BACKGROUND: With the completion of genome sequences belonging to some of the major crop plants, new challenges arise to utilize this data for crop improvement and increased food security. The field of genetical genomics has the potential to identify genes displaying heritable differential expression associated to important phenotypic traits. Here we describe the identification of expression QTLs (eQTLs) in two different potato tissues of a segregating potato population and query the potato genom ...[more]
Project description:BSA pooling experiment for methionine content in a segrating diploid potato population (CxE). RNA of constrasting individuals for methionine content are pooled together based on their tuber methionine content and marker association with either or both of the identified QTLs for methionine content
Project description:BSA expression profiling for tuber flesh color. Extreme individuals segregating for tuber flesh color are selected and RNA is pooled together. Gene expression is profiled using microarray technology. Genes displaying differential expression between the constrasting bulks are considered as candidate genes responsible for the targeted trait and further analyzed using the individual genotypes.
Project description:Methanococcoides burtonii is member of the Archaea that is a valuable model for studying cold adaptation. We developed a Agilent microarray for determing which genes are expressed in operons, and which are differentially expressed at low (4°C) or high (23°C) temperature. Agilent 8 x 15K custom gene expression microarrays containing 15128 probes were designed based on the M. burtonii genome sequence. The Microarrays were constructed using 60-mer oligonucleotides covering 2236 genes (86.7% of the total number) on the coding strand (10153 oligonucleotides) and the complementary strand (3671 oligonucleotides), and a large number of intergenic regions (707 oligonucleotides) (Table 1). Each gene and intergenic region was covered by 1 to 6 oligonucleotides (average of 4 per gene). Eight independent replicates were performed using competitive hybridization comparing 8 cultures grown at 4°C vs 8 grown at 23°C. Due to the fact that different ORFs have different numbers of oligonucleotides (ranging from one to six) and that experiments were performed in 8 different replicates, each gene (or intergenic region) has 8 48 measures of fluorescence.
Project description:We have used RNA immunoprecipitation to identify the set of mRNAs that HIV-1 Tat interacts with in T-cells. We have also performed measurements of relative RNA abundance to determine if Tat binding is associated with an increase in RNA abundance in Tat-expressing T-cells and during HIV infection of primary T-cells. We have also used RNA IP and ChIP-Chip to compare the RNAs with which Tat interacts with to the RNAs that RISC interacts with and the genes associated with pTEF-b.
Project description:RNAs were extracted from entorhinal cortex of human suicide patients with major depression and matched control subjects. The transcription profile was investigated by Agilent microarray platform and quantitative real-time PCR to reveal alterations in neuronal functions in this brain region.
Project description:Total RNAs were extracted from the hippocampus and prefrontal cortex of anxious mice. The transcriptome of the two brain regions were investigated using a custom made Agilent 8 x 15k features oligo microarray.
Project description:Epidemiologic studies have shown a significant inverse correlation between fruit and vegetable consumption and incidence of esophageal adenocarcinoma. Procyanidins are polymeric flavanols found in many fruits and vegetables, and have been shown to possess anti-carcinogenic/chemopreventive properties. We previously showed that an oligomeric procyanidin extracted from apples with an average degree of polymerisation of 3.9 induced cell cycle arrest and apoptosis in the esophageal adenocarcinoma cell line OE33. In order to understand the mechanism of action of this procyanidin we determined genome-wide transcriptomic changes induced by procyanidin treatment of OE33 cells. Pathway analysis of these data implicated the MAP kinase signalling pathways in eliciting these responses. An investigation into the role of these pathways showed that procyanidin specifically induced the activation of the stress-activated protein (SAP) kinases JNK1/2 and p38-? and ? leading to the increased expression of JUN and the phosphatases DUSP1 and -10. Gene-specific knockdown of the expression of JNK1, JNK2, p38-?, p38-? or JUN diminished procyanidin-induced effects on apoptosis demonstrating a clear role for these pathways. JUN is a component of the transcription factor AP-1 and AP-1 binding sites are over-represented in the promoters of procyanidin-induced genes, which together with the demonstration that JUN occupies several such promoters highlight the importance of this transcription factor in mediating the cellular response to procyanidin. These data provide a mechanistic understanding of how procyanidin specifically targets distinct pathways involved in the induction of apoptosis in esophageal adenocarcinoma cells and will inform future studies investigating its use as a chemopreventive/therapeutic agent.
Project description:SKBR3 cells, which bear both an HER2 and a RARA gene amplification, were treated for 12 or 48 hours with 100 nM retinoic acid, 100 nM lapatinib or the combination.The two drugs synergize and induce massive apoptosis. The aim is to find the molecular mechanism(s) of this synergism. Gene expression profiling was performed using Agilent two-color 4X44K arrays. Original processed data are available in the archive: http://www.ebi.ac.uk/arrayexpress/files/E-MEXP-3192/E-MEXP-3192.additional.zip
Project description:We observed extensive neurite formation in NG108-15 cells cultured in the presence of the flavonoid, isoquercitrin. To help determine the mechanism of neuritogenesis, microarray analysis was performed on samples treated with 40 uM isoquercitrin for 24 hrs.