Time-course expression QTL atlas of the global transcriptional response of wheat to Fusarium graminearum
ABSTRACT: We have captured transcriptomes of 196 doubled haploid wheat lines segregating for Fusarium head blight resistance after inoculation with the pathogen Fusarium graminearum at 30 and 50 hours after inoculation. The pathogen switches from biotrophic to nectrotrophic lifestyle in course of disease development forcing its host to adapt its defence strategies. We performed an eQTL analysis on both time points and describe the changing segregating response to the pathogen in time. Our analysis describes three major regulatory hotspots that govern the expression of 1000s of genes and eQTL colocalizing with phenotypic resistance QTL.
Project description:1ml plasma from 10 age- and sex-matched patients (GC stage II with recurrence: sample number 1-5; and stage III without recurrence: sample number 6-10) were arrayed for differential expressed miRNAs so as to look for miRNAs that were associated with GC recurrence. Raw CT values were shown in this dataset.
Project description:For transcript analysis, total RNA was isolated as described (Noens et al, 2007) from surface-grown mycelia of S. coelicolor M145 and its rok7B7 null mutant, cultivated on MM agar plates with mannitol (1% w/v) as the sole carbon source (plates were covered with cellophane discs). Two independent biological replicate experiments were performed. Samples were taken at 14h (early vegetative growth), 24 h (vegetative growth), 30 h (early aerial growth), 36 h (aerial growth), 42 h (early sporulation) and 54 h (sporulation). Total RNA was purified using the Kirby-mix protocol (Kieser et al, 2000). DNaseI treatment was used to fully remove any traces of DNA. Before use, the RNA samples were checked for integrity on an Agilent 2100 Bioanalyzer (Agilent Technologies). cDNA preparation and labeling was performed as previously described (Bucca et al, 1997, Bucca et al, 2009). The filtered data sets were analyzed using rank products analysis (Breitling et al, 2004) via the Rank-ProdIt tool (Laing and Smith, 2010). Differentially expressed genes were identified as demonstrating a > 2 fold change in expression between the parental strain M145 (wild-type) and the rok7B7 mutant.
Project description:22 day old Arabidopsis Col-0 plants were sprayed with 0.5 mM sodium nitroprusside (SNP), corresponding controls were sprayed with water, and leaves harvested 3 hours after spraying and frozen in liquid nitrogen.
Project description:We compared gene expression patterns between the occipital cortex tissues of four male and four female individuals in three species: an ape (human, Homo sapiens), an Old World monkey (macaque; Macaca fascicularis), and a New World monkey (marmoset; Callithrix jacchus). To do so, we hybridized cDNA from each sample (n = 24) to a human cDNA microarray that contains 46,128 probes. (Human 46k cDNA, http://www.biotech.kth.se/molbio/microarray/). We used a loop hybridization study design restricted to within-species comparisons only, in which we co-hybridized on each slide samples from the opposite sex.
Project description:Peripheral infusion of human umbilical cord mesenchymal stem cells (hUC-MSCs) can profoundly suppress the activation of c-Mos and remarkably improve hepatic histology, suppress the systemic inflammatory reaction, and promote animal survival in a large non-human primate model of acute liver failure (ALF). The mechanism through which hUC-MSCs inhibits c-Mos activation in vivo remains unclear. We hypothesized that hUC-MSCs can adaptively produce certain inhibitory cytokines in response to the pro-inflammatory microenvironment. To confirm this, we stimulated cultured hUC-MSCs with inflammatory monkey serum (serum isolated at day 1 following toxin challenge). After a 30-min stimulation, the cells were collected for microarray gene expression analysis. A whole human genome oligo microarray analysis was performed to reveal the altered gene expression profiles of the hUC-MSCs