Project description:Experimentally mapped transcriptome structure of Methanococcus maripaludis S2 by hybridizing total RNA (including RNA species <200 nt) to genome-wide high-density tiling arrays (60 mer probes tiled every 14 nt). Methanococcus maripaludis MM901, a wild type Methanococcus maripaludis S2 with an in frame deletion of the uracil phosphoribosyltransferase gene (Proc. Natl. Acad. Sci. U S A 107: 11050-11055) growth curve experiments were conducted in batch culture. Reference samples were cultured at mid-log phase (OD660 = 0.804). Eight samples were collected that spanned the key phases of the growth curve. Total RNA from samples of growth curve and reference were directly labeled with Cy3 or Cy5, and were hybridized to the tiling array. Dye-flip experiments were done for each sample. Log ratios were calculated for each probe (growth curve sample/reference). Transcriptome browser is available at http://baliga.systemsbiology.net/enigma/.
Project description:Methanococcus maripaludis is a methanogenic Archaea that conserves energy from molecular hydrogen to reduce carbon dioxide to methane. Chemostat grown cultures limited for hydrogen, phosphate, or leucine were compared to determine the regulatory response to hydrogen limitation. This was done by comparing hydrogen limited cultures to both leucine limited and phosphate limited cultures. Slow and rapid growing samples limited for either hydrogen or phosphate were compared to determine the regulatory effects of growth rate. Keywords: archaea, hydrogen, leucine, phosphate, nutrient limitation, growth rate, methanogen
Project description:Experimentally mapped transcriptome structure of Methanococcus maripaludis S2 by hybridizing total RNA (including RNA species <200 nt) to genome-wide high-density tiling arrays (60 mer probes tiled every 14 nt).
