Project description:The alkaliphilic halotolerant bacterium Bacillus sp. N16-5 often faces salt stress in its natural habitats. One-color microarrays was used to investigate transcriptome expression profiles of Bacillus sp. N16-5 adaptation reactions to prolonged grown at different salinities (0%, 2%, 8% and 15% NaCl) and the initial reaction to suddenly alter salinity from 0% to 8% NaCl. Salt induced gene expression was measured when culture was grown on different salinities (0%, 2%, 8% and 15% NaCl) to mid-logarithmic phase. And salt induced gene expression was also measured at 0 min, 10 min, 30 min, 60min, 120min after a sudden change salinity from 0% to 8% NaCl.
Project description:Alkaline hemicellulytic bacteria Bacillus sp. N16-5 has abroad substrate spectrum and exhibits great growth ability on complex carbohydrates. In order to get insight into its carbohydrate utilization mechanism, global transcriptional profiles were separately determined for growth on glucose, fructose, mannose, galactose, arabinose, xylose, galactomannan, xylan, pectin and carboxymethyl cellulose by using one-color microarrays. Substrate induced gene expression was measured when culture was grown on glucose, fructose, mannose, galactose, arabinose, xylose, galactomannan, xylan and CMC to mid-logarithmic phase.
Project description:Side populations have recently been identified in ovarian cancers and may play an important role in post treatment relapse and resistance to chemotherapeutic drugs. In this study, we aimed to identify the differential expression between IGROV1 SP and NSP on Affymetrix HG-U133plus2 microarrays. We found ovarian tumour SP cells frequently over-express the multi-drug resistance associated P-glycoprotein (ABCB1) by Rank Product (FDR<0.05), and by geneset enrichment analysis, embryonic stem cell-associated ‘NOS’ signature (Notch/Oct4/Sox2 regulated genes) and Polycomb Repressive Complex 2 (PRC2) genes were over-expressed, while PRC2-repressed target genes were significantly under-expressed in the SP from ovarian cell lines compared to non-SP (FDR<10-4). Overall design: Cells were isolated using Hoechst 33342 cell sorting without other treatment. The experiment was carried out in triplicates: 3 SP samples and 3 non-SP samples
Project description:Corneal epithelial stem cells reside in the limbus that is the transitional zone between the cornea and conjunctiva, and are essential to maintain the homeostasis of corneal epithelium. However, their characterization is poorly understood. Therefore, we constructed gene expression profiles of limbal epithelial SP and non-SP cell using RNA-sequencing. As a result, limbal epithelial SP cells have immature cell phenotypes with endothelial/mesenchymal cell markers, while limbal epithelial non-SP cells have epithelial progenitor cell markers. Overall design: Examination of rabbit limbal epithelial SP and non-SP cells
Project description:Here we have compared adult wildtype (N2) C. elegans gene expression when grown on different bacterial environments/fod sources in an effort to model naturally occuring nematode-bacteria interactions at the Konza Prairie. We hypothesize that human-induced changes to natural environments, such as the addition of nitrogen fertalizer, have effects on the bacterial community in soils and this drives downstream changes in the structure on soil bacterial-feeding nematode community structure. Here we have used transcriptional profiling to identify candidate genes involved in the interaction of nematodes and bacteria in nature. Overall design: Here we have performed 36 microarrays and because channels were analyzed separately we have uploaded channels separately. We used six biological replicates of C. elegans grown in four bacterial environments (E. coli OP50, Micrococcus luteus, Bacillus megaterium, and Pseudomonas sp.). For each of those biological replicates we have performed three technical replicates because we made all six pair-wise comparisons amoungst the four bacterial environments. Dye swaps were performed. > Biological replicates (technical replicates) < Micrococcus luteus 1 (GSM399039,GSM399094,GSM399119) Micrococcus luteus 2 (GSM399426,GSM399431,GSM399459) Micrococcus luteus 3 (GSM399467,GSM399482,GSM399486) Micrococcus luteus 4 (GSM399489,GSM399493,GSM399500) Micrococcus luteus 5 (GSM399514,GSM399533,GSM399534) Micrococcus luteus 6 (GSM399539,GSM399544,GSM399547) E. coli OP50 1 (GSM399108,GSM399118,GSM399125) E. coli OP50 2 (GSM399427,GSM399428,GSM399465) E. coli OP50 3 (GSM399480,GSM399485,GSM399487) E. coli OP50 4 (GSM399490,GSM399492,GSM399495) E. coli OP50 5 (GSM399510,GSM399513,GSM399535) E. coli OP50 6 (GSM399541,GSM399542,GSM399546) Bacillus megaterium 1 (GSM399089,GSM399097,GSM399123) Bacillus megaterium 2 (GSM399429,GSM399437,GSM399458) Bacillus megaterium 3 (GSM399468,GSM399479,GSM399484) Bacillus megaterium 4 (GSM399496,GSM399498,GSM399505) Bacillus megaterium 5 (GSM399512,GSM399531,GSM399536) Bacillus megaterium 6 (GSM399538,GSM399543,GSM399549) Pseudomonas sp. 1 (GSM399029,GSM399082,GSM399113) Pseudomonas sp. 2 (GSM399432,GSM399457,GSM399464) Pseudomonas sp. 3 (GSM399481,GSM399483,GSM399488) Pseudomonas sp. 4 (GSM399491,GSM399494,GSM399509) Pseudomonas sp. 5 (GSM399511,GSM399532,GSM399537) Pseudomonas sp. 6 (GSM399540,GSM399545,GSM399548)