Project description:Serum-free Fibrocytes, Serum-containing Fibrocytes, CD14++CD16- Monocytes, CD14++CD16+ Monocytes, CD14+CD16++ Monocytes, Macrophages were all generated from up to 3 biological replicates from each of 3 separate donors. RNA was extracted (Ambion RNAqueous), labelled with cy3, mixed with cy5 labelled human reference (Stratagene), and hybridised to slides printed with Human AROS v4.0 oligonucleotides (Operon). Slides were scanned using a Perkin Elmer GX plus, and the data then normalised with GEPAS v4.0 and collated. Final data analysis was carried out using TMEV 4.0. SAM was performed using a 0.1% FDR. PCA were plotted from this list, and interrogation carried out using DAVID to determine pathway enrichment.
Project description:Fibroblasts, Serum-free Fibrocytes, Serum-containing Fibrocytes, Monocytes, Macrophages, Osteoclasts, immature Dendritic Cells, and mature Dendritic Cells were all generated from 3 biological replicates from each of 3 separate donors. RNA was extracted (Ambion RNAqueous), labelled with cy3, mixed with cy5 labelled human reference (Stratagene), and hybridised to slides printed with Human AROS v4.0 oligonucleotides (Operon). Slides were scanned using a Perkin Elmer GX plus, and the data then normalised with GEPAS v4.0 and collated. Final data analysis was carried out using TMEV 4.0. SAM was performed using a 0.1% FDR. HCL and PCA were plotted from this list, and interrogation carried out using DAVID to determine pathway enrichment. After initial analysis, the Fibroblast cell type was found to significantly bias the data. Due to this, these samples were removed from the analysis, and the data re-normalised. This second data file will be submitted separately.
Project description:The objective of the study was to identify the genes up and down-regulated during the interaction of P. brassicae with a partial resistant genotype of Arabidopsis. The transcriptome pattern of inoculated and non-inoculated plants of Arabidopsis was compared at three time points after inoculation (24 hours, 48 hours and one-week ai).<br> Sixty plants were studied by comparison (inoculated-non inoculated) and by kinetic point. RNAs of the 30 inoculated plants and the RNAs of the 30 non-inoculated plants were pooled to eliminate variability between individual plants and thus to target for genes for which differences in expression were linked to the inoculation by the pathogen. Five comparisons have been performed: inoculated-non inoculated at 24 hours ai; inoculated-non inoculated 48 hours ai; inoculated-non inoculated one-week ai; inoculated 24h ai-inoculated 48h ai; inoculated 48h ai- inoculated one-week ai. The entire experiment was repeated (biological repetition) and each comparison was performed in two independent hybridisations (technical repetition).
Project description:three pairs of isogenic human mammary epithelial and fibroblast cells, were used to characterized cell type specific dna methylation using using methyla cytosin immunoprecipitation
Project description:Arabidopsis thaliana transcriptome analysis in response to plant growth promoting rhizobacteria (PGPR)<br> Experiment 1 : Changes in gene expression profile triggered during root architecture response to Phyllobacterium.<br> Biological question : Which genes are up- or down-regulated in Arabidopsis thaliana cultivated in vitro with increased lateral root development in response to Phyllobacterium STM196 inoculation.<br> Experiment description: Seeds of wild-type Arabidopsis thaliana (ecotype Columbia) were surface-sterilized and sown on agar mineral medium (see below). 4 days after storage in the dark at 4C, seedling were cultivated 6 days in a growth chamber (16 h daily, 20-22C) and then transferred on a fresh agar mineral medium inoculated or not with Phyllobacterium STM196 (2.108 cfu/ml). 6 days later, root and leaves were collected, froze on liquid nitrogen and stored at -80C.<br> <br> Experiment 2 : Changes in gene expression profile triggered during induced systemic resistance (ISR)<br> Biological question : Which genes are up- or down-regulated during the ISR triggered by a rhizobacteria, in comparison with those affected by a pathogenic interaction. <br> Experiment description: Seeds were sown on 0.8% (W/V) agar mineral medium (see below). 4 days after storage in the dark at 4C, seedling were cultivated 6 days in a growth chamber (16 h daily, 20-22C) and then transferred on soil inoculated or not with 107 cfu.g-1 of Bradyrhizobium strain ORS278. Three weeks later, 3 leaves per plant were infiltrated with a suspension of Pseudomonas syringae pv. tomato (2.105 cfu.ml-1) or with MgSO4 10 mM alone for control plants. Infiltrated leaves were collected 24h later.<br> <br> Experiment 3 : Comparison of the effects of 3 rhizobacteria on Arabidopsis thaliana transcriptome<br> Biological question : which genes are specifically induced or repressed in Arabidopsis thaliana by inoculation of the soil with a PGPR vs a bacteria that has the ability to trigger nodule formation in a Legume. <br> Experiment description: Seeds of wild-type Arabidopsis thaliana (ecotype Columbia) were surface-sterilized and sown on agar mineral medium. Four days after storage in the dark at 4C, seedlings were cultivated 6 days in a growth chamber (16 h daily, 20-22C) and then transferred on soil inoculated or not with 108 cfu.g-1 of Mesorhizobium loti, or 108 cfu.g-1 of Phyllobacterium STM196, or 107 cfu.g-1 of Bradyrhizobium ORS278.
Project description:HCT116 (kRas mt) cells and HKH2 (Kras wt) cells were implanted into the right and left flanks of nude mice and either untreated or treated with a MEK inhibitor (AZD6244) over time. Tumours were excised and harvested for RNA extraction at the end of the experiment and hybridised to the Colorectal DSA.
Project description:CD4 T cells taken from 6 donors were sorted into CD25hi CD45RA+ (na�ve Treg), CD25hi CD45RO+ (memory Treg), CD25- CD45RA+ (na�ve responder) and CD25- CD45RO+ (memory responder) populations. <br><br>RNA was extracted (Ambion RNAqueous), amplified (SMART), labelled with cy3, mixed with cy5 labelled human reference (Stratagene), and hybridised to slides printed with Human AROS v4.0 oligonucleotides (Operon).<br><br>Slides were scanned using a Perkin Elmer GX plus, and the data then normalised with GEPAS v4.0 and collated. One sample was deemed to be of too low hybridisation quality, and was hence removed at this point.<br><br>Final data analysis was carried out using TMEV 4.0. SAM was performed using a 10% FDR. HCL and PCA were plotted from this list, and interrogation carried out using DAVID to determine pathway enrichment<br>
Project description:Pre-treatment metastatic (liver) biopsies were harvested prior to 5-FU and oxaliplatin therapy. CT imaging for response evaluation using WHO criteria was performed every 6 weeks.