Project description:Transcriptional profiling of N. gonorrhoeae grown in anaerobic conditions (with sodium nitrite supplied by adding 20% w/v solution to a final concentration of 5mM) compared to a control grown in capnoaerobic conditions (normal atmosphere +5% CO2)
Project description:Transcriptional profiling of N. meningitidis grown in anaerobic conditions (with sodium nitrite supplied by adding 40ul 20% w/v solution onto a sterile disc in the centre of the plate) compared to a control grown in capnoaerobic conditions (normal atmosphere +5% CO2)
Project description:Wild type Neisseria gonorrhoea strain FA1090 and N. meningitidis strain MC58 were grown on normal GC plate at either 35 degree celsius (for control samples) or 40 degree celsius (for test samples)
Project description:Transcriptional profiling of N. gonorrhoeae grown in anaerobic conditions (with sodium nitrite supplied by adding 40ul 20% w/v solution onto a sterile disc in the centre of the plate) compared to a control grown in capnoaerobic conditions (normal atmosphere +5% CO2)
Project description:In order to identify novel regulators of haematopoietic stem cell emergence in the mouse embryonic AGM region, 3 different types of gene expression comparisons were performed. In the first one, whole dorsal aortas from embryonic day (E) 11 embryos and E9 embryos were dissected, tissues from each time point were pooled and their expression profile compared (whole aorta (WA) E9 vs E11). 3 different pools/biological replicas were obtained for each time point, a dye swap was included in each experiment, a technical replicate was performed for each pool (including the dye swap) and 2 self-self hybridisation controls were included. In the second comparison, GFP+ cells were isolated by fluorescence-activated cell sorting from pooled E9 and E11 aortas from transgenic embryos that express GFP under the regulatory elements of the Ly-6A gene. We obtained one pool for each time point and compared their transcription profile (GFP E9 vs E11). This comparison also contained a dye swap and a technical replicate (also of the dye swap). In the third comparison, the E11 aorta was cut into 3 roughly equal parts. Pools were obtained of the middle region ("m") and the two outer regions, rostral and caudal, together ("r+c") and their expression profile compared (11AO m vs r+c). There was one pool of each population, and the experiment included a dye swap and a technical replicate (also of the dye swap) and one self-self hybridisation control. Isolated RNA was amplified by T7-mediated in vitro transcription, with one round for the first and the third comparison and two rounds for the second comparison (sorted GFP+ cells). Probes were labelled during the reverse transcription step. Within array normalisation was achieved with Lowess Smooth and between arrays with Z scores. ANOVA analysis identified differentially expressed genes and K means clustering was used to segregate them into upregulated and downregulated genes.
Project description:Each labeled cDNA sample constituted a unique combination of UV dose (2J, 4J or 8J), time point (-30min, 0h, 2h, 4h, 8h and 24h) and photoreactivation status (PR or non-PR) that defined a distinctive matrix point. All samples were hybridized to non-irradiated, non-photoreactivated MDFs of the pertinent time point. As a consequence, the net observed differences in gene expression profiles between treated and non-treated cells depicted only the time-dependent expression profiles of significant gene entries upon a 2J, 4J or 8J of UV-C irradiation and subsequent photoreactivation or not. <br> To allow for the estimation and removal of gene specific dye effects, all samples were reversed labeled during the total RNA reverse transcription step. A pair of self-hybridizations (dye-reversed) preceded each batch of six microarrays. <br> Any deviation from a ratio of 1 (centered to 0 for log ratio data) in self-hybridizations was therefore assigned to either dye effect or residual error. <br> Dye-reversed hybridizations were considered as technical replicates that allowed gene-specific dye effects to be averaged out during clustering while enabled us to <br> exclude dye-dependent variances during the ANOVA analysis. In order to assure a balanced design, the same number of technical dye-reversed replicates was used for all samples and experimental conditions. <br> To account for inherent experimental variation, all samples were each represented by a pool of five <br> (occasionally six) MDF culture dishes that were subjected under identical experimental conditions.
Project description:The Goal of this study is to explore the transcriptional differences between angiogenic and non-angiogenic tumors generated in Dr. Folkman's Lab, Harvard Medical School.<br>Referneces:<br>Almog N, Henke V, Flores L, Hlatky L, Kung AL, Wright RD, Berger R, Hutchinson L, Naumov GN, Bender E, Akslen LA, Achilles EG, Folkman J.<br>Prolonged dormancy of human liposarcoma is associated with impaired tumor angiogenesis.<br>FASEB J. 2006 May;20(7):947-9.<br><br>Naumov GN, Bender E, Zurakowski D, Kang SY, Sampson D, Flynn E, Watnick RS, Straume O, Akslen LA, Folkman J, Almog N.<br>A model of human tumor dormancy: an angiogenic switch from the nonangiogenic phenotype.<br>J Natl Cancer Inst. 2006 Mar 1;98(5):316-25.<br>