treated roots. Of these, 3960 genes were differentially expressed at 24 hours post inoculation and 5521 genes were differentially expressed at 48 hours post inoculation. Gene ontology analysis of DETs suggested substantial transcriptional reprogramming of diverse cellular processes particularly the biotic stress response pathways in Carrizo citrange roots. Many R genes, transcription factors, and several other genes putatively involved in plant immunity were differentially modulated in citrus roots in response to P. parasitica infection. Analysis reported here lays out a strong foundation for future studies aimed at improving resistance of citrus rootstocks to P. parasitica.
Project description:In this dataset, we include the gene expression and exon splicing variants of two Ewing sarcoma cell lines (RDES and TC-32) after knockdown of the transcription factor SOX6 in order to obtain differentially expressed genes and different exon splicing variants.
Project description:Eosinophilic granulomatosis with polyangiitis (EGPA) is a rare and heterogeneous disease of unknown etiology, classified among ANCA-associated vasculitis, with an insatisfactory response to treatment. The aims of the current project are: 1) To investigate pathogenic pathways involved in EGPA that could be potentially druggable or provide clinically useful biomarkers by a cross-sectional study determining gene-expression profile of peripheral blood CD4+T lymphocytes in clinically stable patients with EGPA, patients with asthma and healthy controls. By using gene set expression analysis (GSEA) we will identify the main differentially expressed pathways. The most signficant differentially expressed transcripts will be validated as potential biomarkers by quantitative real time RT-PCR and by serum ELISA if encoding for a soluble product in an additional cohort. 2) To determine the heterogeneity of the EGPA by analyzing its transcriptome according to subgroups of patients defined by clinical variables and response to treatment. If we obtain significant differentially expressed genes for each category defined by clinical variables, these genes will be also validated in an additional cohort. 3) Moreover, an unsurpervised clustering analysis will be performed in order to identify non-predefined subtypes. With this study, we aim to contribute to the characterization of the molecular basis of the heterogeneity of EGPA patients and to identify pathways potentially involved in disease pathogenesis.
Project description:In order to obtain a global view about the strategies used by phytopathogenic bacteria, in response to physiologically relevant temperature changes. We used the DNA microarray technology to compare gene expression profile in the model bacterial pathogen P. syringae pv. phaseolicola NPS3121 grown at 18 ºC and 28ºC.
Project description:Our lab has previously shown that treatment of murine heart valve explants with ATRA promotes calcification in vitro. In order to fully explore gene expression changes in the valve in response to ATRA or LE540, a high throughput microarray was performed. In this data set, we include expression data from dissected murine post natal aortic valve explants treated with ATRA or DMSO as a vehicle control. These data are used to obtain 432 probe sets that are differentially expressed in response to ATRA treatment, with 118 being downregulated and 314 increased.