Project description:Small RNA Sequencing from Pyrococcus furiosus Keywords: Small RNA Analysis Analysis of Small RNA from one sample of Pyrococcus furiosus
Project description:Semiconductor sequencing of alkaline degraded total RNA from Pyrococcus furiosus annotated for ”The 23S ribosomal RNA from Pyrococcus furiosus is circularly permuted” published in Frontiers in Microbiology”
Project description:Analysis of CRISPR RNAs from both total Pyrococcus furiosus RNA and those that co-purify with the Cmr complex, which has been predicted to be involved in RNA-mediated targeting of foreign RNAs in prokaryotes. Small RNAs (20 - 70 nts) were isolated either from total Pyrococcus furiosus RNA or RNAs isolated from immunopurified Cmr complexes. The RNAs were cloned and sequenced using the Illumina platform. Results provide insight into the anatomy of Cmr2-associated CRISPR RNAs.
Project description:Analysis of CRISPR RNAs from both total Pyrococcus furiosus RNA and those that co-purify with the Cmr complex, which has been predicted to be involved in RNA-mediated targeting of foreign RNAs in prokaryotes. Small RNAs (20 - 70 nts) were isolated either from total Pyrococcus furiosus RNA or RNAs isolated from immunopurified Cmr complexes. The RNAs were cloned and sequenced using the Illumina platform. Results provide insight into the anatomy of Cmr2-associated CRISPR RNAs. 2 Samples: total small RNAs vs Cmr2-associated small RNAs
Project description:Experimentally mapped transcriptome structure of Pyrococcus furiosus DSM 3638 by hybridizing total RNA (including RNA species <200 nt) to genome-wide high-density tiling arrays (60 mer probes tiled every 16 nt).
Project description:The transcriptional regulator TrmBL1 from the hyperthermophilic euryarchaeon Pyrococcus furiosus functions as repressor as well as activator of genes encoding enzymes mainly involved in sugar uptake, glykolysis and gluconeogenesis. The aim of this study was to explore the genome-wide binding sites of TrmBL1 in Pyrococus furiosus by ChIP-seq in vivo. Two different growth conditions were tested. Pyrococcus furiosus was cultured on pyruvate to induce gluconeogenic growth and on starch to induce glycolytic growth.
Project description:We designed an experimental setup to investigate the transcriptomic and proteomic responses of the hyperthermophilic archaeon Pyrococcus furiosus to heat and cold shock. P. furiosus is a model organism for studying microbial adaptation to extreme environments, including deep-sea hydrothermal vents with temperature gradients ranging from 1°C to 400°C. We aimed to simulate critical conditions where P. furiosus cannot grow and to examine the immediate response to thermal stress as well as the recovery process.
Project description:Experimentally mapped transcriptome structure of Pyrococcus furiosus DSM 3638 by hybridizing total RNA (including RNA species <200 nt) to genome-wide high-density tiling arrays (60 mer probes tiled every 16 nt). Pyrococcus furiosus DSM 3638 growth curve experiments were conducted in batch culture. Reference samples were cultured at mid-log phase (OD600 = 0.096). Seven 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/.